{"entity": "journal", "iuid": "195595009e0546a29b69d3586c38783f", "timestamp": "2026-06-17T07:41:06.589Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/BMC%20Genomics.json"}, "display": {"href": "https://publications.scilifelab.se/journal/BMC%20Genomics"}}, "title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "publications_count": 97, "publications": [{"entity": "publication", "iuid": "192bc0ba645d4a9babc3be3256ac2d23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/192bc0ba645d4a9babc3be3256ac2d23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/192bc0ba645d4a9babc3be3256ac2d23"}}, "title": "Breeding for climate adaptation: genetic variation and genomic selection for drought response in Scots pine.", "authors": [{"family": "Chaudhary", "given": "Rajiv", "initials": "R"}, {"family": "Estravis Barcala", "given": "Maximiliano", "initials": "M"}, {"family": "Fundova", "given": "Irena", "initials": "I"}, {"family": "Funda", "given": "Tomas", "initials": "T"}, {"family": "Chen", "given": "Zhi-Qiang", "initials": "ZQ"}, {"family": "Wu", "given": "Harry X", "initials": "HX"}], "type": "journal article", "published": "2026-04-27", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "27", "issue": "1", "issn-l": "1471-2164"}, "abstract": "Drought intensity and frequency are increasing under global warming in the boreal forests, and breeding for drought resistance will facilitate adaptation of new planting material to changing climate conditions. We used a tree-ring dataset of 559 individuals to study Scots pine genetic variation and the efficiency of genomic selection of drought-response traits (drought resistance, recovery and resilience), for the first time. From genotyping-by-sequencing (GBS), 31,101 SNPs were generated and used for the study.\n\nSignificant genetic variation was detected for drought-response and other growth, wood-anatomy and wood density traits. Heritability estimates for wood-anatomical traits were higher than those for drought-response and growth traits. Genetic correlations between drought-response and wood-anatomical traits were generally high but mostly nonsignificant. In contrast, drought resistance and recovery showed positive and significant correlations with basal area increment and height. We found that the predictive ability and accuracy for drought-response traits were lower than those for wood-anatomical traits, and were comparable between GBLUP and ABLUP. Greater genetic gain per year can be achieved through genomic selection relative to pedigree-based selection if the generation interval is reduced.\n\nThe positive genetic correlation between drought-response and growth traits will enable simultaneous selection for improved growth and increased drought resistant trees in Scots pine breeding through either pedigreed-based and genomic selection.\n\nThe online version contains supplementary material available at 10.1186/s12864-026-12849-x.", "doi": "10.1186/s12864-026-12849-x", "pmid": "42045837", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13122877"}, {"db": "pii", "key": "10.1186/s12864-026-12849-x"}], "notes": [], "created": "2026-05-11T12:13:32.454Z", "modified": "2026-05-11T12:13:32.461Z"}, {"entity": "publication", "iuid": "46c0df4f63584b799ce7923246580642", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46c0df4f63584b799ce7923246580642.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46c0df4f63584b799ce7923246580642"}}, "title": "Unique sex chromosome translocations and evolutionary strata in two Sylvioidea songbird families.", "authors": [{"family": "Brown", "given": "Thomas J", "initials": "TJ", "orcid": "0000-0002-4235-0856", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f23ec5a35d142de898840b16172fdfb.json"}}, {"family": "Ellerstrand", "given": "Simon J", "initials": "SJ", "orcid": "0000-0003-2674-6997", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ed13c7732674cc992f2356848b97a7b.json"}}, {"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Melo", "given": "Martim", "initials": "M", "orcid": "0000-0003-1394-4361", "researcher": {"href": "https://publications.scilifelab.se/researcher/a42199d6eca542c48290db65ae34d940.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2026-04-20", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "27", "issue": "1", "issn-l": "1471-2164"}, "abstract": "Avian genomes are typically stable, yet instances of chromosome fissions, fusions and translocations are known across various lineages. For example, multiple sex chromosome translocations have been described in the superfamily Sylvioidea. In this study, we examine the sex chromosomes in two Sylvioidea families, Nicatoridae and Cisticolidae, using whole-genome data. We found sex-linkage of chromosomes Z and 4A, consistent with findings in other Sylvioidea species. We also identify sex-linkage of parts of chromosome 4, marking a novel discovery for Nicatoridae and a previously documented feature in Cisticolidae. These families are non-sister taxa, and the size of the translocated region of chromosome 4 differs between them, supporting independent translocation events. We uncover variation in recombination suppression and evolutionary strata on chromosome 4 between families, as well as between two genera within Cisticolidae. This study reveals both recurrent and independent trajectories in sex chromosome evolution, deepening our understanding of complex genomes.\n\nThe online version contains supplementary material available at 10.1186/s12864-026-12861-1.", "doi": "10.1186/s12864-026-12861-1", "pmid": "42010480", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13097842"}, {"db": "pii", "key": "10.1186/s12864-026-12861-1"}], "notes": [], "created": "2026-05-27T11:37:59.563Z", "modified": "2026-05-27T11:38:00.060Z"}, {"entity": "publication", "iuid": "fdb2a58a717e4bbca202566f67f5792b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdb2a58a717e4bbca202566f67f5792b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdb2a58a717e4bbca202566f67f5792b"}}, "title": "A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila", "authors": [{"family": "Papachristos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0002-4777-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf7a545a218455fa134b3dd8bb1b895.json"}}, {"family": "Miller", "given": "Wolfgang J", "initials": "WJ"}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications.scilifelab.se/researcher/409de77af489419db6d2b599b590d02f.json"}}], "type": "journal-article", "published": "2025-12-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "27", "issue": "1", "pages": "41", "issn-l": "1471-2164"}, "abstract": "Long-term persistent symbiotic associations may result in co-speciation and can be inferred if species trees of hosts and symbionts are congruent in topology and divergence times. Co-speciation has been seen to occur relatively frequently in obligate associations, but is less common in parasitic or facultative ones, mainly due to the difference in horizontal transmission rates. The long-term vertical inheritance and close host association of obligate endosymbionts also generally result in smaller genomes than in facultative endosymbionts. Here, we investigate co-speciation and genome reduction using highly similar strains of the endosymbiont Wolbachia infecting Drosophila species from the willistoni and saltans groups, where only one strain, wPau, infecting D. paulistorum, is obligate.\n\nWe sequenced the Wolbachia genomes from five species of the willistoni and saltans groups and constructed phylogenies. Topological congruence was found between these Wolbachia strains and the nuclear DNA of their hosts, except for wPau and D. paulistorum, but full topological congruence was observed between Wolbachia and the host mitochondrial DNA. However, assuming temporal congruence, we estimated extremely low evolutionary rates in Wolbachia of 10- 10-10- 11 changes/site/year. Additionally, the obligate wPau strain was found to have a larger genome than closely related facultative strains, mainly due to an ongoing expansion of an IS4 element. Furthermore, wPau has lost a large proportion of its prophage WO genes, but the cif genes, known to be involved in the CI phenotype, are intact. Finally, nine of the eleven genes from the prophage WO-associated Undecim cluster are uniquely duplicated.\n\nThe congruent topologies between Wolbachia and their willistoni and saltans group hosts indicate co-speciation. However, the high similarity between Wolbachia strains, which results in low mutation rate estimates, challenges this interpretation. Contrary to the expectations of the genome reduction theory, we observed an increase in genome size in the obligate wPau strain, potentially driven by a decreased population size. Finally, the duplication of the Undecim cluster, despite a major loss of other prophage-associated genes, suggests that the genes in the Undecim cluster are under strong selection and potentially play a role in the obligate association between wPau and their D. paulistorum hosts.", "doi": "10.1186/s12864-025-12340-z", "pmid": "41366724", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12801941"}, {"db": "pii", "key": "10.1186/s12864-025-12340-z"}], "notes": [], "created": "2026-01-19T08:58:08.199Z", "modified": "2026-01-20T07:53:24.298Z"}, {"entity": "publication", "iuid": "88ca53dd11f14b3191a5c1a38499a985", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88ca53dd11f14b3191a5c1a38499a985.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88ca53dd11f14b3191a5c1a38499a985"}}, "title": "Genome of the extinct Gotland cattle breed.", "authors": [{"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}}], "type": "journal article", "published": "2025-12-03", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "1093", "issn-l": "1471-2164"}, "abstract": "The extinct cattle breed Gotland cattle lived on the island of Gotland in the Baltic Sea until the beginning of the 1950s. We sequenced the genomes of two Gotland cattle isolated from skulls from a local museum on Gotland.\n\nThe depth of coverage was 2.7X and 3.3X, respectively, with a breadth of coverage of 85% and 89%. Based on coverage of the sex chromosomes, both animals appeared to be female. We detected 19 million single nucleotide variants and 2.8 million indels in the joint dataset of Gotland cattle jointly called with modern Swedish cattle. In a principal component analysis, the two Gotland cattle placed the closest to Swedish Red cattle, rather than among the southern or northern traditional breeds. In terms of mitochondrial haplotypes, they were similar to clusters of related haplotypes involving multiple other breeds, including Swedish Mountain cattle, Swedish Red Polled and several Finnish cattle breeds.\n\nIn summary, our results suggest that Gotland cattle were genetically closer to the ancestors of Swedish Red cattle than to the extant traditional Swedish breeds.", "doi": "10.1186/s12864-025-12382-3", "pmid": "41340033", "labels": {"Ancient DNA": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-025-12382-3"}], "notes": [], "created": "2025-12-10T09:59:37.512Z", "modified": "2025-12-10T09:59:37.679Z"}, {"entity": "publication", "iuid": "5736722e01b74b29baf8fe43d4ce6819", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5736722e01b74b29baf8fe43d4ce6819.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5736722e01b74b29baf8fe43d4ce6819"}}, "title": "RNA-seq analysis identifies key genes enhancing hoof strength to withstand barefoot racing in Standardbred trotters.", "authors": [{"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Alameddine", "given": "Asmaa", "initials": "A"}, {"family": "Sp\u00f6rndly-Nees", "given": "Ellinor", "initials": "E"}, {"family": "Montigny", "given": "Mathilde", "initials": "M"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R", "orcid": "0000-0002-3610-4341", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae740ff060a5499fa477891138e95117.json"}}, {"family": "Jansson", "given": "Anna", "initials": "A"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.json"}}], "type": "journal article", "published": "2025-08-18", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "751", "issn-l": "1471-2164"}, "abstract": "Racing without protective shoes is common in the Swedish harness racing industry, as it can enhance horses' performance on the track. Trainers typically decide whether a horse will race barefoot based on practical experience rather than objective measures. However, this practice can sometimes lead to excessive hoof wear, posing potential welfare concerns for racing horses. Gene expression differences may help reveal the underlying genetic mechanisms associated with different phenotypic traits. To explore an objective measure for assessing which horses are best suited for barefoot racing, we conducted a polyA-selected RNA-seq experiment on tissue from the growth zone at the coronary band of the hoof. This experiment compared tissues from Standardbred trotters capable of repeatedly racing barefoot without injury (n = 11) to those that could not (n = 7). By combining stringent phenotyping with racing records and trainer interviews, we aimed to elucidate the biological factors related to hoof strength in barefoot racing, focusing on differential abundant genes.\n\nThe RNA-seq analysis identified five significantly downregulated genes in horses capable of competing barefoot across consecutive races. These genes are associated with various biological processes relevant for hoof strength: ACCS, IRX2 and TRAPPAC6A contribute to enhancing the structural integrity of the hoof; MT2A regulates its metal homeostasis and SLC35F3 likely influences local vasoconstriction in the hoof. These gene findings suggest a coordinated genetic basis for structural reinforcement and physiological support of the hoof, which may be critical for sustaining performance under barefoot conditions.\n\nOur findings suggest that the ability of Standardbred trotters to race barefoot in consecutive events is reflected in distinct gene expression patterns, underscoring a genetic basis for hoof strength. This supports further genome-wide scans aimed at identifying genetic markers for hoof durability in these horses. The focused design of our study- comparing horses that could consistently race barefoot with those that could not- enabled us to isolate a select group of genes involved in diverse aspects of hoof biology essential for quality and resilience of horse hooves. This insight could ultimately be applied to augment both the performance and wellbeing of equine athletes across disciplines.", "doi": "10.1186/s12864-025-11814-4", "pmid": "40826322", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12363045"}, {"db": "pii", "key": "10.1186/s12864-025-11814-4"}], "notes": [], "created": "2025-09-08T07:04:42.067Z", "modified": "2025-09-09T13:14:43.091Z"}, {"entity": "publication", "iuid": "e4171e3c321d427eab5134bacfa87814", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4171e3c321d427eab5134bacfa87814.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4171e3c321d427eab5134bacfa87814"}}, "title": "Cross-generational genomic prediction of Norway spruce (Picea abies) wood properties: an evaluation using independent validation.", "authors": [{"family": "Hayatgheibi", "given": "Haleh", "initials": "H"}, {"family": "Hallingb\u00e4ck", "given": "Henrik R", "initials": "HR"}, {"family": "Gezan", "given": "Salvador A", "initials": "SA"}, {"family": "Lundqvist", "given": "Sven-Olof", "initials": "SO"}, {"family": "Grahn", "given": "Thomas", "initials": "T"}, {"family": "Scheepers", "given": "Gerhard", "initials": "G"}, {"family": "Ranade", "given": "Sonali Sachin", "initials": "SS"}, {"family": "K\u00e4rkk\u00e4inen", "given": "Katri", "initials": "K"}, {"family": "Garc\u00eda Gil", "given": "M Rosario", "initials": "MR"}], "type": "journal article", "published": "2025-07-21", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "680", "issn-l": "1471-2164"}, "abstract": "The evaluation of genomic selection (GS) efficiency in forestry has primarily relied on cross-validation schemes that split the same population within a single generation for both training and validation. While useful, this approach may not be reliable for multigenerational breeding. To our knowledge, this is the first study to assess genomic prediction in Norway spruce using a large dataset spanning two generations in two environments. We trained pedigree-based (ABLUP) and marker-based (GBLUP) prediction models under three approaches: forward prediction, backward prediction, and across-environment prediction. The models were evaluated for ring-width, solid-wood and tracheid characteristics, using ~ 6,000 phenotyped and ~ 2,500 genotyped individual. Predictive ability (PA) and prediction accuracy (ACC) were estimated using an independent validation method, ensuring no individuals were shared between training and validation datasets. To assess the trade-off between comprehensive radial history and practical direct methods, we compared GBLUP models trained with cumulative area-weighted density (AWE-GBLUP) and single annual-ring density (SAD-GBLUP) from mother plus-trees. These models were validated using early and mature-stage progeny density measurements across two trials.\n\nDespite the smaller number of individuals used in the GBLUP models, both PA and ACC were generally comparable to those of the ABLUP model, particularly for cross-environment predictions. Overall, forward and backward predictions were significantly higher for density-related and tracheid properties, suggesting that across-generation predictions are feasible for wood properties but may be challenging for growth and low-heritability traits. Notably, SAD-GBLUP provided comparable prediction accuracies to AWE-GBLUP, supporting the use of more practical and cost-effective phenotyping methods in operational breeding programs.\n\nOur findings highlight the need for context-specific models to improve the accuracy and reliability of genomic prediction in forest tree breeding. Future efforts might aim to expand training populations, incorporate non-additive genetic effects, and validate model performance across cambial ages while accounting for climatic variability during the corresponding growth years. Overall, this study offers a valuable foundation for implementing GS in Norway spruce breeding programs.", "doi": "10.1186/s12864-025-11861-x", "pmid": "40691535", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12278512"}, {"db": "pii", "key": "10.1186/s12864-025-11861-x"}], "notes": [], "created": "2025-11-17T16:50:45.625Z", "modified": "2025-11-17T16:50:45.629Z"}, {"entity": "publication", "iuid": "59b7b1a3171445408a05b3c342c2dc3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59b7b1a3171445408a05b3c342c2dc3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59b7b1a3171445408a05b3c342c2dc3b"}}, "title": "Genome-wide comparison reveals large structural variants in cassava landraces.", "authors": [{"family": "Landi", "given": "Michael", "initials": "M"}, {"family": "Carluccio", "given": "Anna Vittoria", "initials": "AV"}, {"family": "Shah", "given": "Trushar", "initials": "T"}, {"family": "Niazi", "given": "Adnan", "initials": "A"}, {"family": "Stavolone", "given": "Livia", "initials": "L"}, {"family": "Falquet", "given": "Laurent", "initials": "L"}, {"family": "Gisel", "given": "Andreas", "initials": "A"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2025-04-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "362", "issn-l": "1471-2164"}, "abstract": "Structural variants (SVs) are critical for plant genomic diversity and phenotypic variation. This study investigates a large, 9.7 Mbp highly repetitive segment on chromosome 12 of TMEB117, a region not previously characterized in cassava (Manihot esculenta Crantz). We aim to explore its presence and variability across multiple cassava landraces, providing insights into its genomic significance and potential implications.\n\nWe validated the presence of the 9.7 Mbp segment in the TMEB117 genome, distinguishing it from other published cassava genome assemblies. By mapping short-read sequencing data from 16 cassava landraces to TMEB117 chromosome 12, we observed variability in read mapping, suggesting that while all genotypes contain the insertion region, some exhibit missing segments or sequence differences. Further analysis revealed two unique genes associated with deacetylase activity, HDA14 and SRT2, within the insertion. Additionally, the MUDR-Mutator transposable element was significantly overrepresented in this region.\n\nThis study uncovers a large structural variant in the TMEB117 cassava genome, highlighting its variability among different genotypes. The enrichment of HDA14 and SRT2 genes and the MUDR-Mutator elements within the insertion suggests potential functional significance, though further research is needed to explore this. These findings provide important insights into the role of structural variations in shaping cassava genomic diversity.", "doi": "10.1186/s12864-025-11523-y", "pmid": "40211122", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11987339"}, {"db": "pii", "key": "10.1186/s12864-025-11523-y"}], "notes": [], "created": "2025-09-08T06:59:22.722Z", "modified": "2025-09-08T06:59:22.728Z"}, {"entity": "publication", "iuid": "6af44bc75c7b4fe19763db841169ec45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6af44bc75c7b4fe19763db841169ec45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6af44bc75c7b4fe19763db841169ec45"}}, "title": "Genetic and neuro-epigenetic effects of divergent artificial selection for feather pecking behaviour in chickens.", "authors": [{"family": "de Haas", "given": "Elske N", "initials": "EN"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Kjaer", "given": "Joergen B", "initials": "JB"}, {"family": "Jensen", "given": "Per", "initials": "P", "orcid": "0000-0001-5491-0649", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83892cd7d6a46898629107a11205254.json"}}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}], "type": "journal article", "published": "2024-12-19", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "1219", "issn-l": "1471-2164"}, "abstract": "Feather pecking (FP) is a repetitive behaviour in chickens, influenced by genetic, epigenetic, and environmental factors, similar to behaviours seen in human developmental disorders (e.g., hyperactivity, autism). This study examines genetic and neuro-epigenetic factors in the thalamus of chickens from lines selected for seven generations for high or low FP behaviour (HFP or LFP). We integrate data on Differentially Methylated Regions (DMRs), Single Nucleotide Polymorphisms (SNPs), and Copy Number Variations (CNVs) in this controlled artificial selection process. Significant differences in behaviour, immunology, and neurology have been reported in these lines. We identified 710 SNPs in these lines that indicate new potentially important genes for FP such as TMPRSS6 (implicated in autism), and SST and ARNT2 (somatostatin function). CNV were the omic level most affected during selection. The largest CNVs found were in RIC3 (gain in HFP) and SH3RF2 (gain in LFP) genes, linked to nicotinic acetylcholine receptor regulation and human oncogenesis, respectively. Our study also suggests that promoters and introns are hotspots for CpG depletion. The overlapping of the omic levels investigated here with data from a public FP Quantitative Trait Loci (QTL) database revealed novel candidate genes for understanding repetitive behaviours, such as RTKN2, associated with Alzheimer's disease in humans. This study suggests CNVs as a crucial initial step for genomic diversification, potentially more impactful than SNPs.", "doi": "10.1186/s12864-024-11137-w", "pmid": "39702044", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11657628"}, {"db": "pii", "key": "10.1186/s12864-024-11137-w"}], "notes": [], "created": "2025-02-28T14:22:16.646Z", "modified": "2025-04-07T07:29:14.100Z"}, {"entity": "publication", "iuid": "b7114b93d21a4ff785520ac2615494a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7114b93d21a4ff785520ac2615494a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7114b93d21a4ff785520ac2615494a6"}}, "title": "Unraveling the ancient fungal DNA from the Iceman gut.", "authors": [{"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Sandionigi", "given": "Anna", "initials": "A"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Canini", "given": "Fabiana", "initials": "F"}, {"family": "Turchetti", "given": "Benedetta", "initials": "B"}, {"family": "Zucconi", "given": "Laura", "initials": "L"}, {"family": "Mimmo", "given": "Tanja", "initials": "T"}, {"family": "Buzzini", "given": "Pietro", "initials": "P"}, {"family": "Borruso", "given": "Luigimaria", "initials": "L"}], "type": "journal article", "published": "2024-12-19", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "1225", "issn-l": "1471-2164"}, "abstract": "Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of \u00d6tzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).\n\nA robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.\n\nWe revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.\n\nWe suggest that \u00d6tzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.", "doi": "10.1186/s12864-024-11123-2", "pmid": "39701966", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11660557"}, {"db": "pii", "key": "10.1186/s12864-024-11123-2"}], "notes": [], "created": "2025-11-21T13:36:48.522Z", "modified": "2025-11-21T13:36:48.531Z"}, {"entity": "publication", "iuid": "2a14fd27a1034c0a88a19ff85f785d19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a14fd27a1034c0a88a19ff85f785d19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a14fd27a1034c0a88a19ff85f785d19"}}, "title": "Characteristics of gene expression in epicardial adipose tissue and subcutaneous adipose tissue in patients at risk for heart failure undergoing coronary artery bypass grafting.", "authors": [{"family": "Frisk", "given": "Christoffer", "initials": "C"}, {"family": "Ekstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Eriksson", "given": "Maria J", "initials": "MJ"}, {"family": "Corbascio", "given": "Matthias", "initials": "M"}, {"family": "Hage", "given": "Camilla", "initials": "C"}, {"family": "Persson", "given": "Hans", "initials": "H"}, {"family": "Linde", "given": "Cecilia", "initials": "C"}, {"family": "Persson", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2024-10-07", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "938", "issn-l": "1471-2164"}, "abstract": "Epicardial adipose tissue (EAT) surrounds the heart and is hypothesised to play a role in the development of heart failure (HF). In this study, we first investigated the differences in gene expression between epicardial adipose tissue (EAT) and subcutaneous adipose tissue (SAT) in patients undergoing elective coronary artery bypass graft (CABG) surgery (n = 21; 95% male). Secondly, we examined the association between EAT and SAT in patients at risk for HF stage A (n = 12) and in pre-HF patients, who show signs but not symptoms of HF, stage B (n = 9).\n\nThe study confirmed a distinct separation between EAT and SAT. In EAT 17 clusters of genes were present, of which several novel gene modules are associated with characteristics of HF. Notably, seven gene modules showed significant correlation to measures of HF, such as end diastolic left ventricular posterior wall thickness, e'mean, deceleration time and BMI. One module was particularly distinct in EAT when compared to SAT, featuring key genes such as FLT4, SEMA3A, and PTX3, which are implicated in angiogenesis, inflammation regulation, and tissue repair, suggesting a unique role in EAT linked to left ventricular dysfunction. Genetic expression was compared in EAT across all pre-HF and normal phenotypes, revealing small genetic changes in the form of 18 differentially expressed genes in ACC/AHA Stage A vs. Stage B.\n\nThe roles of subcutaneous and epicardial fat are clearly different. We highlight the gene expression difference in search of potential modifiers of HF progress. The true implications of our findings should be corroborated in other studies since HF ACC/AHA stage B patients are common and carry a considerable risk for progression to symptomatic HF.", "doi": "10.1186/s12864-024-10851-9", "pmid": "39375631", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11457432"}, {"db": "pii", "key": "10.1186/s12864-024-10851-9"}], "notes": [], "created": "2024-10-31T12:36:52.295Z", "modified": "2025-02-28T14:22:11.481Z"}, {"entity": "publication", "iuid": "2d32c6ca69dd464487cda795b12e8a67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d32c6ca69dd464487cda795b12e8a67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d32c6ca69dd464487cda795b12e8a67"}}, "title": "Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies.", "authors": [{"family": "Sigur\u00f0ard\u00f3ttir", "given": "Hei\u00f0r\u00fan", "initials": "H"}, {"family": "Ablondi", "given": "Michela", "initials": "M"}, {"family": "Kristjansson", "given": "Thorvaldur", "initials": "T"}, {"family": "Lindgren", "given": "Gabriella", "initials": "G"}, {"family": "Eriksson", "given": "Susanne", "initials": "S"}], "type": "journal article", "published": "2024-08-08", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "772", "issn-l": "1471-2164"}, "abstract": "The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds.\n\nHO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20).\n\nEvaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.", "doi": "10.1186/s12864-024-10682-8", "pmid": "39118059", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11308356"}, {"db": "pii", "key": "10.1186/s12864-024-10682-8"}], "notes": [], "created": "2024-11-12T11:52:50.819Z", "modified": "2024-11-12T11:52:50.827Z"}, {"entity": "publication", "iuid": "53f9468fbc74451191f9dcfd1c77d21f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53f9468fbc74451191f9dcfd1c77d21f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53f9468fbc74451191f9dcfd1c77d21f"}}, "title": "Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology.", "authors": [{"family": "Biswas", "given": "Twinkle", "initials": "T", "orcid": "0000-0001-6106-0611", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e4bf354cc1240edbec52c1478249950.json"}}, {"family": "Vogel", "given": "Heiko", "initials": "H", "orcid": "0000-0001-9821-7731", "researcher": {"href": "https://publications.scilifelab.se/researcher/a64cd168fc814737830d2d01bacc78d6.json"}}, {"family": "Biedermann", "given": "Peter H W", "initials": "PHW", "orcid": "0000-0003-4234-5659", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cbd5bd2cf0445ca996d99377179272c.json"}}, {"family": "Lehenberger", "given": "Maximilian", "initials": "M", "orcid": "0000-0001-9097-9715", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5b54a1d9485441a9512d310f5025680.json"}}, {"family": "Yuvaraj", "given": "Jothi Kumar", "initials": "JK", "orcid": "0000-0002-5702-3751", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e338cdc27804e5795dfab4f8763424f.json"}}, {"family": "Andersson", "given": "Martin N", "initials": "MN", "orcid": "0000-0001-9807-8524", "researcher": {"href": "https://publications.scilifelab.se/researcher/42bc7f90fad040c292fceed405df5ac3.json"}}], "type": "journal article", "published": "2024-08-06", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "764", "issn-l": "1471-2164"}, "abstract": "Chemoreception is crucial for insect fitness, underlying for instance food-, host-, and mate finding. Chemicals in the environment are detected by receptors from three divergent gene families: odorant receptors (ORs), gustatory receptors (GRs), and ionotropic receptors (IRs). However, how the chemoreceptor gene families evolve in parallel with ecological specializations remains poorly understood, especially in the order Coleoptera. Hence, we sequenced the genome and annotated the chemoreceptor genes of the specialised ambrosia beetle Trypodendron lineatum (Coleoptera, Curculionidae, Scolytinae) and compared its chemoreceptor gene repertoires with those of other scolytines with different ecological adaptations, as well as a polyphagous cerambycid species.\n\nWe identified 67 ORs, 38 GRs, and 44 IRs in T. lineatum ('Tlin'). Across gene families, T. lineatum has fewer chemoreceptors compared to related scolytines, the coffee berry borer Hypothenemus hampei and the mountain pine beetle Dendroctonus ponderosae, and clearly fewer receptors than the polyphagous cerambycid Anoplophora glabripennis. The comparatively low number of chemoreceptors is largely explained by the scarcity of large receptor lineage radiations, especially among the bitter taste GRs and the 'divergent' IRs, and the absence of alternatively spliced GR genes. Only one non-fructose sugar receptor was found, suggesting several sugar receptors have been lost. Also, we found no orthologue in the 'GR215 clade', which is widely conserved across Coleoptera. Two TlinORs are orthologous to ORs that are functionally conserved across curculionids, responding to 2-phenylethanol (2-PE) and green leaf volatiles (GLVs), respectively.\n\nTrypodendron lineatum reproduces inside the xylem of decaying conifers where it feeds on its obligate fungal mutualist Phialophoropsis ferruginea. Like previous studies, our results suggest that stenophagy correlates with small chemoreceptor numbers in wood-boring beetles; indeed, the few GRs may be due to its restricted fungal diet. The presence of TlinORs orthologous to those detecting 2-PE and GLVs in other species suggests these compounds are important for T. lineatum. Future functional studies should test this prediction, and chemoreceptor annotations should be conducted on additional ambrosia beetle species to investigate whether few chemoreceptors is a general trait in this specialized group of beetles.", "doi": "10.1186/s12864-024-10678-4", "pmid": "39107741", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11302349"}, {"db": "pii", "key": "10.1186/s12864-024-10678-4"}], "notes": [], "created": "2024-08-15T12:16:43.573Z", "modified": "2024-11-25T10:30:07.491Z"}, {"entity": "publication", "iuid": "b1b22be3de694e3fa3f3b9a3ba9f6c78", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1b22be3de694e3fa3f3b9a3ba9f6c78.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1b22be3de694e3fa3f3b9a3ba9f6c78"}}, "title": "Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis.", "authors": [{"family": "Rosling", "given": "Anna", "initials": "A"}, {"family": "Eshghi Sahraei", "given": "Shadi", "initials": "S"}, {"family": "Kalsoom Khan", "given": "Faheema", "initials": "F"}, {"family": "Desir\u00f2", "given": "Alessandro", "initials": "A"}, {"family": "Bryson", "given": "Abigail E", "initials": "AE"}, {"family": "Mondo", "given": "Stephen J", "initials": "SJ"}, {"family": "Grigoriev", "given": "Igor V", "initials": "IV"}, {"family": "Bonito", "given": "Gregory", "initials": "G"}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M"}], "type": "journal article", "published": "2024-05-29", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "529", "issn-l": "1471-2164"}, "abstract": "The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid.\n\nIn this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89.\n\nBased on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.", "doi": "10.1186/s12864-024-10391-2", "pmid": "38811885", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11134847"}, {"db": "pii", "key": "10.1186/s12864-024-10391-2"}], "notes": [], "created": "2024-11-25T10:30:02.327Z", "modified": "2025-02-28T14:22:06.272Z"}, {"entity": "publication", "iuid": "f984c2d2de4c4dd39b5ce3c3921595b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f984c2d2de4c4dd39b5ce3c3921595b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f984c2d2de4c4dd39b5ce3c3921595b7"}}, "title": "Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring.", "authors": [{"family": "Mohamadnejad Sangdehi", "given": "Fahime", "initials": "F"}, {"family": "Jamsandekar", "given": "Minal S", "initials": "MS"}, {"family": "Enbody", "given": "Erik D", "initials": "ED"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2024-05-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "459", "issn-l": "1471-2164"}, "abstract": "Genome-wide comparisons of populations are widely used to explore the patterns of nucleotide diversity and sequence divergence to provide knowledge on how natural selection and genetic drift affect the genome. In this study we have compared whole-genome sequencing data from Atlantic and Pacific herring, two sister species that diverged about 2 million years ago, to explore the pattern of genetic differentiation between the two species.\n\nThe genome comparison of the two species revealed high genome-wide differentiation but with islands of remarkably low genetic differentiation, as measured by an FST analysis. However, the low FST observed in these islands is not caused by low interspecies sequence divergence (dxy) but rather by exceptionally high estimated intraspecies nucleotide diversity (\u03c0). These regions of low differentiation and elevated nucleotide diversity, termed high-diversity regions in this study, are not enriched for repeats but are highly enriched for immune-related genes. This enrichment includes genes from both the adaptive immune system, such as immunoglobulin, T-cell receptor and major histocompatibility complex genes, as well as a substantial number of genes with a role in the innate immune system, e.g. novel immune-type receptor, tripartite motif and tumor necrosis factor receptor genes. Analysis of long-read based assemblies from two Atlantic herring individuals revealed extensive copy number variation in these genomic regions, indicating that the elevated intraspecies nucleotide diversities were partially due to the cross-mapping of short reads.\n\nThis study demonstrates that copy number variation is a characteristic feature of immune trait loci in herring. Another important implication is that these loci are blind spots in classical genome-wide screens for genetic differentiation using short-read data, not only in herring, likely also in other species harboring qualitatively similar variation at immune trait loci. These loci stood out in this study because of the relatively high genome-wide baseline for FST values between Atlantic and Pacific herring.", "doi": "10.1186/s12864-024-10380-5", "pmid": "38730342", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11088111"}, {"db": "pii", "key": "10.1186/s12864-024-10380-5"}], "notes": [], "created": "2024-08-02T12:07:07.600Z", "modified": "2025-02-28T14:22:01.056Z"}, {"entity": "publication", "iuid": "1fe7298fac0643f4aad58a25d24aa7d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fe7298fac0643f4aad58a25d24aa7d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fe7298fac0643f4aad58a25d24aa7d0"}}, "title": "Loss of chromosome Y in regulatory T cells.", "authors": [{"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Bruhn-Olszewska", "given": "Bo\u017cena", "initials": "B"}, {"family": "Olszewski", "given": "Pawe\u0142", "initials": "P"}, {"family": "Danielsson", "given": "Marcus", "initials": "M"}, {"family": "Bjurling", "given": "Josefin", "initials": "J"}, {"family": "Lindberg", "given": "Amanda", "initials": "A"}, {"family": "Zaghlool", "given": "Ammar", "initials": "A"}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Forsberg", "given": "Lars A", "initials": "LA"}], "type": "journal article", "published": "2024-03-05", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "243", "issn-l": "1471-2164"}, "abstract": "Mosaic loss of chromosome Y (LOY) in leukocytes is the most prevalent somatic aneuploidy in aging humans. Men with LOY have increased risks of all-cause mortality and the major causes of death, including many forms of cancer. It has been suggested that the association between LOY and disease risk depends on what type of leukocyte is affected with Y loss, with prostate cancer patients showing higher levels of LOY in CD4 + T lymphocytes. In previous studies, Y loss has however been observed at relatively low levels in this cell type. This motivated us to investigate whether specific subsets of CD4 + T lymphocytes are particularly affected by LOY. Publicly available, T lymphocyte enriched, single-cell RNA sequencing datasets from patients with liver, lung or colorectal cancer were used to study how LOY affects different subtypes of T lymphocyte. To validate the observations from the public data, we also generated a single-cell RNA sequencing dataset comprised of 23 PBMC samples and 32 CD4 + T lymphocytes enriched samples.\n\nRegulatory T cells had significantly more LOY than any other studied T lymphocytes subtype. Furthermore, LOY in regulatory T cells increased the ratio of regulatory T cells compared with other T lymphocyte subtypes, indicating an effect of Y loss on lymphocyte differentiation. This was supported by developmental trajectory analysis of CD4 + T lymphocytes culminating in the regulatory T cells cluster most heavily affected by LOY. Finally, we identify dysregulation of 465 genes in regulatory T cells with Y loss, many involved in the immunosuppressive functions and development of regulatory T cells.\n\nHere, we show that regulatory T cells are particularly affected by Y loss, resulting in an increased fraction of regulatory T cells and dysregulated immune functions. Considering that regulatory T cells plays a critical role in the process of immunosuppression; this enrichment for regulatory T cells with LOY might contribute to the increased risk for cancer observed among men with Y loss in leukocytes.", "doi": "10.1186/s12864-024-10168-7", "pmid": "38443832", "labels": {"NGI Single cell": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10913415"}, {"db": "pii", "key": "10.1186/s12864-024-10168-7"}], "notes": [], "created": "2024-03-06T13:04:09.255Z", "modified": "2025-02-28T14:21:55.540Z"}, {"entity": "publication", "iuid": "999556e1041547b49d0a807a80249103", "links": {"self": {"href": "https://publications.scilifelab.se/publication/999556e1041547b49d0a807a80249103.json"}, "display": {"href": "https://publications.scilifelab.se/publication/999556e1041547b49d0a807a80249103"}}, "title": "Single-cell RNA-seq mapping of chicken peripheral blood leukocytes.", "authors": [{"family": "Maxwell", "given": "Matilda", "initials": "M"}, {"family": "S\u00f6derlund", "given": "Robert", "initials": "R"}, {"family": "H\u00e4rtle", "given": "Sonja", "initials": "S"}, {"family": "Wattrang", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2024-01-29", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "124", "issn-l": "1471-2164"}, "abstract": "Single-cell transcriptomics provides means to study cell populations at the level of individual cells. In leukocyte biology this approach could potentially aid the identification of subpopulations and functions without the need to develop species-specific reagents. The present study aimed to evaluate single-cell RNA-seq as a tool for identification of chicken peripheral blood leukocytes. For this purpose, purified and thrombocyte depleted leukocytes from 4 clinically healthy hens were subjected to single-cell 3' RNA-seq. Bioinformatic analysis of data comprised unsupervised clustering of the cells, and annotation of clusters based on expression profiles. Immunofluorescence phenotyping of the cell preparations used was also performed.\n\nComputational analysis identified 31 initial cell clusters and based on expression of defined marker genes 28 cluster were identified as comprising mainly B-cells, T-cells, monocytes, thrombocytes and red blood cells. Of the remaining clusters, two were putatively identified as basophils and eosinophils, and one as proliferating cells of mixed origin. In depth analysis on gene expression profiles within and between the initial cell clusters allowed further identification of cell identity and possible functions for some of them. For example, analysis of the group of monocyte clusters revealed subclusters comprising heterophils, as well as putative monocyte subtypes. Also, novel aspects of TCR\u03b3/\u03b4 + T-cell subpopulations could be inferred such as evidence of at least two subtypes based on e.g., different expression of transcription factors MAF, SOX13 and GATA3. Moreover, a novel subpopulation of chicken peripheral B-cells with high SOX5 expression was identified. An overall good correlation between mRNA and cell surface phenotypic cell identification was shown.\n\nTaken together, we were able to identify and infer functional aspects of both previously well known as well as novel chicken leukocyte populations although some cell types. e.g., T-cell subtypes, proved more challenging to decipher. Although this methodology to some extent is limited by incomplete annotation of the chicken genome, it definitively has benefits in chicken immunology by expanding the options to distinguish identity and functions of immune cells also without access to species specific reagents.", "doi": "10.1186/s12864-024-10044-4", "pmid": "38287279", "labels": {"NGI Single cell": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10826067"}, {"db": "pii", "key": "10.1186/s12864-024-10044-4"}], "notes": [], "created": "2024-01-31T13:03:41.480Z", "modified": "2024-11-25T10:29:46.749Z"}, {"entity": "publication", "iuid": "0533fbff25544d368a04f51d1e5e1a3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0533fbff25544d368a04f51d1e5e1a3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0533fbff25544d368a04f51d1e5e1a3b"}}, "title": "Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds.", "authors": [{"family": "Harish", "given": "Ajith", "initials": "A"}, {"family": "Lopes Pinto", "given": "Fernando A", "initials": "FA"}, {"family": "Eriksson", "given": "Susanne", "initials": "S"}, {"family": "Johansson", "given": "Anna M", "initials": "AM"}], "type": "journal article", "published": "2024-01-22", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "89", "issn-l": "1471-2164"}, "abstract": "Several indigenous cattle breeds in Sweden are endangered. Conservation of their genetic diversity and genomic characterization is a priority.Whole-genome sequences (WGS) with a mean coverage of 25X, ranging from 14 to 41X were obtained for 30 individuals of the breeds Fj\u00e4llko, Fj\u00e4lln\u00e4ra, Bohuskulla, R\u00f6dkulla, Ringam\u00e5la, and V\u00e4neko. WGS-based genotyping revealed 22,548,028 variants in total, comprising 18,876,115 single nucleotide polymorphisms (SNPs) and 3,671,913 indels. Out of these, 1,154,779 SNPs and 304,467 indels were novel. Population stratification based on roughly 19 million SNPs showed two major groups of the breeds that correspond to northern and southern breeds. Overall, a higher genetic diversity was observed in the southern breeds compared to the northern breeds. While the population stratification was consistent with previous genome-wide SNP array-based analyses, the genealogy of the individuals inferred from WGS based estimates turned out to be more complex than expected from previous SNP-array based estimates. Polymorphisms and their predicted phenotypic consequences were associated with differences in the coat color phenotypes between the northern and southern breeds. Notably, these high-consequence polymorphisms were not represented in SNP arrays, which are used routinely for genotyping of cattle breeds.This study is the first WGS-based population genetic analysis of Swedish native cattle breeds. The genetic diversity of native breeds was found to be high. High-consequence polymorphisms were linked with desirable phenotypes using whole-genome genotyping, which highlights the pressing need for intensifying WGS-based characterization of the native breeds.", "doi": "10.1186/s12864-024-09959-9", "pmid": "38254050", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10802049"}, {"db": "pii", "key": "10.1186/s12864-024-09959-9"}], "notes": [], "created": "2024-03-21T08:57:34.995Z", "modified": "2024-03-21T08:57:34.998Z"}, {"entity": "publication", "iuid": "9e395d12b51d4220bb42dc2a6d4227d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e395d12b51d4220bb42dc2a6d4227d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e395d12b51d4220bb42dc2a6d4227d1"}}, "title": "Functional annotation of a divergent genome using sequence and structure-based similarity.", "authors": [{"family": "Svedberg", "given": "Dennis", "initials": "D", "orcid": "0000-0001-5799-4075", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9273749dce544ee85e251fab9edbb70.json"}}, {"family": "Winiger", "given": "Rahel R", "initials": "RR", "orcid": "0000-0001-9796-5543", "researcher": {"href": "https://publications.scilifelab.se/researcher/75de6abd5afa48e5813919deb9132c85.json"}}, {"family": "Berg", "given": "Alexandra", "initials": "A", "orcid": "0000-0003-3609-2878", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1d5f2e44c4ab8bdd18c4b783f6dd4.json"}}, {"family": "Sharma", "given": "Himanshu", "initials": "H", "orcid": "0000-0001-9518-4671", "researcher": {"href": "https://publications.scilifelab.se/researcher/1be529a4b9854c9eba83cb99ce77a074.json"}}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C", "orcid": "0000-0003-0502-3693", "researcher": {"href": "https://publications.scilifelab.se/researcher/982873aade554b38b26b877298db5115.json"}}, {"family": "Debrunner-Vossbrinck", "given": "Bettina A", "initials": "BA"}, {"family": "Vossbrinck", "given": "Charles R", "initials": "CR", "orcid": "0000-0002-2929-9718", "researcher": {"href": "https://publications.scilifelab.se/researcher/436b6e437ad343f5bb21f6bdd1c56761.json"}}, {"family": "Barandun", "given": "Jonas", "initials": "J", "orcid": "0000-0003-2971-8190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2456fbe0b6bf406889842ab9f0267c22.json"}}], "type": "journal article", "published": "2024-01-02", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "6", "issn-l": "1471-2164"}, "abstract": "Microsporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on sequence similarity. As a result, many of the microsporidian genomes sequenced to date contain numerous genes of unknown function. Recent innovations in rapid and accurate structure prediction and comparison, together with the growing amount of data in structural databases, provide new opportunities to assist in the functional annotation of newly sequenced genomes.\n\nIn this study, we established a workflow that combines sequence and structure-based functional gene annotation approaches employing a ChimeraX plugin named ANNOTEX (Annotation Extension for ChimeraX), allowing for visual inspection and manual curation. We employed this workflow on a high-quality telomere-to-telomere sequenced tetraploid genome of Vairimorpha necatrix. First, the 3080 predicted protein-coding DNA sequences, of which 89% were confirmed with RNA sequencing data, were used as input. Next, ColabFold was used to create protein structure predictions, followed by a Foldseek search for structural matching to the PDB and AlphaFold databases. The subsequent manual curation, using sequence and structure-based hits, increased the accuracy and quality of the functional genome annotation compared to results using only traditional annotation tools. Our workflow resulted in a comprehensive description of the V. necatrix genome, along with a structural summary of the most prevalent protein groups, such as the ricin B lectin family. In addition, and to test our tool, we identified the functions of several previously uncharacterized Encephalitozoon cuniculi genes.\n\nWe provide a new functional annotation tool for divergent organisms and employ it on a newly sequenced, high-quality microsporidian genome to shed light on this uncharacterized intracellular pathogen of Lepidoptera. The addition of a structure-based annotation approach can serve as a valuable template for studying other microsporidian or similarly divergent species.", "doi": "10.1186/s12864-023-09924-y", "pmid": "38166563", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10759460"}, {"db": "pii", "key": "10.1186/s12864-023-09924-y"}], "notes": [], "created": "2024-01-10T09:47:15.771Z", "modified": "2025-02-28T14:21:50.443Z"}, {"entity": "publication", "iuid": "5f21ede989334e04a527a393eddf2ae8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f21ede989334e04a527a393eddf2ae8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f21ede989334e04a527a393eddf2ae8"}}, "title": "Improved detection of clinically relevant fusion transcripts in cancer by machine learning classification.", "authors": [{"family": "Hafsta\u00f0", "given": "V\u00f6lundur", "initials": "V"}, {"family": "H\u00e4kkinen", "given": "Jari", "initials": "J"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Staaf", "given": "Johan", "initials": "J"}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J"}, {"family": "Persson", "given": "Helena", "initials": "H"}], "type": "journal article", "published": "2023-12-18", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "24", "issue": "1", "pages": "783", "issn-l": "1471-2164"}, "abstract": "Genomic rearrangements in cancer cells can create fusion genes that encode chimeric proteins or alter the expression of coding and non-coding RNAs. In some cancer types, fusions involving specific kinases are used as targets for therapy. Fusion genes can be detected by whole genome sequencing (WGS) and targeted fusion panels, but RNA sequencing (RNA-Seq) has the advantageous capability of broadly detecting expressed fusion transcripts.\n\nWe developed a pipeline for validation of fusion transcripts identified in RNA-Seq data using matched WGS data from The Cancer Genome Atlas (TCGA) and applied it to 910 tumors from 11 different cancer types. This resulted in 4237 validated gene fusions, 3049 of them with at least one identified genomic breakpoint. Utilizing validated fusions as true positive events, we trained a machine learning classifier to predict true and false positive fusion transcripts from RNA-Seq data. The final precision and recall metrics of the classifier were 0.74 and 0.71, respectively, in an independent dataset of 249 breast tumors. Application of this classifier to all samples with RNA-Seq data from these cancer types vastly extended the number of likely true positive fusion transcripts and identified many potentially targetable kinase fusions. Further analysis of the validated gene fusions suggested that many are created by intrachromosomal amplification events with microhomology-mediated non-homologous end-joining.\n\nA classifier trained on validated fusion events increased the accuracy of fusion transcript identification in samples without WGS data. This allowed the analysis to be extended to all samples with RNA-Seq data, facilitating studies of tumor biology and increasing the number of detected kinase fusions. Machine learning could thus be used in identification of clinically relevant fusion events for targeted therapy. The large dataset of validated gene fusions generated here presents a useful resource for development and evaluation of fusion transcript detection algorithms.", "doi": "10.1186/s12864-023-09889-y", "pmid": "38110872", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10726539"}, {"db": "pii", "key": "10.1186/s12864-023-09889-y"}], "notes": [], "created": "2024-01-16T12:11:57.715Z", "modified": "2024-11-25T10:29:36.525Z"}, {"entity": "publication", "iuid": "644ff655a61e46c08a5438a23c82830c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/644ff655a61e46c08a5438a23c82830c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/644ff655a61e46c08a5438a23c82830c"}}, "title": "RecView: an interactive R application for locating recombination positions using pedigree data.", "authors": [{"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2023-11-25", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "24", "issue": "1", "pages": "712", "issn-l": "1471-2164"}, "abstract": "Recombination reshuffles alleles at linked loci, allowing genes to evolve independently and consequently enhancing the efficiency of selection. This makes quantifying recombination along chromosomes an important goal for understanding how selection and drift are acting on genes and chromosomes.\n\nWe present RecView, an interactive R application and its homonymous R package, to facilitate locating recombination positions along chromosomes or scaffolds using whole-genome genotype data of a three-generation pedigree. RecView analyses and plots the grandparent-of-origin of all informative alleles along each chromosome of the offspring in the pedigree, and infers recombination positions with either of two built-in algorithms: one based on change in the proportion of the alleles with specific grandparent-of-origin, and one on the degree of continuity of alleles with the same grandparent-of-origin. RecView handles multiple offspring and chromosomes simultaneously, and all putative recombination positions are reported in base pairs together with an estimated precision based on the local density of informative alleles. We demonstrate RecView using genotype data of a passerine bird with an available reference genome, the great reed warbler (Acrocephalus arundinaceus), and show that recombination events can be located to specific positions.\n\nRecView is an easy-to-use and highly effective application for locating recombination positions with high precision. RecView is available on GitHub ( https://github.com/HKyleZhang/RecView.git ).", "doi": "10.1186/s12864-023-09807-2", "pmid": "38007417", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10676570"}, {"db": "pii", "key": "10.1186/s12864-023-09807-2"}], "notes": [], "created": "2024-01-08T16:11:18.459Z", "modified": "2024-01-16T13:48:31.644Z"}, {"entity": "publication", "iuid": "2e31abdf99b245178c96a47d5696b8da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e31abdf99b245178c96a47d5696b8da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e31abdf99b245178c96a47d5696b8da"}}, "title": "Seasonal and age-related changes in sperm quality of farmed arctic charr (Salvelinus alpinus).", "authors": [{"family": "Kurta", "given": "Khrystyna", "initials": "K"}, {"family": "Jeuthe", "given": "Henrik", "initials": "H"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R"}, {"family": "de Koning", "given": "Dirk-Jan", "initials": "DJ"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C"}], "type": "journal article", "published": "2023-09-04", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "24", "issue": "1", "pages": "519", "issn-l": "1471-2164"}, "abstract": "Substantial variation in male fertility is regularly observed in farmed Arctic charr. However, detailed investigations of its fluctuation during a reproductive season and across years are lacking. Furthermore, information about the effect of underlying genetic factors influencing sperm quality is scarce. The current study focused on seasonal and age-related factors that may affect sperm quality characteristics in males reared in natural and delayed photoperiods. Animals were sampled three times for two consecutive years, and sperm quality parameters were recorded using a computer-assisted sperm analysis (CASA) system. Thereafter, high-throughput sequencing technologies were applied, aiming to identify genomic regions related to the variation of sperm quality throughout the reproductive season.\n\nAn across-season variation in the recorded sperm quality parameters was evident. Overall, 29% and 42% of males from the natural and delayed spawning groups had a highly variable total progressive motility. Males at four years of age showed significantly higher sperm motility and velocities during the early October and November recordings compared to the following year when the same animals were five years of age. On the other hand, the opposite was observed regarding sperm concentration during the last sampling. A genome-wide FST scan detected SNP differentiation among males with high and low variability in total progressive motility (PM) on eight chromosomes (FST > 0.17), Genome wide windows with the highest FST contained SNPs in proximity (within 250 kb up- and downstream distance) to 16 genes with sperm quality biological functions in mammalian species.\n\nOur findings provide a detailed view of seasonal, age-related, and genetic effects on sperm quality and can be used to guide decisions on broodstock selection and hatchery management.", "doi": "10.1186/s12864-023-09614-9", "pmid": "37667174", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10478403"}, {"db": "pii", "key": "10.1186/s12864-023-09614-9"}], "notes": [], "created": "2023-11-29T10:58:03.579Z", "modified": "2023-11-29T10:58:03.583Z"}, {"entity": "publication", "iuid": "cfaa7d44c1834ba79dee356633f30546", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cfaa7d44c1834ba79dee356633f30546.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cfaa7d44c1834ba79dee356633f30546"}}, "title": "T-RHEX-RNAseq - a tagmentation-based, rRNA blocked, random hexamer primed RNAseq method for generating stranded RNAseq libraries directly from very low numbers of lysed cells.", "authors": [{"family": "Gustafsson", "given": "Charlotte", "initials": "C"}, {"family": "Hauenstein", "given": "Julia", "initials": "J"}, {"family": "Frengen", "given": "Nicolai", "initials": "N"}, {"family": "Krstic", "given": "Aleksandra", "initials": "A"}, {"family": "Luc", "given": "Sidinh", "initials": "S"}, {"family": "M\u00e5nsson", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2023-04-17", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "24", "issue": "1", "pages": "205", "issn-l": "1471-2164"}, "abstract": "RNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming - to allow analysis of a broader range of transcripts - remains challenging.\n\nWe here describe a tagmentation-based, rRNA blocked, random hexamer primed RNAseq approach (T-RHEX-RNAseq) for generating stranded RNAseq libraries from very low numbers of FACS sorted cells without RNA purification steps.\n\nT-RHEX-RNAseq provides an easy-to-use, time efficient and automation compatible method for generating stranded RNAseq libraries from rare cells.", "doi": "10.1186/s12864-023-09279-4", "pmid": "37069502", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10111750"}, {"db": "pii", "key": "10.1186/s12864-023-09279-4"}], "notes": [], "created": "2023-11-27T21:59:21.543Z", "modified": "2024-01-16T13:48:33.691Z"}, {"entity": "publication", "iuid": "a447417a7c664b86a0308dd49ea05b31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a447417a7c664b86a0308dd49ea05b31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a447417a7c664b86a0308dd49ea05b31"}}, "title": "The genetic basis of wing spots in Pieris canidia butterflies.", "authors": [{"family": "Wee", "given": "Jocelyn Liang Qi", "initials": "JLQ"}, {"family": "Murugesan", "given": "Suriya Narayanan", "initials": "SN"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Monteiro", "given": "Ant\u00f3nia", "initials": "A"}], "type": "journal article", "published": "2023-04-04", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "24", "issue": "1", "pages": "169", "issn-l": "1471-2164"}, "abstract": "Spots in pierid butterflies and eyespots in nymphalid butterflies are likely non-homologous wing colour pattern elements, yet they share a few features in common. Both develop black scales that depend on the function of the gene spalt, and both might have central signalling cells. This suggests that both pattern elements may be sharing common genetic circuitry. Hundreds of genes have already been associated with the development of nymphalid butterfly eyespot patterns, but the genetic basis of the simpler spot patterns on the wings of pierid butterflies has not been investigated. To facilitate studies of pierid wing patterns, we report a high-quality draft genome assembly for Pieris canidia, the Indian cabbage white. We then conducted transcriptomic analyses of pupal wing tissues sampled from the spot and non-spot regions of P. canidia at 3-6 h post-pupation. A total of 1352 genes were differentially regulated between wing tissues with and without the black spot, including spalt, Kr\u00fcppel-like factor 10, genes from the Toll, Notch, TGF-\u03b2, and FGFR signalling pathways, and several genes involved in the melanin biosynthetic pathway. We identified 14 genes that are up-regulated in both pierid spots and nymphalid eyespots and propose that spots and eyespots share regulatory modules despite their likely independent origins.", "doi": "10.1186/s12864-023-09261-0", "pmid": "37016295", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10074818"}, {"db": "pii", "key": "10.1186/s12864-023-09261-0"}], "notes": [], "created": "2024-03-14T12:56:18.609Z", "modified": "2024-03-14T12:56:18.614Z"}, {"entity": "publication", "iuid": "86aa459ca48c418cbf4991eda32b3d72", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86aa459ca48c418cbf4991eda32b3d72.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86aa459ca48c418cbf4991eda32b3d72"}}, "title": "Preselection of QTL markers enhances accuracy of genomic selection in Norway spruce.", "authors": [{"family": "Chen", "given": "Zhi-Qiang", "initials": "ZQ"}, {"family": "Klingberg", "given": "Adam", "initials": "A"}, {"family": "Hallingb\u00e4ck", "given": "Henrik R", "initials": "HR"}, {"family": "Wu", "given": "Harry X", "initials": "HX"}], "type": "journal article", "published": "2023-03-27", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "24", "issue": "1", "pages": "147", "issn-l": "1471-2164"}, "abstract": "Genomic prediction (GP) or genomic selection is a method to predict the accumulative effect of all quantitative trait loci (QTLs) in a population by estimating the realized genomic relationships between the individuals and by capturing the linkage disequilibrium between markers and QTLs. Thus, marker preselection is considered a promising method to capture Mendelian segregation effects. Using QTLs detected in a genome-wide association study (GWAS) may improve GP. Here, we performed GWAS and GP in a population with 904 clones from 32 full-sib families using a newly developed 50 k SNP Norway spruce array. Through GWAS we identified 41 SNPs associated with budburst stage (BB) and the largest effect association explained 5.1% of the phenotypic variation (PVE). For the other five traits such as growth and wood quality traits, only 2 - 13 associations were observed and the PVE of the strongest effects ranged from 1.2% to 2.0%. GP using approximately 100 preselected SNPs, based on the smallest p-values from GWAS showed the greatest predictive ability (PA) for the trait BB. For the other traits, a preselection of 2000-4000 SNPs, was found to offer the best model fit according to the Akaike information criterion being minimized. But PA-magnitudes from GP using such selections were still similar to that of GP using all markers. Analyses on both real-life and simulated data also showed that the inclusion of a large QTL SNP in the model as a fixed effect could improve PA and accuracy of GP provided that the PVE of the QTL was \u2265 2.5%.", "doi": "10.1186/s12864-023-09250-3", "pmid": "36973641", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10041705"}, {"db": "pii", "key": "10.1186/s12864-023-09250-3"}], "notes": [], "created": "2023-05-17T08:57:46.051Z", "modified": "2024-01-16T13:48:33.802Z"}, {"entity": "publication", "iuid": "60891ce7bff2454680910f942c1a0ea5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60891ce7bff2454680910f942c1a0ea5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60891ce7bff2454680910f942c1a0ea5"}}, "title": "Stochastic nuclear organization and host-dependent allele contribution in Rhizophagus irregularis.", "authors": [{"family": "van Creij", "given": "Jelle", "initials": "J"}, {"family": "Auxier", "given": "Ben", "initials": "B"}, {"family": "An", "given": "Jianyong", "initials": "J"}, {"family": "Wijfjes", "given": "Ra\u00fal Y", "initials": "RY"}, {"family": "Bergin", "given": "Claudia", "initials": "C"}, {"family": "Rosling", "given": "Anna", "initials": "A"}, {"family": "Bisseling", "given": "Ton", "initials": "T"}, {"family": "Pan", "given": "Zhiyong", "initials": "Z"}, {"family": "Limpens", "given": "Erik", "initials": "E", "orcid": "0000-0002-9668-4085", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7051d73c8c34cd68395ee015701fb5c.json"}}], "type": "journal article", "published": "2023-01-28", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "24", "issue": "1", "pages": "53", "issn-l": "1471-2164"}, "abstract": "Arbuscular mycorrhizal (AM) fungi are arguably the most important symbionts of plants, offering a range of benefits to their hosts. However, the provisioning of these benefits does not appear to be uniform among AM fungal individuals, with genetic variation between fungal symbionts having a substantial impact on plant performance. Interestingly, genetic variation has also been reported within fungal individuals, which contain millions of haploid nuclei sharing a common cytoplasm. In the model AM fungus, Rhizophagus irregularis, several isolates have been reported to be dikaryotes, containing two genetically distinct types of nuclei recognized based on their mating-type (MAT) locus identity. However, their extremely coenocytic nature and lack of a known single nucleus stage has raised questions on the origin, distribution and dynamics of this genetic variation.\n\nHere we performed DNA and RNA sequencing at the mycelial individual, single spore and single nucleus levels to gain insight into the dynamic genetic make-up of the dikaryote-like R. irregularis C3 isolate and the effect of different host plants on its genetic variation. Our analyses reveal that parallel spore and root culture batches can have widely variable ratios of two main genotypes in C3. Additionally, numerous polymorphisms were found with frequencies that deviated significantly from the general genotype ratio, indicating a diverse population of slightly different nucleotypes. Changing host plants did not show consistent host effects on nucleotype ratio's after multiple rounds of subculturing. Instead, we found a major effect of host plant-identity on allele-specific expression in C3.\n\nOur analyses indicate a highly dynamic/variable genetic organization in different isolates of R. irregularis. Seemingly random fluctuations in nucleotype ratio's upon spore formation, recombination events, high variability of non-tandemly repeated rDNA sequences and host-dependent allele expression all add levels of variation that may contribute to the evolutionary success of these widespread symbionts.", "doi": "10.1186/s12864-023-09126-6", "pmid": "36709253", "labels": {"Microbial Single Cell Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9883914"}, {"db": "pii", "key": "10.1186/s12864-023-09126-6"}], "notes": [], "created": "2023-04-28T09:35:18.507Z", "modified": "2023-04-28T09:36:39.678Z"}, {"entity": "publication", "iuid": "f6085b6a093542799cfce5d77056cf6d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6085b6a093542799cfce5d77056cf6d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6085b6a093542799cfce5d77056cf6d"}}, "title": "Early changes in gene expression profiles in AML patients during induction chemotherapy.", "authors": [{"family": "Jakobsen", "given": "Ingrid", "initials": "I", "orcid": "0000-0003-4450-0333", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf014a7141ae4ebe854146cee082c6b2.json"}}, {"family": "Sundkvist", "given": "Max", "initials": "M"}, {"family": "Bj\u00f6rn", "given": "Niclas", "initials": "N", "orcid": "0000-0001-6806-4527", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39cecc1714f4331b08a47f1f1bbe7ac.json"}}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H", "orcid": "0000-0002-8015-5728", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d92037931f64b70b8d4bf78dab628b4.json"}}, {"family": "Lotfi", "given": "Kourosh", "initials": "K", "orcid": "0000-0001-5797-7232", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c292ca46bf444fd8b79adc76555e722.json"}}], "type": "journal article", "published": "2022-11-14", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "23", "issue": "1", "pages": "752"}, "abstract": "Elucidation of the genetic mechanisms underlying treatment response to standard induction chemotherapy in AML patients is warranted, in order to aid in risk-adapted treatment decisions as novel treatments are emerging. In this pilot study, we explored the treatment-induced expression patterns in a small cohort of AML patients by analyzing differential gene expression (DGE) over the first 2 days of induction chemotherapy.\n\nBlood samples were collected from ten AML patients at baseline (before treatment initiation) and during the first 2 days of treatment (Day 1; approximately 24 h, and Day 2; approximately 48 h after treatment initiation, respectively) and RNA was extracted for subsequent RNA sequencing. DGE between time points were assessed by pairwise analysis using the R package edgeR version 3.18.1 in all patients as well as in relation to treatment response (complete remission, CR, vs non-complete remission, nCR). Ingenuity Pathway Analysis (Qiagen) software was used for pathway analysis and visualization.\n\nAfter initial data quality control, two patients were excluded from further analysis, resulting in a final cohort of eight patients with data from all three timepoints. DGE analysis demonstrated activation of pathways with genes directly or indirectly associated with NF-\u03baB signaling. Significant activation of the NF-\u03baB pathway was seen in 50% of the patients 2 days after treatment start, while iNOS pathway effects could be identified already after 1 day. nCR patients displayed activation of pathways associated with cell cycle progression, oncogenesis and anti-apoptotic behavior, including the STAT3 pathway and Salvage pathways of pyrimidine ribonucleotides. Notably, a significant induction of cytidine deaminase, an enzyme responsible for the deamination of Ara-C, could be observed between baseline and Day 2 in the nCR patients but not in patients achieving CR.\n\nIn conclusion, we show that time-course analysis of gene expression represents a feasible approach to identify relevant pathways affected by standard induction chemotherapy in AML patients. This poses as a potential method for elucidating new drug targets and biomarkers for categorizing disease aggressiveness and evaluating treatment response. However, more studies on larger cohorts are warranted to elucidate the transcriptional basis for drug response.", "doi": "10.1186/s12864-022-08960-4", "pmid": "36376859", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9664790"}, {"db": "pii", "key": "10.1186/s12864-022-08960-4"}], "notes": [], "created": "2022-12-19T10:42:55.959Z", "modified": "2023-10-16T15:31:03.123Z"}, {"entity": "publication", "iuid": "78ffb8b1ccac450ba856236c88120517", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78ffb8b1ccac450ba856236c88120517.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78ffb8b1ccac450ba856236c88120517"}}, "title": "Genomic trajectories of a near-extinction event in the Chatham Island black robin.", "authors": [{"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Sigeman", "given": "Hanna", "initials": "H"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Knapp", "given": "Michael", "initials": "M"}, {"family": "Kardailsky", "given": "Olga", "initials": "O"}, {"family": "Robertson", "given": "Fiona", "initials": "F"}, {"family": "Hale", "given": "Marie", "initials": "M"}, {"family": "Houston", "given": "Dave", "initials": "D"}, {"family": "Kennedy", "given": "Euan", "initials": "E"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Massaro", "given": "Melanie", "initials": "M"}, {"family": "Robertson", "given": "Bruce C", "initials": "BC"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}], "type": "journal article", "published": "2022-11-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "23", "issue": "1", "pages": "747"}, "abstract": "Understanding the micro--evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation.\n\nWe found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations.\n\nOur results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.", "doi": "10.1186/s12864-022-08963-1", "pmid": "36357860", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9647977"}, {"db": "pii", "key": "10.1186/s12864-022-08963-1"}], "notes": [], "created": "2022-12-19T10:39:30.158Z", "modified": "2023-10-16T15:12:57.954Z"}, {"entity": "publication", "iuid": "52583936c1024a468226e9c12527aaaa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52583936c1024a468226e9c12527aaaa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52583936c1024a468226e9c12527aaaa"}}, "title": "Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA.", "authors": [{"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK"}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF"}, {"family": "Ramesh", "given": "Malavika", "initials": "M"}, {"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA"}], "type": "journal article", "published": "2022-10-15", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "23", "issue": "1", "pages": "704"}, "abstract": "The Mycobacterium genus encompasses at least 192 named species, many of which cause severe diseases such as tuberculosis. Non-tuberculosis mycobacteria (NTM) can also infect humans and animals. Some are of emerging concern because they show high resistance to commonly used antibiotics while others are used and evaluated in bioremediation or included in anticancer vaccines.\r\n\r\nWe provide the genome sequences for 114 mycobacterial type strains and together with 130 available mycobacterial genomes we generated a phylogenetic tree based on 387 core genes and supported by average nucleotide identity (ANI) data. The 244 genome sequences cover most of the species constituting the Mycobacterium genus. The genome sizes ranged from 3.2 to 8.1 Mb with an average of 5.7 Mb, and we identified 14 new plasmids. Moreover, mycobacterial genomes consisted of phage-like sequences ranging between 0 and 4.64% dependent on mycobacteria while the number of IS elements varied between 1 and 290. Our data also revealed that, depending on the mycobacteria, the number of tRNA and non-coding (nc) RNA genes differ and that their positions on the chromosome varied. We identified a conserved core set of 12 ncRNAs, 43 tRNAs and 18 aminoacyl-tRNA synthetases among mycobacteria.\r\n\r\nPhages, IS elements, tRNA and ncRNAs appear to have contributed to the evolution of the Mycobacterium genus where several tRNA and ncRNA genes have been horizontally transferred. On the basis of our phylogenetic analysis, we identified several isolates of unnamed species as new mycobacterial species or strains of known mycobacteria. The predicted number of coding sequences correlates with genome size while the number of tRNA, rRNA and ncRNA genes does not. Together these findings expand our insight into the evolution of the Mycobacterium genus and as such they establish a platform to understand mycobacterial pathogenicity, their evolution, antibiotic resistance/tolerance as well as the function and evolution of ncRNA among mycobacteria.", "doi": "10.1186/s12864-022-08927-5", "pmid": "36243697", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-022-08927-5"}, {"db": "pmc", "key": "PMC9569102"}], "notes": [], "created": "2022-11-21T10:04:26.689Z", "modified": "2024-01-16T13:48:34.732Z"}, {"entity": "publication", "iuid": "f727437a58c3458fbfbb061c7872de44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f727437a58c3458fbfbb061c7872de44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f727437a58c3458fbfbb061c7872de44"}}, "title": "Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Sinclair", "given": "Bella", "initials": "B"}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2022-04-27", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "23", "issue": "1", "pages": "328", "issn-l": "1471-2164"}, "abstract": "Sex chromosomes have evolved numerous times, as revealed by recent genomic studies. However, large gaps in our knowledge of sex chromosome diversity across the tree of life remain. Filling these gaps, through the study of novel species, is crucial for improved understanding of why and how sex chromosomes evolve. Characterization of sex chromosomes in already well-studied organisms is also important to avoid misinterpretations of population genomic patterns caused by undetected sex chromosome variation.\n\nHere we present findZX, an automated Snakemake-based computational pipeline for detecting and visualizing sex chromosomes through differences in genome coverage and heterozygosity between any number of males and females. A main feature of the pipeline is the option to perform a genome coordinate liftover to a reference genome of another species. This allows users to inspect sex-linked regions over larger contiguous chromosome regions, while also providing important between-species synteny information. To demonstrate its effectiveness, we applied findZX to publicly available genomic data from species belonging to widely different taxonomic groups (mammals, birds, reptiles, and fish), with sex chromosome systems of different ages, sizes, and levels of differentiation. We also demonstrate that the liftover method is robust over large phylogenetic distances (> 80 million years of evolution).\n\nWith findZX we provide an easy-to-use and highly effective tool for identification of sex chromosomes. The pipeline is compatible with both Linux and MacOS systems, and scalable to suit different computational platforms.", "doi": "10.1186/s12864-022-08432-9", "pmid": "35477344", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9044604"}, {"db": "pii", "key": "10.1186/s12864-022-08432-9"}], "notes": [], "created": "2022-05-19T14:57:04.550Z", "modified": "2024-01-16T13:48:36.973Z"}, {"entity": "publication", "iuid": "64118dce7d1343469bcff7d1753b674f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64118dce7d1343469bcff7d1753b674f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64118dce7d1343469bcff7d1753b674f"}}, "title": "Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line.", "authors": [{"family": "Lewerentz", "given": "Jacob", "initials": "J", "orcid": "0000-0001-5013-9498", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb6f36f637804d6e9a9d58d28ce5bd92.json"}}, {"family": "Johansson", "given": "Anna-Mia", "initials": "A"}, {"family": "Larsson", "given": "Jan", "initials": "J"}, {"family": "Stenberg", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2022-04-07", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "23", "issue": "1", "pages": "276"}, "abstract": "Immortalized cell lines are widely used model systems whose genomes are often highly rearranged and polyploid. However, their genome structure is seldom deciphered and is thus not accounted for during analyses. We therefore used linked short- and long-read sequencing to perform haplotype-level reconstruction of the genome of a Drosophila melanogaster cell line (S2-DRSC) with a complex genome structure.\r\n\r\nUsing a custom implementation (that is designed to use ultra-long reads in complex genomes with nested rearrangements) to call structural variants (SVs), we found that the most common SV was repetitive sequence insertion or deletion (> 80% of SVs), with Gypsy retrotransposon insertions dominating. The second most common SV was local sequence duplication. SNPs and other SVs were rarer, but several large chromosomal translocations and mitochondrial genome insertions were observed. Haplotypes were highly similar at the nucleotide level but structurally very different. Insertion SVs existed at various haplotype frequencies and were unlinked on chromosomes, demonstrating that haplotypes have different structures and suggesting the existence of a mechanism that allows SVs to propagate across haplotypes. Finally, using public short-read data, we found that transposable element insertions and local duplications are common in other D. melanogaster cell lines.\r\n\r\nThe S2-DRSC cell line evolved through retrotransposon activity and vast local sequence duplications, that we hypothesize were the products of DNA re-replication events. Additionally, mutations can propagate across haplotypes (possibly explained by mitotic recombination), which enables fine-tuning of mutational impact and prevents accumulation of deleterious events, an inherent problem of clonal reproduction. We conclude that traditional linear homozygous genome representation conceals the complexity when dealing with rearranged and heterozygous clonal cells.", "doi": "10.1186/s12864-022-08472-1", "pmid": "35392795", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8991648"}, {"db": "pii", "key": "10.1186/s12864-022-08472-1"}], "notes": [], "created": "2022-08-19T08:37:15.097Z", "modified": "2024-01-16T13:48:37.069Z"}, {"entity": "publication", "iuid": "4f8f700e79bb4eaf93c08f95fc56854b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f8f700e79bb4eaf93c08f95fc56854b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f8f700e79bb4eaf93c08f95fc56854b"}}, "title": "TC-hunter: identification of the insertion site of a transgenic gene within the host genome.", "authors": [{"family": "B\u00f6rjesson", "given": "Vanja", "initials": "V"}, {"family": "Martinez-Monleon", "given": "Angela", "initials": "A"}, {"family": "Fransson", "given": "Susanne", "initials": "S"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Johnsen", "given": "John Inge", "initials": "JI"}, {"family": "Milosevic", "given": "Jelena", "initials": "J"}, {"family": "L\u00f3pez", "given": "Marcela D\u00e1vila", "initials": "MD"}], "type": "journal article", "published": "2022-02-20", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "23", "issue": "1", "pages": "149"}, "abstract": "Transgenic animal models are crucial for the study of gene function and disease, and are widely utilized in basic biological research, agriculture and pharma industries. Since the current methods for generating transgenic animals result in the random integration of the transgene under study, the phenotype may be compromised due to disruption of known genes or regulatory regions. Unfortunately, most of the tools that predict transgene insertion sites from high-throughput data are not publicly available or not properly maintained.\r\n\r\nWe implemented TC-hunter, Transgene-Construct hunter, an open tool that identifies transgene insertion sites and provides simple reports and visualization aids. It relies on common tools used in the analysis of high-throughput data and makes use of chimeric reads and discordant read pairs to identify and support the transgenic insertion site. To demonstrate its applicability, we applied TC-hunter to four transgenic mice samples harboring the human PPM1D gene, a model used in the study of malignant tumor development. We identified the transgenic insertion site in each sample and experimentally validated them with Touchdown-polymerase chain reaction followed by Sanger sequencing.\r\n\r\nTC-hunter is an accessible bioinformatics tool that can automatically identify transgene insertion sites from DNA sequencing data with high sensitivity (98%) and precision (92.45%). TC-hunter is a valuable tool that can aid in evaluating any potential phenotypic complications due to the random integration of the transgene and can be accessed at https://github.com/bcfgothenburg/SSF .", "doi": "10.1186/s12864-022-08376-0", "pmid": "35184734", "labels": {"Clinical Genomics Gothenburg": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC8859905"}, {"db": "pii", "key": "10.1186/s12864-022-08376-0"}], "notes": [], "created": "2022-12-02T12:22:47.042Z", "modified": "2023-05-15T16:38:32.835Z"}, {"entity": "publication", "iuid": "14134f63018347aa8d6babcae10aa9ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14134f63018347aa8d6babcae10aa9ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14134f63018347aa8d6babcae10aa9ee"}}, "title": "Mutation analysis of disease causing genes in patients with early onset or familial forms of Alzheimer's disease and frontotemporal dementia.", "authors": [{"family": "Pagnon de la Vega", "given": "Mar\u00eda", "initials": "M"}, {"family": "N\u00e4slund", "given": "Carl", "initials": "C"}, {"family": "Brundin", "given": "RoseMarie", "initials": "R"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "L\u00f6wenmark", "given": "Malin", "initials": "M"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}], "type": "journal article", "published": "2022-02-04", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "23", "issue": "1", "pages": "99", "issn-l": "1471-2164"}, "abstract": "Most dementia disorders have a clear genetic background and a number of disease genes have been identified. Mutations in the tau gene (MAPT) lead to frontotemporal dementia (FTD), whereas mutations in the genes for the amyloid-\u03b2 precursor protein (APP) and the presenilins (PSEN1, PSEN2) cause early-onset, dominantly inherited forms of Alzheimer's disease (AD). Even if mutations causing Mendelian forms of these diseases are uncommon, elucidation of the pathogenic effects of such mutations have proven important for understanding the pathogenic processes. Here, we performed a screen to identify novel pathogenic mutations in known disease genes among patients undergoing dementia investigation.\n\nUsing targeted exome sequencing we have screened all coding exons in eleven known dementia genes (PSEN1, PSEN2, APP, MAPT, APOE, GRN, TARDBP, CHMP2B, TREM2, VCP and FUS) in 102 patients with AD, FTD, other dementia diagnoses or mild cognitive impairment. We found three AD patients with two previously identified pathogenic mutations in PSEN1 (Pro264Leu and Met146Val). In this screen, we also identified the recently reported APP mutation in two siblings with AD. This mutation, named the Uppsala mutation, consists of a six amino acid intra-amyloid \u03b2 deletion. In addition, we found several potentially pathogenic mutations in PSEN2, FUS, MAPT, GRN and APOE. Finally, APOE \u03b54 was prevalent in this patient group with an allele frequency of 54%.\n\nAmong the 102 screened patients, we found two disease causing mutations in PSEN1 and one in APP, as well as several potentially pathogenic mutations in other genes related to neurodegenerative disorders. Apart from giving important information to the clinical investigation, the identification of disease mutations can contribute to an increased understanding of disease mechanisms.", "doi": "10.1186/s12864-022-08343-9", "pmid": "35120450", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-022-08343-9"}, {"db": "pmc", "key": "PMC8817590"}], "notes": [], "created": "2022-03-29T18:38:39.114Z", "modified": "2022-03-29T18:38:39.120Z"}, {"entity": "publication", "iuid": "f0f3387de08d4dc0b0afc2190d780578", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0f3387de08d4dc0b0afc2190d780578.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0f3387de08d4dc0b0afc2190d780578"}}, "title": "Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes.", "authors": [{"family": "Anderson", "given": "Benjamin M", "initials": "BM", "orcid": "0000-0001-9755-4365", "researcher": {"href": "https://publications.scilifelab.se/researcher/30ef70433a5b4f728ce4a274b995d880.json"}}, {"family": "Krause", "given": "Kirsten", "initials": "K"}, {"family": "Petersen", "given": "Gitte", "initials": "G"}], "type": "journal article", "published": "2021-11-12", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "22", "issue": "1", "pages": "816", "issn-l": "1471-2164"}, "abstract": "The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus.\n\nThe mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT.\n\nThe lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences.", "doi": "10.1186/s12864-021-08105-z", "pmid": "34772334", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-021-08105-z"}, {"db": "pmc", "key": "PMC8588681"}], "notes": [], "created": "2022-11-09T15:41:08.525Z", "modified": "2024-01-16T13:48:38.141Z"}, {"entity": "publication", "iuid": "b71d176fed2e46f98495d913d952268b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b71d176fed2e46f98495d913d952268b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b71d176fed2e46f98495d913d952268b"}}, "title": "Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis.", "authors": [{"family": "Hallingb\u00e4ck", "given": "Henrik R", "initials": "HR"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "R\u00f6nnberg-W\u00e4stljung", "given": "Ann Christin", "initials": "AC"}, {"family": "Berlin", "given": "Sofia", "initials": "S"}], "type": "journal article", "published": "2021-10-02", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "22", "issue": "1", "pages": "710", "issn-l": "1471-2164"}, "abstract": "Sex chromosomes are in some species largely undifferentiated (homomorphic) with restricted sex determination regions. Homomorphic but different sex chromosomes are found in the closely related genera Populus and Salix indicating flexible sex determination systems, ideal for studies of processes involved in sex chromosome evolution. We have performed genome-wide association studies of sex and analysed sex chromosomes in a population of 265 wild collected Salix viminalis accessions and studied the sex determining locus.\n\nA total of 19,592 markers were used in association analyses using both Fisher's exact tests and a single-marker mixed linear model, which resulted in 48 and 41 sex-associated (SA) markers respectively. Across all 48 SA markers, females were much more often heterozygous than males, which is expected if females were the heterogametic sex. The majority of the SA markers were, based on positions in the S. purpurea genome, located on chromosome 15, previously demonstrated to be the sex chromosome. Interestingly, when mapping the genotyping-by-sequencing sequence tag harbouring the two SA markers with the highest significance to the S. viminalis genomic scaffolds, five regions of very high similarity were found: three on a scaffold that represents a part of chromosome 15, one on a scaffold that represents a part of chromosome 9 and one on a scaffold not anchored to the genome. Based on segregation differences of the alleles at the two marker positions and on differences in PCR amplification between females and males we conclude that females had multiple copies of this DNA fragment (chromosome 9 and 15), whereas males only had one (chromosome 9). We therefore postulate that the female specific sequences have been copied from chromosome 9 and inserted on chromosome 15, subsequently developing into a hemizygous W chromosome linked region.\n\nOur results support that sex determination in S. viminalis is controlled by one locus on chromosome 15. The segregation patterns observed at the SA markers furthermore confirm that S. viminalis females are the heterogametic sex. We also identified a translocation from chromosome 9 to the W chromosome.", "doi": "10.1186/s12864-021-08021-2", "pmid": "34600471", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-021-08021-2"}, {"db": "pmc", "key": "PMC8487499"}], "notes": [], "created": "2021-10-07T06:20:09.208Z", "modified": "2024-01-16T13:48:38.292Z"}, {"entity": "publication", "iuid": "4f73084862574e6a8c628f2ab94e8780", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f73084862574e6a8c628f2ab94e8780.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f73084862574e6a8c628f2ab94e8780"}}, "title": "Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens.", "authors": [{"family": "Sandholt", "given": "Arnar K S", "initials": "AKS"}, {"family": "Wattrang", "given": "Eva", "initials": "E"}, {"family": "Lilja", "given": "Tobias", "initials": "T"}, {"family": "Ahola", "given": "Harri", "initials": "H"}, {"family": "Lund\u00e9n", "given": "Anna", "initials": "A"}, {"family": "Troell", "given": "Karin", "initials": "K"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}, {"family": "S\u00f6derlund", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2021-09-14", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "22", "issue": "1", "pages": "660", "issn-l": "1471-2164"}, "abstract": "Coccidiosis is an infectious disease with large negative impact on the poultry industry worldwide. It is an enteric infection caused by unicellular Apicomplexan parasites of the genus Eimeria. The present study aimed to gain more knowledge about interactions between parasites and the host immune system during the early asexual replication phase of E. tenella in chicken caeca. For this purpose, chickens were experimentally infected with E. tenella oocysts, sacrificed on days 1-4 and 10 after infection and mRNA from caecal tissues was extracted and sequenced.\n\nDual RNA-seq analysis revealed time-dependent changes in both host and parasite gene expression during the course of the infection. Chicken immune activation was detected from day 3 and onwards with the highest number of differentially expressed immune genes recorded on day 10. Among early (days 3-4) responses up-regulation of genes for matrix metalloproteinases, several chemokines, interferon (IFN)-\u03b3 along with IFN-stimulated genes GBP, IRF1 and RSAD2 were noted. Increased expression of genes with immune suppressive/regulatory effects, e.g. IL10, SOCS1, SOCS3, was also observed among early responses. For E. tenella a general up-regulation of genes involved in protein expression and energy metabolism as well as a general down-regulation genes for DNA and RNA processing were observed during the infection. Specific E. tenella genes with altered expression during the experiment include those for proteins in rhoptry and microneme organelles.\n\nThe present study provides novel information on both the transcriptional activity of E. tenella during schizogony in ceacal tissue and of the local host responses to parasite invasion during this phase of infection. Results indicate a role for IFN-\u03b3 and IFN-stimulated genes in the innate defence against Eimeria replication.", "doi": "10.1186/s12864-021-07959-7", "pmid": "34521339", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-021-07959-7"}, {"db": "pmc", "key": "PMC8438895"}], "notes": [], "created": "2021-12-08T13:53:57.547Z", "modified": "2024-01-16T13:48:38.495Z"}, {"entity": "publication", "iuid": "ed820a56d6594ec48ebf8d5d78c801d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed820a56d6594ec48ebf8d5d78c801d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed820a56d6594ec48ebf8d5d78c801d1"}}, "title": "Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires.", "authors": [{"family": "Elfstrand", "given": "Malin", "initials": "M"}, {"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Cleary", "given": "Michelle", "initials": "M"}, {"family": "Halecker", "given": "Sandra", "initials": "S"}, {"family": "Ihrmark", "given": "Katarina", "initials": "K"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}, {"family": "Davydenko", "given": "Kateryna", "initials": "K"}, {"family": "Stenlid", "given": "Jan", "initials": "J"}, {"family": "Stadler", "given": "Marc", "initials": "M"}, {"family": "Durling", "given": "Mikael Brandstr\u00f6m", "initials": "MB"}], "type": "journal article", "published": "2021-07-04", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "22", "issue": "1", "pages": "503", "issn-l": "1471-2164"}, "abstract": "The dieback epidemic decimating common ash (Fraxinus excelsior) in Europe is caused by the invasive fungus Hymenoscyphus fraxineus. In this study we analyzed the genomes of H. fraxineus and H. albidus, its native but, now essentially displaced, non-pathogenic sister species, and compared them with several other members of Helotiales. The focus of the analyses was to identify signals in the genome that may explain the rapid establishment of H. fraxineus and displacement of H. albidus.\n\nThe genomes of H. fraxineus and H. albidus showed a high level of synteny and identity. The assembly of H. fraxineus is 13 Mb longer than that of H. albidus', most of this difference can be attributed to higher dispersed repeat content (i.e. transposable elements [TEs]) in H. fraxineus. In general, TE families in H. fraxineus showed more signals of repeat-induced point mutations (RIP) than in H. albidus, especially in Long-terminal repeat (LTR)/Copia and LTR/Gypsy elements. Comparing gene family expansions and 1:1 orthologs, relatively few genes show signs of positive selection between species. However, several of those did appeared to be associated with secondary metabolite genes families, including gene families containing two of the genes in the H. fraxineus-specific, hymenosetin biosynthetic gene cluster (BGC).\n\nThe genomes of H. fraxineus and H. albidus show a high degree of synteny, and are rich in both TEs and BGCs, but the genomic signatures also indicated that H. albidus may be less well equipped to adapt and maintain its ecological niche in a rapidly changing environment.", "doi": "10.1186/s12864-021-07837-2", "pmid": "34217229", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-021-07837-2"}, {"db": "pmc", "key": "PMC8254937"}], "notes": [], "created": "2021-12-07T21:36:40.820Z", "modified": "2021-12-07T21:36:40.833Z"}, {"entity": "publication", "iuid": "8761638859a04c37a88380e214272f9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8761638859a04c37a88380e214272f9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8761638859a04c37a88380e214272f9f"}}, "title": "A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses.", "authors": [{"family": "Rosengren", "given": "Maria K", "initials": "MK", "orcid": "0000-0003-0144-7034", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b771ed57d3e4c409c2a208173945786.json"}}, {"family": "Sigur\u00f0ard\u00f3ttir", "given": "Hei\u00f0r\u00fan", "initials": "H"}, {"family": "Eriksson", "given": "Susanne", "initials": "S"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R"}, {"family": "Jouni", "given": "Ahmad", "initials": "A"}, {"family": "Novoa-Bravo", "given": "Miguel", "initials": "M"}, {"family": "Albertsd\u00f3ttir", "given": "Elsa", "initials": "E"}, {"family": "Kristj\u00e1nsson", "given": "\u00deorvaldur", "initials": "\u00de"}, {"family": "Rhodin", "given": "Marie", "initials": "M"}, {"family": "Viklund", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Velie", "given": "Brandon D", "initials": "BD"}, {"family": "Negro", "given": "Juan J", "initials": "JJ"}, {"family": "Sol\u00e9", "given": "Marina", "initials": "M"}, {"family": "Lindgren", "given": "Gabriella", "initials": "G"}], "type": "journal article", "published": "2021-04-14", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "22", "issue": "1", "pages": "267", "issn-l": "1471-2164"}, "abstract": "The back plays a vital role in horse locomotion, where the spine functions as a spring during the stride cycle. A complex interaction between the spine and the muscles of the back contribute to locomotion soundness, gait ability, and performance of riding and racehorses. Conformation is commonly used to select horses for breeding and performance in multiple horse breeds, where the back and croup conformation plays a significant role. The conformation of back and croup plays an important role on riding ability in Icelandic horses. However, the genes behind this trait are still unknown. Therefore, the aim of this study was to identify genomic regions associated with conformation of back and croup in Icelandic horses and to investigate their effects on riding ability. One hundred seventy-seven assessed Icelandic horses were included in the study. A genome-wide association analysis was performed using the 670 K+ Axiom Equine Genotyping Array, and the effects of different haplotypes in the top associated region were estimated for riding ability and additional conformation traits assessed during breeding field tests.\n\nA suggestive quantitative trait loci (QTL) for the score of back and croup was detected on Equus caballus (ECA) 22 (p-value = 2.67 \u00d7 10- 7). Haplotype analysis revealed two opposite haplotypes, which resulted in higher and lower scores of the back and croup, respectively (p-value < 0.001). Horses with the favorable haplotype were more inclined to have a well-balanced backline with an uphill conformation and had, on average, higher scores for the lateral gaits t\u00f6lt (p-value = 0.02) and pace (p-value = 0.004). This genomic region harbors three genes: C20orf85, ANKRD60 and LOC100056167. ANKRD60 is associated with body height in humans. C20orf85 and ANKRD60 are potentially linked to adolescent idiopathic scoliosis in humans.\n\nOur results show that the detected QTL for conformation of back and croup is of importance for quality of lateral gaits in Icelandic horses. These findings could result in a genetic test to aid in the selection of breeding horses, thus they are of major interest for horse breeders. The results may also offer a gateway to comparative functional genomics by potentially linking both motor laterality and back inclination in horses with scoliosis in humans.", "doi": "10.1186/s12864-021-07454-z", "pmid": "33853519", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-021-07454-z"}, {"db": "pmc", "key": "PMC8048352"}], "notes": [], "created": "2021-05-11T06:11:20.472Z", "modified": "2024-01-16T13:48:40.082Z"}, {"entity": "publication", "iuid": "238f626b7a75464994d9f84456327dc7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/238f626b7a75464994d9f84456327dc7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/238f626b7a75464994d9f84456327dc7"}}, "title": "Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons.", "authors": [{"family": "Lindner", "given": "Melanie", "initials": "M", "orcid": "0000-0003-2931-265X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf37b79d5336408fb72f72c29b363a1b.json"}}, {"family": "Verhagen", "given": "Irene", "initials": "I"}, {"family": "Viitaniemi", "given": "Heidi M", "initials": "HM"}, {"family": "Laine", "given": "Veronika N", "initials": "VN"}, {"family": "Visser", "given": "Marcel E", "initials": "ME"}, {"family": "Husby", "given": "Arild", "initials": "A"}, {"family": "van Oers", "given": "Kees", "initials": "K"}], "type": "journal article", "published": "2021-01-07", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "22", "issue": "1", "pages": "36"}, "abstract": "DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of DNA methylation we need simultaneous within-individual assessment of methylation changes and gene expression changes over time. Within-individual repeated sampling of tissues, which are essential for trait expression is, however, unfeasible (e.g. specific brain regions, liver and ovary for reproductive timing). Here, we explore to what extend between-individual changes in DNA methylation in a tissue accessible for repeated sampling (red blood cells (RBCs)) reflect such patterns in a tissue unavailable for repeated sampling (liver) and how these DNA methylation patterns are associated with gene expression in such inaccessible tissues (hypothalamus, ovary and liver). For this, 18 great tit (Parus major) females were sacrificed at three time points (n = 6 per time point) throughout the pre-laying and egg-laying period and their blood, hypothalamus, ovary and liver were sampled.\n\nWe simultaneously assessed DNA methylation changes (via reduced representation bisulfite sequencing) and changes in gene expression (via RNA-seq and qPCR) over time. In general, we found a positive correlation between changes in CpG site methylation in RBCs and liver across timepoints. For CpG sites in close proximity to the transcription start site, an increase in RBC methylation over time was associated with a decrease in the expression of the associated gene in the ovary. In contrast, no such association with gene expression was found for CpG site methylation within the gene body or the 10 kb up- and downstream regions adjacent to the gene body.\n\nTemporal changes in DNA methylation are largely tissue-general, indicating that changes in RBC methylation can reflect changes in DNA methylation in other, often less accessible, tissues such as the liver in our case. However, associations between temporal changes in DNA methylation with changes in gene expression are mostly tissue- and genomic location-dependent. The observation that temporal changes in DNA methylation within RBCs can relate to changes in gene expression in less accessible tissues is important for a better understanding of how environmental conditions shape traits that temporally change in expression in wild populations.", "doi": "10.1186/s12864-020-07329-9", "pmid": "33413102", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-07329-9"}, {"db": "pmc", "key": "PMC7792223"}], "notes": [], "created": "2021-02-22T10:20:10.020Z", "modified": "2024-01-16T13:48:40.957Z"}, {"entity": "publication", "iuid": "7c65da05f8c44cc08507b044f77cc22e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c65da05f8c44cc08507b044f77cc22e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c65da05f8c44cc08507b044f77cc22e"}}, "title": "Moose genomes reveal past glacial demography and the origin of modern lineages.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Alberti", "given": "Federica", "initials": "F"}, {"family": "Heino", "given": "Matti T", "initials": "MT"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "R"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Ryman", "given": "Nils", "initials": "N"}, {"family": "Laikre", "given": "Linda", "initials": "L"}, {"family": "Ahlgren", "given": "Hans", "initials": "H"}, {"family": "Askeyev", "given": "Igor V", "initials": "IV"}, {"family": "Askeyev", "given": "Oleg V", "initials": "OV"}, {"family": "Shaymuratova", "given": "Dilyara N", "initials": "DN"}, {"family": "Askeyev", "given": "Arthur O", "initials": "AO"}, {"family": "D\u00f6ppes", "given": "Doris", "initials": "D"}, {"family": "Friedrich", "given": "Ronny", "initials": "R"}, {"family": "Lindauer", "given": "Susanne", "initials": "S"}, {"family": "Rosendahl", "given": "Wilfried", "initials": "W"}, {"family": "Aspi", "given": "Jouni", "initials": "J"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Lid\u00e9n", "given": "Kerstin", "initials": "K"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}], "type": "journal article", "published": "2020-12-02", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "21", "issue": "1", "pages": "854"}, "abstract": "Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America.\r\n\r\nWe found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines.\r\n\r\nTaken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.", "doi": "10.1186/s12864-020-07208-3", "pmid": "33267779", "labels": {"NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-07208-3"}, {"db": "pmc", "key": "PMC7709250"}], "notes": [], "created": "2020-12-07T16:36:41.615Z", "modified": "2023-09-07T14:58:17.282Z"}, {"entity": "publication", "iuid": "3e21cc6163c14d55a5a03727b870e2d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e21cc6163c14d55a5a03727b870e2d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e21cc6163c14d55a5a03727b870e2d1"}}, "title": "Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.", "authors": [{"family": "Feuerborn", "given": "Tatiana R", "initials": "TR"}, {"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Ure\u00f1a", "given": "Irene", "initials": "I"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}], "type": "journal article", "published": "2020-11-30", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "844", "issn-l": "1471-2164"}, "abstract": "After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.\n\nHere we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.\n\nWe propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.", "doi": "10.1186/s12864-020-07229-y", "pmid": "33256612", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-07229-y"}, {"db": "pmc", "key": "PMC7708127"}], "notes": [], "created": "2020-12-07T16:36:42.754Z", "modified": "2024-01-16T13:48:41.282Z"}, {"entity": "publication", "iuid": "4eaba3d139bf427eb332f2f93f77bf0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4eaba3d139bf427eb332f2f93f77bf0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4eaba3d139bf427eb332f2f93f77bf0a"}}, "title": "Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine.", "authors": [{"family": "Calleja-Rodriguez", "given": "Ainhoa", "initials": "A"}, {"family": "Pan", "given": "Jin", "initials": "J"}, {"family": "Funda", "given": "Tomas", "initials": "T"}, {"family": "Chen", "given": "Zhiqiang", "initials": "Z"}, {"family": "Baison", "given": "John", "initials": "J"}, {"family": "Isik", "given": "Fikret", "initials": "F"}, {"family": "Abrahamsson", "given": "Sara", "initials": "S"}, {"family": "Wu", "given": "Harry X", "initials": "HX"}], "type": "journal article", "published": "2020-11-16", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "796", "issn-l": "1471-2164"}, "abstract": "Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (Pinus sylvestris L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers.\n\nGenomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143% higher than the traditional pedigree-based selection.\n\nAlthough prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50%.", "doi": "10.1186/s12864-020-07188-4", "pmid": "33198692", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-07188-4"}, {"db": "pmc", "key": "PMC7667760"}], "notes": [], "created": "2020-12-08T23:32:05.662Z", "modified": "2024-01-16T13:48:41.324Z"}, {"entity": "publication", "iuid": "aad98531594443b3bdf72d5748622b1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aad98531594443b3bdf72d5748622b1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aad98531594443b3bdf72d5748622b1e"}}, "title": "Combined transcriptome and proteome profiling of the pancreatic \u03b2-cell response to palmitate unveils key pathways of \u03b2-cell lipotoxicity.", "authors": [{"family": "Lytrivi", "given": "Maria", "initials": "M"}, {"family": "Ghaddar", "given": "Kassem", "initials": "K"}, {"family": "Lopes", "given": "Miguel", "initials": "M"}, {"family": "Rosengren", "given": "Victoria", "initials": "V"}, {"family": "Piron", "given": "Anthony", "initials": "A"}, {"family": "Yi", "given": "Xiaoyan", "initials": "X"}, {"family": "Johansson", "given": "Henrik", "initials": "H"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Igoillo-Esteve", "given": "Mariana", "initials": "M"}, {"family": "Cunha", "given": "Daniel A", "initials": "DA"}, {"family": "Marselli", "given": "Lorella", "initials": "L"}, {"family": "Marchetti", "given": "Piero", "initials": "P"}, {"family": "Orts\u00e4ter", "given": "Henrik", "initials": "H"}, {"family": "Eizirik", "given": "Decio L", "initials": "DL"}, {"family": "Cnop", "given": "Miriam", "initials": "M", "orcid": "0000-0002-5112-1692", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0d855a049344a42bbb571e7c8e688b0.json"}}], "type": "journal article", "published": "2020-08-26", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "590", "issn-l": "1471-2164"}, "abstract": "Prolonged exposure to elevated free fatty acids induces \u03b2-cell failure (lipotoxicity) and contributes to the pathogenesis of type 2 diabetes. In vitro exposure of \u03b2-cells to the saturated free fatty acid palmitate is a valuable model of lipotoxicity, reproducing features of \u03b2-cell failure observed in type 2 diabetes. In order to map the \u03b2-cell response to lipotoxicity, we combined RNA-sequencing of palmitate-treated human islets with iTRAQ proteomics of insulin-secreting INS-1E cells following a time course exposure to palmitate.\n\nCrossing transcriptome and proteome of palmitate-treated \u03b2-cells revealed 85 upregulated and 122 downregulated genes at both transcript and protein level. Pathway analysis identified lipid metabolism, oxidative stress, amino-acid metabolism and cell cycle pathways among the most enriched palmitate-modified pathways. Palmitate induced gene expression changes compatible with increased free fatty acid mitochondrial import and \u03b2-oxidation, decreased lipogenesis and modified cholesterol transport. Palmitate modified genes regulating endoplasmic reticulum (ER) function, ER-to-Golgi transport and ER stress pathways. Furthermore, palmitate modulated cAMP/protein kinase A (PKA) signaling, inhibiting expression of PKA anchoring proteins and downregulating the GLP-1 receptor. SLC7 family amino-acid transporters were upregulated in response to palmitate but this induction did not contribute to \u03b2-cell demise. To unravel critical mediators of lipotoxicity upstream of the palmitate-modified genes, we identified overrepresented transcription factor binding sites and performed network inference analysis. These identified LXR, PPAR\u03b1, FOXO1 and BACH1 as key transcription factors orchestrating the metabolic and oxidative stress responses to palmitate.\n\nThis is the first study to combine transcriptomic and sensitive time course proteomic profiling of palmitate-exposed \u03b2-cells. Our results provide comprehensive insight into gene and protein expression changes, corroborating and expanding beyond previous findings. The identification of critical drivers and pathways of the \u03b2-cell lipotoxic response points to novel therapeutic targets for type 2 diabetes.", "doi": "10.1186/s12864-020-07003-0", "pmid": "32847508", "labels": {"Global Proteomics and Proteogenomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-07003-0"}, {"db": "pmc", "key": "PMC7448506"}], "notes": [], "created": "2021-01-12T18:17:43.722Z", "modified": "2021-11-10T12:48:00.690Z"}, {"entity": "publication", "iuid": "d191a7af04da4afea9d0e9e07fe20a75", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d191a7af04da4afea9d0e9e07fe20a75.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d191a7af04da4afea9d0e9e07fe20a75"}}, "title": "The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution.", "authors": [{"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Strempfl", "given": "Katharina", "initials": "K"}, {"family": "Fogelholm", "given": "Jesper", "initials": "J"}, {"family": "Wright", "given": "Dominic", "initials": "D"}, {"family": "Henriksen", "given": "Rie", "initials": "R", "orcid": "0000-0002-7290-6376", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca679685607b4187bffa818ee1168c81.json"}}], "type": "journal article", "published": "2020-07-29", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "518", "issn-l": "1471-2164"}, "abstract": "Large difference in cerebrum size exist between avian species and populations of the same species and is believed to reflect differences in processing power, i.e. in the speed and efficiency of processing information in this brain region. During domestication chickens developed a larger cerebrum compared to their wild progenitor, the Red jungle fowl. The underlying mechanisms that control cerebrum size and the extent to which genetic regulation is similar across brain regions is not well understood. In this study, we combine measurement of cerebrum size with genome-wide genetical genomics analysis to identify the genetic architecture of the cerebrum, as well as compare the regulation of gene expression in this brain region with gene expression in other regions of the brain (the hypothalamus) and somatic tissue (liver).\n\nWe identify one candidate gene that putatively regulates cerebrum size (MTF2) as well as a large number of eQTL that regulate the transcriptome in cerebrum tissue, with the majority of these eQTL being trans-acting. The overall regulation of gene expression variation in the cerebrum was markedly different to the hypothalamus, with relatively few eQTL in common. In comparison, the cerebrum tissue shared more eQTL with a distant tissue (liver) than with a neighboring tissue (hypothalamus).\n\nThe candidate gene for cerebrum size (MTF2) has previously been linked to brain development making it a good candidate for further investigation as a regulator of inter-population variation in cerebrum size. The lack of shared eQTL between the two brain regions implies that genetic regulation of gene expression appears to be relatively independent between the two brain regions and suggest that coevolution between these two brain regions might be more functionally driven than developmental. These findings have relevance for current brain size evolution theories.", "doi": "10.1186/s12864-020-06908-0", "pmid": "32727510", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-06908-0"}, {"db": "pmc", "key": "PMC7392834"}], "notes": [], "created": "2020-08-04T14:50:06.953Z", "modified": "2024-01-16T13:48:42.102Z"}, {"entity": "publication", "iuid": "15981a63f8c94a17ab3bf14f021ef2bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15981a63f8c94a17ab3bf14f021ef2bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15981a63f8c94a17ab3bf14f021ef2bc"}}, "title": "Seamless integration of image and molecular analysis for spatial transcriptomics workflows.", "authors": [{"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2020-07-14", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "482", "issn-l": "1471-2164"}, "abstract": "Recent advancements in in situ gene expression technologies constitute a new and rapidly evolving field of transcriptomics. With the recent launch of the 10x Genomics Visium platform, such methods have started to become widely adopted. The experimental protocol is conducted on individual tissue sections collected from a larger tissue sample. The two-dimensional nature of this data requires multiple consecutive sections to be collected from the sample in order to construct a comprehensive three-dimensional map of the tissue. However, there is currently no software available that lets the user process the images, align stacked experiments, and finally visualize them together in 3D to create a holistic view of the tissue.\n\nWe have developed an R package named STUtility that takes 10x Genomics Visium data as input and provides features to perform standardized data transformations, alignment of multiple tissue sections, regional annotation, and visualizations of the combined data in a 3D model framework.\n\nSTUtility lets the user process, analyze and visualize multiple samples of spatially resolved RNA sequencing and image data from the 10x Genomics Visium platform. The package builds on the Seurat framework and uses familiar APIs and well-proven analysis methods. An introduction to the software package is available at https://ludvigla.github.io/STUtility_web_site/ .", "doi": "10.1186/s12864-020-06832-3", "pmid": "32664861", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-06832-3"}, {"db": "pmc", "key": "PMC7386244"}], "notes": [], "created": "2020-12-07T16:28:50.026Z", "modified": "2024-01-16T13:48:42.159Z"}, {"entity": "publication", "iuid": "194d913bd2654246bcdf9732ca06b6e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/194d913bd2654246bcdf9732ca06b6e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/194d913bd2654246bcdf9732ca06b6e2"}}, "title": "An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells.", "authors": [{"family": "Onsbring", "given": "Henning", "initials": "H"}, {"family": "Tice", "given": "Alexander K", "initials": "AK"}, {"family": "Barton", "given": "Brandon T", "initials": "BT"}, {"family": "Brown", "given": "Matthew W", "initials": "MW"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG", "orcid": "0000-0002-6898-6377", "researcher": {"href": "https://publications.scilifelab.se/researcher/42fc4acc111f4c488b23fa41341705e2.json"}}], "type": "journal article", "published": "2020-06-29", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "448", "issn-l": "1471-2164"}, "abstract": "Most diversity in the eukaryotic tree of life is represented by microbial eukaryotes, which is a polyphyletic group also referred to as protists. Among the protists, currently sequenced genomes and transcriptomes give a biased view of the actual diversity. This biased view is partly caused by the scientific community, which has prioritized certain microbes of biomedical and agricultural importance. Additionally, some protists remain difficult to maintain in cultures, which further influences what has been studied. It is now possible to bypass the time-consuming process of cultivation and directly analyze the gene content of single protist cells. Single-cell genomics was used in the first experiments where individual protists cells were genomically explored. Unfortunately, single-cell genomics for protists is often associated with low genome recovery and the assembly process can be complicated because of repetitive intergenic regions. Sequencing repetitive sequences can be avoided if single-cell transcriptomics is used, which only targets the part of the genome that is transcribed.\n\nIn this study we test different modifications of Smart-seq2, a single-cell RNA sequencing protocol originally developed for mammalian cells, to establish a robust and more cost-efficient workflow for protists. The diplomonad Giardia intestinalis was used in all experiments and the available genome for this species allowed us to benchmark our results. We could observe increased transcript recovery when freeze-thaw cycles were added as an extra step to the Smart-seq2 protocol. Further we reduced the reaction volume and purified the amplified cDNA with alternative beads to test different cost-reducing changes of Smart-seq2. Neither improved the procedure, and reducing the volumes by half led to significantly fewer genes detected. We also added a 5' biotin modification to our primers and reduced the concentration of oligo-dT, to potentially reduce generation of artifacts. Except adding freeze-thaw cycles and reducing the volume, no other modifications lead to a significant change in gene detection. Therefore, we suggest adding freeze-thaw cycles to Smart-seq2 when working with protists and further consider our other modification described to improve cost and time-efficiency.\n\nThe presented single-cell RNA sequencing workflow represents an efficient method to explore the diversity and cell biology of individual protist cells.", "doi": "10.1186/s12864-020-06858-7", "pmid": "32600266", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Microbial Single Cell Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-06858-7"}, {"db": "pmc", "key": "PMC7325058"}], "notes": [], "created": "2020-07-03T05:25:51.570Z", "modified": "2021-11-10T12:44:49.955Z"}, {"entity": "publication", "iuid": "65338b6f4c55448b9e4454def5c0cc0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65338b6f4c55448b9e4454def5c0cc0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65338b6f4c55448b9e4454def5c0cc0d"}}, "title": "LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function.", "authors": [{"family": "Jhamat", "given": "Naveed", "initials": "N"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Guo", "given": "Yongzhi", "initials": "Y"}, {"family": "Chanrot", "given": "Metasu", "initials": "M"}, {"family": "Ivanova", "given": "Elena", "initials": "E"}, {"family": "Kelsey", "given": "Gavin", "initials": "G"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Humblot", "given": "Patrice", "initials": "P"}], "type": "journal article", "published": "2020-06-03", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "385", "issn-l": "1471-2164"}, "abstract": "Lipopolysaccharide (LPS) endotoxin stimulates pro-inflammatory pathways and is a key player in the pathological mechanisms involved in the development of endometritis. This study aimed to investigate LPS-induced DNA methylation changes in bovine endometrial epithelial cells (bEECs), which may affect endometrial function. Following in vitro culture, bEECs from three cows were either untreated (0) or exposed to 2 and 8 \u03bcg/mL LPS for 24 h.\n\nDNA samples extracted at 0 h and 24 h were sequenced using reduced representation bisulfite sequencing (RRBS). When comparing DNA methylation results at 24 h to time 0 h, a larger proportion of hypomethylated regions were identified in the LPS-treated groups, whereas the trend was opposite in controls. When comparing LPS groups to controls at 24 h, a total of 1291 differentially methylated regions (DMRs) were identified (55% hypomethylated and 45% hypermethylated). Integration of DNA methylation data obtained here with our previously published gene expression data obtained from the same samples showed a negative correlation (r = - 0.41 for gene promoter, r = - 0.22 for gene body regions, p < 0.05). Differential methylation analysis revealed that effects of LPS treatment were associated with methylation changes for genes involved in regulation of immune and inflammatory responses, cell adhesion, and external stimuli. Gene ontology and pathway analyses showed that most of the differentially methylated genes (DMGs) were associated with cell proliferation and apoptotic processes; and pathways such as calcium-, oxytocin- and MAPK-signaling pathways with recognized roles in innate immunity. Several DMGs were related to systemic inflammation and tissue re-modelling including HDAC4, IRAK1, AKT1, MAP3K6, Wnt7A and ADAMTS17.\n\nThe present results show that LPS altered the DNA methylation patterns of bovine endometrial epithelial cells. This information, combined with our previously reported changes in gene expression related to endometrial function, confirm that LPS activates pro-inflammatory mechanisms leading to perturbed immune balance and cell adhesion processes in the endometrium.", "doi": "10.1186/s12864-020-06777-7", "pmid": "32493210", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-06777-7"}, {"db": "pmc", "key": "PMC7268755"}], "notes": [], "created": "2020-06-09T14:54:11.383Z", "modified": "2024-01-16T13:48:42.410Z"}, {"entity": "publication", "iuid": "cd9171508710494ba8bad2c1d95b8651", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd9171508710494ba8bad2c1d95b8651.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd9171508710494ba8bad2c1d95b8651"}}, "title": "Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs.", "authors": [{"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645ef0e04a245f0ac9e7d7498b2bd69.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Mur\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Sundberg", "given": "Katarina", "initials": "K"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Rosengren Pielberg", "given": "Gerli", "initials": "G"}], "type": "journal article", "published": "2020-04-16", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "307", "issn-l": "1471-2164"}, "abstract": "Hypothyroidism is a common complex endocrinopathy that typically has an autoimmune etiology, and it affects both humans and dogs. Genetic and environmental factors are both known to play important roles in the disease development. In this study, we sought to identify the genetic risk factors potentially involved in the susceptibility to the disease in the high-risk Giant Schnauzer dog breed.\n\nBy employing genome-wide association followed by fine-mapping (top variant p-value = 5.7 \u00d7 10- 6), integrated with whole-genome resequencing and copy number variation analysis, we detected a ~ 8.9 kbp deletion strongly associated (p-value = 0.0001) with protection against development of hypothyroidism. The deletion is located between two predicted Interferon alpha (IFNA) genes and it may eliminate functional elements potentially involved in the transcriptional regulation of these genes. Remarkably, type I IFNs have been extensively associated to human autoimmune hypothyroidism and general autoimmunity. Nonetheless, the extreme genomic complexity of the associated region on CFA11 warrants further long-read sequencing and annotation efforts in order to ascribe functions to the identified deletion and to characterize the canine IFNA gene cluster in more detail.\n\nOur results expand the current knowledge on genetic determinants of canine hypothyroidism by revealing a significant link with the human counterpart disease, potentially translating into better diagnostic tools across species, and may contribute to improved canine breeding strategies.", "doi": "10.1186/s12864-020-6700-3", "pmid": "32299354", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-6700-3"}, {"db": "pmc", "key": "PMC7160888"}], "notes": [], "created": "2020-07-08T13:04:54.893Z", "modified": "2024-01-16T13:48:42.606Z"}, {"entity": "publication", "iuid": "4914e822a6ff4ce4ad8cafdded9ef574", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4914e822a6ff4ce4ad8cafdded9ef574.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4914e822a6ff4ce4ad8cafdded9ef574"}}, "title": "Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues.", "authors": [{"family": "Berglund", "given": "Emelie", "initials": "E"}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S"}, {"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Bergenstr\u00e5hle", "given": "Ludvig", "initials": "L"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}], "type": "journal article", "published": "2020-04-15", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "298", "issn-l": "1471-2164"}, "abstract": "Interest in studying the spatial distribution of gene expression in tissues is rapidly increasing. Spatial Transcriptomics is a novel sequencing-based technology that generates high-throughput information on the distribution, heterogeneity and co-expression of cells in tissues. Unfortunately, manual preparation of high-quality sequencing libraries is time-consuming and subject to technical variability due to human error during manual pipetting, which results in sample swapping and the accidental introduction of batch effects. All these factors complicate the production and interpretation of biological datasets.\n\nWe have integrated an Agilent Bravo Automated Liquid Handling Platform into the Spatial Transcriptomics workflow. Compared to the previously reported Magnatrix 8000+ automated protocol, this approach increases the number of samples processed per run, reduces sample preparation time by 35%, and minimizes batch effects between samples. The new approach is also shown to be highly accurate and almost completely free from technical variability between prepared samples.\n\nThe new automated Spatial Transcriptomics protocol using the Agilent Bravo Automated Liquid Handling Platform rapidly generates high-quality Spatial Transcriptomics libraries. Given the wide use of the Agilent Bravo Automated Liquid Handling Platform in research laboratories and facilities, this will allow many researchers to quickly create robust Spatial Transcriptomics libraries.", "doi": "10.1186/s12864-020-6631-z", "pmid": "32293264", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-6631-z"}, {"db": "pmc", "key": "PMC7158132"}], "notes": [], "created": "2020-07-08T13:03:44.517Z", "modified": "2024-01-16T13:48:42.620Z"}, {"entity": "publication", "iuid": "c982efa83ad042baaaa633f71d3b3cb9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c982efa83ad042baaaa633f71d3b3cb9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c982efa83ad042baaaa633f71d3b3cb9"}}, "title": "Gene regulatory response to hyposalinity in the brown seaweed Fucus vesiculosus.", "authors": [{"family": "Rugiu", "given": "Luca", "initials": "L", "orcid": "0000-0002-9675-7168", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d411b99abcc4474aff904e43247fb7a.json"}}, {"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Pereyra", "given": "Ricardo Tom\u00e1s", "initials": "RT"}, {"family": "Jormalainen", "given": "Veijo", "initials": "V"}], "type": "journal article", "published": "2020-01-13", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "42", "issn-l": "1471-2164"}, "abstract": "Rockweeds are among the most important foundation species of temperate rocky littoral shores. In the Baltic Sea, the rockweed Fucus vesiculosus is distributed along a decreasing salinity gradient from the North Atlantic entrance to the low-salinity regions in the north-eastern margins, thus, demonstrating a remarkable tolerance to hyposalinity. The underlying mechanisms for this tolerance are still poorly understood. Here, we exposed F. vesiculosus from two range-margin populations to the hyposaline (2.5 PSU - practical salinity unit) conditions that are projected to occur in the region by the end of this century as a result of climate change. We used transcriptome analysis (RNA-seq) to determine the gene expression patterns associated with hyposalinity acclimation, and examined the variation in these patterns between the sampled populations.\n\nHyposalinity induced different responses in the two populations: in one, only 26 genes were differentially expressed between salinity treatments, while the other population demonstrated up- or downregulation in 3072 genes. In the latter population, the projected future hyposalinity induced an acute response in terms of antioxidant production. Genes associated with membrane composition and structure were also heavily involved, with the upregulation of fatty acid and actin production, and the downregulation of ion channels and alginate pathways. Changes in gene expression patterns clearly indicated an inhibition of the photosynthetic machinery, with a consequent downregulation of carbohydrate production. Simultaneously, energy consumption increased, as revealed by the upregulation of genes associated with respiration and ATP synthesis. Overall, the genes that demonstrated the largest increase in expression were ribosomal proteins involved in translation pathways. The fixation rate of SNP:s was higher within genes responding to hyposalinity than elsewhere in the transcriptome.\n\nThe high fixation rate in the genes coding for salinity acclimation mechanisms implies strong selection for them. The among-population differentiation that we observed in the transcriptomic response to hyposalinity stress suggests that populations of F. vesiculosus may differ in their tolerance to future desalination, possibly as a result of local adaptation to salinity conditions within the Baltic Sea. These results emphasise the importance of considering interspecific genetic variation when evaluating the consequences of environmental change.", "doi": "10.1186/s12864-020-6470-y", "pmid": "31931708", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-6470-y"}, {"db": "pmc", "key": "PMC6958763"}], "notes": [], "created": "2020-07-08T13:03:42.198Z", "modified": "2024-01-16T13:48:43.072Z"}, {"entity": "publication", "iuid": "50298673c29845b082e21ec46b31ce6c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50298673c29845b082e21ec46b31ce6c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50298673c29845b082e21ec46b31ce6c"}}, "title": "Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce.", "authors": [{"family": "Nakamura", "given": "Miyuki", "initials": "M", "orcid": "0000-0002-8153-7293", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa9f227109b54fa9a1457a1f7af197af.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C"}, {"family": "Hennig", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2019-12-19", "journal": {"volume": "20", "issn": "1471-2164", "issue": "1", "pages": "997", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Small RNAs (sRNAs) are regulatory molecules impacting on gene expression and transposon activity. MicroRNAs (miRNAs) are responsible for tissue-specific and environmentally-induced gene repression. Short interfering RNAs (siRNA) are constitutively involved in transposon silencing across different type of tissues. The male gametophyte in angiosperms has a unique set of sRNAs compared to vegetative tissues, including phased siRNAs from intergenic or genic regions, or epigenetically activated siRNAs. This is contrasted by a lack of knowledge about the sRNA profile of the male gametophyte of gymnosperms.\n\nHere, we isolated mature pollen from male cones of Norway spruce and investigated its sRNA profiles. While 21-nt sRNAs is the major size class of sRNAs in needles, in pollen 21-nt and 24-nt sRNAs are the most abundant size classes. Although the 24-nt sRNAs were exclusively derived from TEs in pollen, both 21-nt and 24-nt sRNAs were associated with TEs. We also investigated sRNAs from somatic embryonic callus, which has been reported to contain 24-nt sRNAs. Our data show that the 24-nt sRNA profiles are tissue-specific and differ between pollen and cell culture.\n\nOur data reveal that gymnosperm pollen, like angiosperm pollen, has a unique sRNA profile, differing from vegetative leaf tissue. Thus, our results reveal that angiosperm and gymnosperm pollen produce new size classes not present in vegetative tissues; while in angiosperm pollen 21-nt sRNAs are generated, in the gymnosperm Norway spruce 24-nt sRNAs are generated. The tissue-specific production of distinct TE-derived sRNAs in angiosperms and gymnosperms provides insights into the diversification process of sRNAs in TE silencing pathways between the two groups of seed plants.", "doi": "10.1186/s12864-019-6385-7", "pmid": "31856707", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-019-6385-7"}, {"db": "pmc", "key": "PMC6923980"}], "notes": [], "created": "2020-01-08T12:42:35.674Z", "modified": "2021-06-16T14:53:11.254Z"}, {"entity": "publication", "iuid": "75c0d2a11d08485782437af9dc2ef53a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/75c0d2a11d08485782437af9dc2ef53a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/75c0d2a11d08485782437af9dc2ef53a"}}, "title": "Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait.", "authors": [{"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Priehodov\u00e1", "given": "Edita", "initials": "E"}, {"family": "Diallo", "given": "Issa", "initials": "I"}, {"family": "Podgorn\u00e1", "given": "Eli\u0161ka", "initials": "E"}, {"family": "Poloni", "given": "Estella S", "initials": "ES"}, {"family": "\u010cern\u00fd", "given": "Viktor", "initials": "V"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM"}], "type": "journal article", "published": "2019-12-02", "journal": {"volume": "20", "issn": "1471-2164", "issue": "1", "pages": "915", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt.\n\nBased on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. We furthermore directly link the T-13910 haplotype with the Lactase Persistence phenotype through a Genome Wide Association study (GWAS) and identify another genomic region in the vicinity of the SPRY2 gene associated with glycaemic measurements after lactose intake.\n\nOur findings suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first GWAS of the lactase persistence trait. We also explored other signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.", "doi": "10.1186/s12864-019-6296-7", "pmid": "31791255", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-019-6296-7"}], "notes": [], "created": "2019-12-04T15:15:34.229Z", "modified": "2024-01-16T13:48:43.354Z"}, {"entity": "publication", "iuid": "047bc081b2be4acc96d3a11e80fc1f69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/047bc081b2be4acc96d3a11e80fc1f69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/047bc081b2be4acc96d3a11e80fc1f69"}}, "title": "Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model", "authors": [{"family": "Kampfraath", "given": "A A", "initials": "AA"}, {"family": "Klasson", "given": "L", "initials": "L"}, {"family": "Anvar", "given": "S Y", "initials": "SY"}, {"family": "Vossen", "given": "R H A M", "initials": "RHAM"}, {"family": "Roelofs", "given": "D", "initials": "D"}, {"family": "Kraaijeveld", "given": "K", "initials": "K"}, {"family": "Ellers", "given": "J", "initials": "J"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "20", "issn": "1471-2164", "issue": "1", "pages": "106", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associated wFol. In this study, we investigate possible processes underlying this genome expansion by comparing a re-annotated wFol genome to other Wolbachia genomes. In addition, we also search for candidate genes related to parthenogenesis induction (PI).\n\nWithin wFol, we found five phage WO regions representing 25.4% of the complete genome, few pseudogenized genes, and an expansion of DNA-repair genes in comparison to other Wolbachia. These signs of genome conservation were mirrored in the wFol host, the springtail F. candida, which also had an expanded DNA-repair gene family and many horizontally transferred genes. Across all Wolbachia genomes, there was a strong correlation between gene numbers of Wolbachia strains and their hosts. In order to identify genes with a potential link to PI, we assembled the genome of an additional PI strain, wLcla. Comparisons between four PI Wolbachia, including wFol and wLcla, and fourteen non-PI Wolbachia yielded a small set of potential candidate genes for further investigation.\n\nThe strong similarities in genome content of wFol and its host, as well as the correlation between host and Wolbachia gene numbers suggest that there may be some form of convergent evolution between endosymbiont and host genomes. If such convergent evolution would be strong enough to overcome the evolutionary forces causing genome reduction, it would enable expanded genomes within long-term obligate endosymbionts.", "doi": "10.1186/s12864-019-5492-9", "pmid": "30727958", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-019-5492-9"}, {"db": "pmc", "key": "PMC6364476"}], "notes": [], "created": "2019-11-25T14:12:15.318Z", "modified": "2024-01-16T13:48:43.434Z"}, {"entity": "publication", "iuid": "9a6efccfa136436c90bdc26ecf092c06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a6efccfa136436c90bdc26ecf092c06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a6efccfa136436c90bdc26ecf092c06"}}, "title": "The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation.", "authors": [{"family": "Bai\u00e3o", "given": "Guilherme C", "initials": "GC"}, {"family": "Schneider", "given": "Daniela I", "initials": "DI"}, {"family": "Miller", "given": "Wolfgang J", "initials": "WJ"}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications.scilifelab.se/researcher/409de77af489419db6d2b599b590d02f.json"}}], "type": "journal article", "published": "2019-06-07", "journal": {"volume": "20", "issn": "1471-2164", "issue": "1", "pages": "465", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The Neotropical fruit fly Drosophila paulistorum (Diptera: Drosophilidae) is a species complex in statu nascendi comprising six reproductively isolated semispecies, each harboring mutualistic Wolbachia strains. Although wild type flies of each semispecies are isolated from the others by both pre- and postmating incompatibilities, mating between semispecies and successful offspring development can be achieved once flies are treated with antibiotics to reduce Wolbachia titer. Here we use RNA-seq to study the impact of Wolbachia on D. paulistorum and investigate the hypothesis that the symbiont may play a role in host speciation. For that goal, we analyze samples of heads and abdomens of both sexes of the Amazonian, Centro American and Orinocan semispecies of D. paulistorum.\n\nWe identify between 175 and 1192 differentially expressed genes associated with a variety of biological processes that respond either globally or according to tissue, sex or condition in the three semispecies. Some of the functions associated with differentially expressed genes are known to be affected by Wolbachia in other species, such as metabolism and immunity, whereas others represent putative novel phenotypes involving muscular functions, pheromone signaling, and visual perception.\n\nOur results show that Wolbachia affect a large number of biological functions in D. paulistorum, particularly when present in high titer. We suggest that the significant metabolic impact of the infection on the host may cause several of the other putative and observed phenotypes. We also speculate that the observed differential expression of genes associated with chemical communication and reproduction may be associated with the emergence of pre- and postmating barriers between semispecies, which supports a role for Wolbachia in the speciation of D. paulistorum.", "doi": "10.1186/s12864-019-5816-9", "pmid": "31174466", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-019-5816-9"}, {"db": "pmc", "key": "PMC6555960"}], "notes": [], "created": "2020-01-08T12:42:20.556Z", "modified": "2021-06-16T14:45:31.213Z"}, {"entity": "publication", "iuid": "0b4fa3160d6649d4942504cfeb8d300d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b4fa3160d6649d4942504cfeb8d300d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b4fa3160d6649d4942504cfeb8d300d"}}, "title": "A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds.", "authors": [{"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "MB"}, {"family": "Childers", "given": "Anna K", "initials": "AK"}, {"family": "Evans", "given": "Jay D", "initials": "JD"}, {"family": "Mikheyev", "given": "Alexander S", "initials": "AS"}, {"family": "Robertson", "given": "Hugh M", "initials": "HM"}, {"family": "Robinson", "given": "Gene E", "initials": "GE"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}], "type": "journal article", "published": "2019-04-08", "journal": {"volume": "20", "issn": "1471-2164", "issue": "1", "pages": "275", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map.\n\nEach of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor >\u200998% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features.\n\nThe improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics.", "doi": "10.1186/s12864-019-5642-0", "pmid": "30961563", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-019-5642-0"}], "notes": [], "created": "2019-04-10T09:44:17.171Z", "modified": "2024-01-16T13:48:44.515Z"}, {"entity": "publication", "iuid": "4ab972d262af414cae7747417e8fbeb0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ab972d262af414cae7747417e8fbeb0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ab972d262af414cae7747417e8fbeb0"}}, "title": "Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model.", "authors": [{"family": "Velie", "given": "Brandon D", "initials": "BD", "orcid": "0000-0001-9359-6138", "researcher": {"href": "https://publications.scilifelab.se/researcher/c39a4ff0532345f58201d6d40a691a46.json"}}, {"family": "Lillie", "given": "Mette", "initials": "M"}, {"family": "Fegraeus", "given": "Kim J\u00e4derkvist", "initials": "KJ"}, {"family": "Rosengren", "given": "Maria K", "initials": "MK"}, {"family": "Sol\u00e9", "given": "Marina", "initials": "M"}, {"family": "Wiklund", "given": "Maja", "initials": "M"}, {"family": "Ihler", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Strand", "given": "Eric", "initials": "E"}, {"family": "Lindgren", "given": "Gabriella", "initials": "G"}], "type": "journal article", "published": "2019-02-04", "journal": {"volume": "20", "issn": "1471-2164", "issue": "1", "pages": "104", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Horses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds often representing closed populations with high phenotypic and genetic uniformity. However, a great deal of variation still exists between breeds, making the horse particularly well suited for genetic studies of athleticism. To identify genomic regions associated with athleticism as it pertains to trotting racing ability in the horse, the current study applies a pooled sequence analysis approach using a unique Nordic horse model.\n\nPooled sequence data from three Nordic horse populations were used for F ST analysis. After strict filtering, FST analysis yielded 580 differentiated regions for trotting racing ability. Candidate regions on equine chromosomes 7 and 11 contained the largest number of SNPs (n = 214 and 147, respectively). GO analyses identified multiple genes related to intelligence, energy metabolism, and skeletal development as potential candidate genes. However, only one candidate region for trotting racing ability overlapped a known racing ability QTL.\n\nNot unexpected for genomic investigations of complex traits, the current study identified hundreds of candidate regions contributing to trotting racing ability in the horse. Likely resulting from the cumulative effects of many variants across the genome, racing ability continues to demonstrate its polygenic nature with candidate regions implicating genes influencing both musculature and neurological development.", "doi": "10.1186/s12864-019-5484-9", "pmid": "30717660", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-019-5484-9"}, {"db": "pmc", "key": "PMC6360714"}], "notes": [], "created": "2019-04-23T09:58:32.755Z", "modified": "2024-01-16T13:48:44.722Z"}, {"entity": "publication", "iuid": "1395e138b69949e3b221577f74c6d32c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1395e138b69949e3b221577f74c6d32c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1395e138b69949e3b221577f74c6d32c"}}, "title": "Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms", "authors": [{"family": "De Wit", "given": "Pierre", "initials": "P"}, {"family": "Durland", "given": "Evan", "initials": "E"}, {"family": "Ventura", "given": "Alexander", "initials": "A"}, {"family": "Langdon", "given": "Chris J", "initials": "CJ"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": null, "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": null, "doi": "10.1186/s12864-018-4519-y", "pmid": "29471790", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Crassostrea gigas embryonic gene expression", "key": "PRJNA306408"}, {"db": "Dryad", "description": "https://datadryad.org/resource/doi:10.5061/dryad.8m5v4", "key": "10.5061/dryad.8m5v4"}], "notes": [], "created": "2018-02-27T13:44:13.067Z", "modified": "2020-01-21T13:56:12.162Z"}, {"entity": "publication", "iuid": "6ffac0923e9747bf8995a9b6c804133a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ffac0923e9747bf8995a9b6c804133a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ffac0923e9747bf8995a9b6c804133a"}}, "title": "Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction", "authors": [{"family": "Bornel\u00f6v", "given": "Susanne", "initials": "S"}, {"family": "Seroussi", "given": "Eyal", "initials": "E"}, {"family": "Yosefi", "given": "Sara", "initials": "S"}, {"family": "Benjamini", "given": "Sharon", "initials": "S"}, {"family": "Miyara", "given": "Shoval", "initials": "S"}, {"family": "Ruzal", "given": "Mark", "initials": "M"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Molin", "given": "Anna Maja", "initials": "AM"}, {"family": "Pendavis", "given": "Ken", "initials": "K"}, {"family": "Burgess", "given": "Shane C", "initials": "SC"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Friedman-Einat", "given": "Miriam", "initials": "M"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": null, "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": null, "doi": "10.1186/s12864-018-4675-0", "pmid": "29695257", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Comparative RNA-seq in chicken reveals new reproductive adipokines", "key": "PRJEB23373"}], "notes": [], "created": "2018-05-03T11:09:55.199Z", "modified": "2024-01-16T13:48:45.125Z"}, {"entity": "publication", "iuid": "b132b31294784723bb2d008456c45f1d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b132b31294784723bb2d008456c45f1d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b132b31294784723bb2d008456c45f1d"}}, "title": "Analysis of porcine body size variation using re-sequencing data of miniature and large pigs", "authors": [{"family": "Reimer", "given": "C", "initials": "C"}, {"family": "Rubin", "given": "C J", "initials": "CJ"}, {"family": "Sharifi", "given": "A R", "initials": "AR"}, {"family": "Ha", "given": "N T", "initials": "NT"}, {"family": "Weigend", "given": "S", "initials": "S"}, {"family": "Waldmann", "given": "K H", "initials": "KH"}, {"family": "Distl", "given": "O", "initials": "O"}, {"family": "Pant", "given": "S D", "initials": "SD"}, {"family": "Fredholm", "given": "M", "initials": "M"}, {"family": "Schlather", "given": "M", "initials": "M"}, {"family": "Simianer", "given": "H", "initials": "H"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": null, "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": null, "doi": "10.1186/s12864-018-5009-y", "pmid": "30231878", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "Dryad", "description": "Data from: Comparative analyses of QTLs influencing obesity and metabolic phenotypes in pigs and humans", "key": "https://doi.org/10.5061/dryad.3jj7f"}, {"db": "SRA", "description": "Data from: Strong signatures of selection in the domestic pig genome", "key": "ERP001813"}, {"db": "SRA", "description": "Data from: The sequence and analysis of a Chinese pig genome", "key": "SRA051254"}, {"db": "SRA", "description": "Data from: Minipig and beagle animal model genomes aid species selection in pharmaceutical discovery and development", "key": "SRR578029"}, {"db": "SRA", "description": "Data from: Minipig and beagle animal model genomes aid species selection in pharmaceutical discovery and development", "key": "SRR578191"}, {"db": "SRA", "description": "Data from: Minipig and beagle animal model genomes aid species selection in pharmaceutical discovery and development", "key": "SRR578192"}, {"db": "BioProject", "description": "Goettingen Miniature Pig and MiniLEWE sequencing", "key": "PRJEB27654"}], "notes": [], "created": "2018-09-24T05:40:33.940Z", "modified": "2024-01-16T13:48:45.140Z"}, {"entity": "publication", "iuid": "f9a8fbd98d754cffa1879583683d108c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9a8fbd98d754cffa1879583683d108c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9a8fbd98d754cffa1879583683d108c"}}, "title": "SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma.", "authors": [{"family": "Jord\u00e1n-Pla", "given": "Antonio", "initials": "A"}, {"family": "Yu", "given": "Simei", "initials": "S"}, {"family": "Waldholm", "given": "Johan", "initials": "J"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "\u00d6stlund Farrants", "given": "Ann-Kristin", "initials": "AK"}, {"family": "Visa", "given": "Neus", "initials": "N"}], "type": "journal article", "published": "2018-05-18", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": "367", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Brahma (BRM) is the only catalytic subunit of the SWI/SNF chromatin-remodeling complex of Drosophila melanogaster. The function of SWI/SNF in transcription has long been attributed to its ability to remodel nucleosomes, which requires the ATPase activity of BRM. However, recent studies have provided evidence for a non-catalytic function of BRM in the transcriptional regulation of a few specific genes.\n\nHere we have used RNA-seq and ChIP-seq to identify the BRM target genes in S2 cells, and we have used a catalytically inactive BRM mutant (K804R) that is unable to hydrolyze ATP to investigate the magnitude of the non-catalytic function of BRM in transcription regulation. We show that 49% of the BRM target genes in S2 cells are regulated through mechanisms that do not require BRM to have an ATPase activity. We also show that the catalytic and non-catalytic mechanisms of SWI/SNF regulation operate on two subsets of genes that differ in promoter architecture and are linked to different biological processes.\n\nThis study shows that the non-catalytic role of SWI/SNF in transcription regulation is far more prevalent than previously anticipated and that the genes that are regulated by SWI/SNF through ATPase-dependent and ATPase-independent mechanisms have specialized roles in different cellular and developmental processes.", "doi": "10.1186/s12864-018-4746-2", "pmid": "29776334", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-018-4746-2"}, {"db": "pmc", "key": "PMC5960078"}, {"db": "GEO", "description": "The distribution of Brahma in the genome of Drosophila melanogaster S2 cells and the roles of Brahma in transcription and pre-mRNA processin", "key": "GSE95236"}], "notes": [], "created": "2018-10-31T19:46:23.156Z", "modified": "2024-01-16T13:48:46.291Z"}, {"entity": "publication", "iuid": "8feeddbbec5040e4a4d84314710c2608", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8feeddbbec5040e4a4d84314710c2608.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8feeddbbec5040e4a4d84314710c2608"}}, "title": "Genetical genomics of growth in a chicken model.", "authors": [{"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Fogelholm", "given": "Jesper", "initials": "J"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D"}], "type": "journal article", "published": "2018-01-23", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": "72", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The genetics underlying body mass and growth are key to understanding a wide range of topics in biology, both evolutionary and developmental. Body mass and growth traits are affected by many genetic variants of small effect. This complicates genetic mapping of growth and body mass. Experimental intercrosses between individuals from divergent populations allows us to map naturally occurring genetic variants for selected traits, such as body mass by linkage mapping. By simultaneously measuring traits and intermediary molecular phenotypes, such as gene expression, one can use integrative genomics to search for potential causative genes.\n\nIn this study, we use linkage mapping approach to map growth traits (N\u2009=\u2009471) and liver gene expression (N\u2009=\u2009130) in an advanced intercross of wild Red Junglefowl and domestic White Leghorn layer chickens. We find 16 loci for growth traits, and 1463 loci for liver gene expression, as measured by microarrays. Of these, the genes TRAK1, OSBPL8, YEATS4, CEP55, and PIP4K2B are identified as strong candidates for growth loci in the chicken. We also show a high degree of sex-specific gene-regulation, with almost every gene expression locus exhibiting sex-interactions. Finally, several trans-regulatory hotspots were found, one of which coincides with a major growth locus.\n\nThese findings not only serve to identify several strong candidates affecting growth, but also show how sex-specificity and local gene-regulation affect growth regulation in the chicken.", "doi": "10.1186/s12864-018-4441-3", "pmid": "29361907", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-018-4441-3"}, {"db": "pmc", "key": "PMC5782384"}, {"db": "ArrayExpress", "description": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5572/", "key": "E-MTAB-5572"}], "notes": [], "created": "2018-05-25T13:31:02.222Z", "modified": "2024-01-16T13:48:47.054Z"}, {"entity": "publication", "iuid": "89f85b8150ec4621b3e38e5f6146d691", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89f85b8150ec4621b3e38e5f6146d691.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89f85b8150ec4621b3e38e5f6146d691"}}, "title": "A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of\u200b \u200b\u200bPopulus\u200b\u200b \u200btrees.", "authors": [{"family": "Obudulu", "given": "Ogonna", "initials": "O"}, {"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Skotare", "given": "Tomas", "initials": "T"}, {"family": "Bygdell", "given": "Joakim", "initials": "J"}, {"family": "Abreu", "given": "Ilka N", "initials": "IN"}, {"family": "Ahnlund", "given": "Maria", "initials": "M"}, {"family": "Latha Gandla", "given": "Madhavi", "initials": "M"}, {"family": "Petterle", "given": "Anna", "initials": "A"}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ"}, {"family": "Wingsle", "given": "Gunnar", "initials": "G"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Tuominen", "given": "Hannele", "initials": "H", "orcid": "0000-0002-4949-3702", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fe575e1cb054ab08b57e05d3a1ee28d.json"}}], "type": "journal article", "published": "2018-01-03", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "19", "issue": "1", "pages": "11", "issn-l": "1471-2164"}, "abstract": "Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32-38 kDa proteins that are involved in membrane trafficking. A systems approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. Phenotypic and multi-omics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3; Potri.019G104000).\n\nThe woody tissues of the transgenic trees displayed increased amounts of both polysaccharides and lignin oligomers, indicating increased deposition of both the carbohydrate and lignin components of the secondary cell walls. This coincided with a tendency towards increased wood density as well as significantly increased thickness of the suberized cork in the transgenic lines. Multivariate OnPLS (orthogonal projections to latent structures) modeling of five different omics datasets (the transcriptome, proteome, GC-MS metabolome, LC-MS metabolome and pyrolysis-GC/MS metabolome) collected from the secondary xylem tissues of the stem revealed systemic variation in the different variables in the transgenic lines, including changes that correlated with the changes in the secondary cell wall composition. The OnPLS model also identified a rather large number of proteins that were more abundant in the transgenic lines than in the wild type. Several of these were related to secretion and/or endocytosis as well as both primary and secondary cell wall biosynthesis.\n\nPopulus SCAMP proteins were shown to influence accumulation of secondary cell wall components, including polysaccharides and phenolic compounds, in the woody tissues of Populus tree stems. Our multi-omics analyses combined with the OnPLS modelling suggest that this function is mediated by changes in membrane trafficking to fine-tune the abundance of cell wall precursors and/or proteins involved in cell wall biosynthesis and transport. The data provides a multi-level source of information for future studies on the function of the SCAMP proteins in plant stem tissues.", "doi": "10.1186/s12864-017-4411-1", "pmid": "29298676", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-4411-1"}, {"db": "pmc", "key": "PMC5753437"}], "notes": [], "created": "2019-01-10T10:03:22.571Z", "modified": "2025-10-17T13:03:18.332Z"}, {"entity": "publication", "iuid": "95528cb576024dc288a66fc3d60df598", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95528cb576024dc288a66fc3d60df598.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95528cb576024dc288a66fc3d60df598"}}, "title": "Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum.", "authors": [{"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "Tzelepis", "given": "Georgios", "initials": "G"}, {"family": "Bejai", "given": "Sarosh", "initials": "S"}, {"family": "Ilb\u00e4ck", "given": "Jonas", "initials": "J"}, {"family": "Schwelm", "given": "Arne", "initials": "A"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2018-01-03", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": "14", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Brassica plant species are attacked by a number of pathogens; among them, the ones with a soil-borne lifestyle have become increasingly important. Verticillium stem stripe caused by Verticillium longisporum is one example. This fungal species is thought to be of a hybrid origin, having a genome composed of combinations of lineages denominated A and D. In this study we report the draft genomes of 2 V. longisporum field isolates sequenced using the Illumina technology. Genomic characterization and lineage composition, followed by selected gene analysis to facilitate the comprehension of its genomic features and potential effector categories were performed.\n\nThe draft genomes of 2 Verticillium longisporum single spore isolates (VL1 and VL2) have an estimated ungapped size of about 70\u00a0Mb. The total number of protein encoding genes identified in VL1 was 20,793, whereas 21,072 gene models were predicted in VL2. The predicted genome size, gene contents, including the gene families coding for carbohydrate active enzymes were almost double the numbers found in V. dahliae and V. albo-atrum. Single nucleotide polymorphisms (SNPs) were frequently distributed in the two genomes but the distribution of heterozygosity and depth was not independent. Further analysis of potential parental lineages suggests that the V. longisporum genome is composed of two parts, A1 and D1, where A1 is more ancient than the parental lineage genome D1, the latter being more closer related to V. dahliae. Presence of the mating-type genes MAT1-1-1 and MAT1-2-1 in the V. longisporum genomes were confirmed. However, the MAT genes in V. dahliae, V. albo-atrum and V. longisporum have experienced extensive nucleotide changes at least partly explaining the present asexual nature of these fungal species.\n\nThe established draft genome of V. longisporum is comparatively large compared to other studied ascomycete fungi. Consequently, high numbers of genes were predicted in the two V. longisporum genomes, among them many secreted proteins and carbohydrate active enzyme (CAZy) encoding genes. The genome is composed of two parts, where one lineage is more ancient than the part being more closely related to V. dahliae. Dissimilar mating-type sequences were identified indicating possible ancient hybridization events.", "doi": "10.1186/s12864-017-4407-x", "pmid": "29298673", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-4407-x"}, {"db": "pmc", "key": "PMC5753508"}], "notes": [], "created": "2018-10-31T19:45:58.528Z", "modified": "2024-01-16T13:48:47.117Z"}, {"entity": "publication", "iuid": "4c60c5b0a8564155ad92ca6e79e2a352", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c60c5b0a8564155ad92ca6e79e2a352.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c60c5b0a8564155ad92ca6e79e2a352"}}, "title": "Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens", "authors": [{"family": "Lillie", "given": "Mette", "initials": "M"}, {"family": "Sheng", "given": "Zheya", "initials": "Z"}, {"family": "Honaker", "given": "Christa F", "initials": "CF"}, {"family": "Dorshorst", "given": "Ben J", "initials": "BJ"}, {"family": "Ashwell", "given": "Christopher M", "initials": "CM"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "18", "issn": "1471-2164", "issue": "1", "pages": null, "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": null, "doi": "10.1186/s12864-016-3414-7", "pmid": "28100171", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP094614"}, {"db": "SRA", "description": "High Antibody Relaxed", "key": "SRX2398013"}, {"db": "SRA", "description": "High Antibody Selected", "key": "SRX2398014"}, {"db": "SRA", "description": "Low Antibody Relaxed", "key": "SRX2398015"}, {"db": "SRA", "description": "Low Antibody Selected", "key": "SRX2398018"}], "notes": [], "created": "2017-10-19T20:19:08.913Z", "modified": "2020-01-21T13:56:11.293Z"}, {"entity": "publication", "iuid": "7c8cc7a768524b84be600507b658f4b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c8cc7a768524b84be600507b658f4b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c8cc7a768524b84be600507b658f4b9"}}, "title": "The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics.", "authors": [{"family": "Gopalakrishnan", "given": "Shyam", "initials": "S"}, {"family": "Samaniego Castruita", "given": "Jose A", "initials": "JA"}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Kuderna", "given": "Lukas F K", "initials": "LFK"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Jannikke", "initials": "J"}, {"family": "Petersen", "given": "Bent", "initials": "B"}, {"family": "Sicheritz-Ponten", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}, {"family": "Larson", "given": "Greger", "initials": "G"}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Hansen", "given": "Anders J", "initials": "AJ"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}], "type": "journal article", "published": "2017-06-29", "journal": {"volume": "18", "issn": "1471-2164", "issue": "1", "pages": "495", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a boxer dog (Canis lupus familiaris). We generated the first de novo wolf genome (Canis lupus lupus) as an additional choice of reference, and explored what implications may arise when previously published dog and wolf resequencing data are remapped to this reference.\n\nReassuringly, we find that regardless of the reference genome choice, most evolutionary genomic analyses yield qualitatively similar results, including those exploring the structure between the wolves and dogs using admixture and principal component analysis. However, we do observe differences in the genomic coverage of re-mapped samples, the number of variants discovered, and heterozygosity estimates of the samples.\n\nIn conclusion, the choice of reference is dictated by the aims of the study being undertaken; if the study focuses on the differences between the different dog breeds or the fine structure among dogs, then using the boxer reference genome is appropriate, but if the aim of the study is to look at the variation within wolves and their relationships to dogs, then there are clear benefits to using the de novo assembled wolf reference genome.", "doi": "10.1186/s12864-017-3883-3", "pmid": "28662691", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-3883-3"}, {"db": "pmc", "key": "PMC5492679"}], "notes": [], "created": "2017-11-03T16:21:39.181Z", "modified": "2021-07-07T20:31:10.838Z"}, {"entity": "publication", "iuid": "f35c109acf9743b79cb359d6a7b17c91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f35c109acf9743b79cb359d6a7b17c91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f35c109acf9743b79cb359d6a7b17c91"}}, "title": "The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish.", "authors": [{"family": "Adrian-Kalchhauser", "given": "Irene", "initials": "I"}, {"family": "Svensson", "given": "Ola", "initials": "O"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Pippel", "given": "Martin", "initials": "M"}, {"family": "Winkler", "given": "Sylke", "initials": "S"}, {"family": "Schloissnig", "given": "Siegfried", "initials": "S"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Burkhardt-Holm", "given": "Patricia", "initials": "P"}], "type": "journal article", "published": "2017-02-16", "journal": {"volume": "18", "issn": "1471-2164", "issue": "1", "pages": "177", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb).\n\nDuring genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16.4\u00a0kb), while the mitochondrial genome of the round goby is much larger than expected for a vertebrate. It is 19\u00a0kb in size and is thus one of the largest fish and even vertebrate mitochondrial genomes known to date. The expansion is attributable to a sequence insertion downstream of the putative transcriptional start site. This insertion carries traces of repeats from the control region, but is mostly novel. To get more information about this phenomenon, we gathered all available mitochondrial genomes of Gobiidae and of nine gobioid species, performed phylogenetic analyses, analysed gene arrangements, and compared gobiid mitochondrial genome sizes, ecological information and other species characteristics with respect to the mitochondrial phylogeny. This allowed us amongst others to identify a unique arrangement of tRNAs among Ponto-Caspian gobies.\n\nOur results indicate that the round goby mitochondrial genome may contain novel features. Since mitochondrial genome organisation is tightly linked to energy metabolism, these features may be linked to its invasion success. Also, the unique tRNA arrangement among Ponto-Caspian gobies may be helpful in studying the evolution of this highly adaptive and invasive species group. Finally, we find that the phylogeny of gobiids can be further refined by the use of longer stretches of linked DNA sequence.", "doi": "10.1186/s12864-017-3550-8", "pmid": "28209125", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-3550-8"}, {"db": "pmc", "key": "PMC5314710"}], "notes": [], "created": "2017-11-01T12:54:58.955Z", "modified": "2024-01-16T13:48:48.415Z"}, {"entity": "publication", "iuid": "d20029cd97e5458ba383b2a258b01fe8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d20029cd97e5458ba383b2a258b01fe8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d20029cd97e5458ba383b2a258b01fe8"}}, "title": "The genome-scale DNA-binding profile of BarR, a \u03b2-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius.", "authors": [{"family": "Liu", "given": "Han", "initials": "H"}, {"family": "Wang", "given": "Kun", "initials": "K"}, {"family": "Lind\u00e5s", "given": "Ann-Christin", "initials": "AC"}, {"family": "Peeters", "given": "Eveline", "initials": "E"}], "type": "journal article", "published": "2016-08-08", "journal": {"volume": "17", "issn": "1471-2164", "issue": null, "pages": "569", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The Leucine-responsive Regulatory Protein (Lrp) family is a widespread family of regulatory transcription factors in prokaryotes. BarR is an Lrp-like transcription factor in the model archaeon Sulfolobus acidocaldarius that activates the expression of a \u03b2-alanine aminotransferase gene, which is involved in \u03b2-alanine degradation. In contrast to classical Lrp-like transcription factors, BarR is not responsive to any of the \u03b1-amino acids but interacts specifically with \u03b2-alanine. Besides the juxtaposed \u03b2-alanine aminotransferase gene, other regulatory targets of BarR have not yet been identified although \u03b2-alanine is the precursor of coenzyme A and thus an important central metabolite. The aim of this study is to extend the knowledge of the DNA-binding characteristics of BarR and of its corresponding regulon from a local to a genome-wide perspective.\n\nWe characterized the genome-wide binding profile of BarR using chromatin immunoprecipation combined with high-throughput sequencing (ChIP-seq). This revealed 21 genomic binding loci. High-enrichment binding regions were validated to interact with purified BarR protein in vitro using electrophoretic mobility shift assays and almost all targets were also shown to harbour a conserved semi-palindromic binding motif. Only a small subset of enriched genomic sites are located in intergenic regions at a relative short distance to a promoter, and qRT-PCR analysis demonstrated that only one additional operon is under activation of BarR, namely the glutamine synthase operon. The latter is also a target of other Lrp-like transcription factors. Detailed inspection of the BarR ChIP-seq profile at the \u03b2-alanine aminotransferase promoter region in combination with binding motif predictions indicate that the operator structure is more complicated than previously anticipated, consisting of multiple (major and auxiliary) operators.\n\nBarR has a limited regulon, and includes also glutamine synthase genes besides the previously characterized \u03b2-alanine aminotransferase. Regulation of glutamine synthase is suggestive of a link between \u03b2-alanine and \u03b1-amino acid metabolism in S. acidocaldarius. Furthermore, this work reveals that the BarR regulon overlaps with that of other Lrp-like regulators.", "doi": "10.1186/s12864-016-2890-0", "pmid": "27502941", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-016-2890-0"}, {"db": "pmc", "key": "PMC4977709"}], "notes": [], "created": "2017-05-03T13:01:07.294Z", "modified": "2020-01-21T13:56:05.381Z"}, {"entity": "publication", "iuid": "9ef8d910663840a9884ea1c71f4d3408", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ef8d910663840a9884ea1c71f4d3408.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ef8d910663840a9884ea1c71f4d3408"}}, "title": "Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes.", "authors": [{"family": "Troell", "given": "Karin", "initials": "K"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Divne", "given": "Anna-Maria", "initials": "AM"}, {"family": "Alsmark", "given": "Cecilia", "initials": "C"}, {"family": "Arrighi", "given": "Romanico", "initials": "R"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Beser", "given": "Jessica", "initials": "J"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2016-06-23", "journal": {"volume": "17", "issn": "1471-2164", "issue": null, "pages": "471", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Infectious disease involving multiple genetically distinct populations of pathogens is frequently concurrent, but difficult to detect or describe with current routine methodology. Cryptosporidium sp. is a widespread gastrointestinal protozoan of global significance in both animals and humans. It cannot be easily maintained in culture and infections of multiple strains have been reported. To explore the potential use of single cell genomics methodology for revealing genome-level variation in clinical samples from Cryptosporidium-infected hosts, we sorted individual oocysts for subsequent genome amplification and full-genome sequencing.\n\nCells were identified with fluorescent antibodies with an 80\u00a0% success rate for the entire single cell genomics workflow, demonstrating that the methodology can be applied directly to purified fecal samples. Ten amplified genomes from sorted single cells were selected for genome sequencing and compared both to the original population and a reference genome in order to evaluate the accuracy and performance of the method. Single cell genome coverage was on average 81\u00a0% even with a moderate sequencing effort and by combining the 10 single cell genomes, the full genome was accounted for. By a comparison to the original sample, biological variation could be distinguished and separated from noise introduced in the amplification.\n\nAs a proof of principle, we have demonstrated the power of applying single cell genomics to dissect infectious disease caused by closely related parasite species or subtypes. The workflow can easily be expanded and adapted to target other protozoans, and potential applications include mapping genome-encoded traits, virulence, pathogenicity, host specificity and resistance at the level of cells as truly meaningful biological units.", "doi": "10.1186/s12864-016-2815-y", "pmid": "27338614", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Microbial Single Cell Genomics": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-016-2815-y"}, {"db": "pmc", "key": "PMC4917956"}], "notes": [], "created": "2017-05-03T12:59:36.710Z", "modified": "2024-01-16T13:48:49.934Z"}, {"entity": "publication", "iuid": "c1101eb867604d37b6e8ce7051cd822c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1101eb867604d37b6e8ce7051cd822c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1101eb867604d37b6e8ce7051cd822c"}}, "title": "Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development.", "authors": [{"family": "Obudulu", "given": "Ogonna", "initials": "O"}, {"family": "Bygdell", "given": "Joakim", "initials": "J"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Wingsle", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2016-02-18", "journal": {"volume": "17", "issn": "1471-2164", "issue": null, "pages": "119", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Wood development is of outstanding interest both to basic research and industry due to the associated cellulose and lignin biomass production. Efforts to elucidate wood formation (which is essential for numerous aspects of both pure and applied plant science) have been made using transcriptomic analyses and/or low-resolution sampling. However, transcriptomic data do not correlate perfectly with levels of expressed proteins due to effects of post-translational modifications and variations in turnover rates. In addition, high-resolution analysis is needed to characterize key transitions. In order to identify protein profiles across the developmental region of wood formation, an in-depth and tissue specific sampling was performed.\n\nWe examined protein profiles, using an ultra-performance liquid chromatography/quadrupole time of flight mass spectrometry system, in high-resolution tangential sections spanning all wood development zones in Populus tremula from undifferentiated cambium to mature phloem and xylem, including cell expansion and cell death zones. In total, we analyzed 482 sections, 20-160 \u03bcm thick, from four 47-year-old trees growing wild in Sweden. We obtained high quality expression profiles for 3,082 proteins exhibiting consistency across the replicates, considering that the trees were growing in an uncontrolled environment. A combination of Principal Component Analysis (PCA), Orthogonal Projections to Latent Structures (OPLS) modeling and an enhanced stepwise linear modeling approach identified several major transitions in global protein expression profiles, pinpointing (for example) locations of the cambial division leading to phloem and xylem cells, and secondary cell wall formation zones. We also identified key proteins and associated pathways underlying these developmental landmarks. For example, many of the lignocellulosic related proteins were upregulated in the expansion to the early developmental xylem zone, and for laccases with a rapid decrease in early xylem zones. We observed upregulation of two forms of xylem cysteine protease (Potri.002G005700.1 and Potri.005G256000.2; Pt-XCP2.1) in early xylem and their downregulation in late maturing xylem. Our data also show that Pt-KOR1.3 (Potri.003G151700.2) exhibits an expression pattern that supports the hypothesis put forward in previous studies that this is a key xyloglucanase involved in cellulose biosynthesis in primary cell walls and reduction of cellulose crystallinity in secondary walls.\n\nOur novel multivariate approach highlights important processes and provides confirmatory insights into the molecular foundations of wood development.", "doi": "10.1186/s12864-016-2458-z", "pmid": "26887814", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-016-2458-z"}, {"db": "pmc", "key": "PMC4758094"}], "notes": [], "created": "2017-05-03T12:59:41.476Z", "modified": "2025-10-17T13:03:19.747Z"}, {"entity": "publication", "iuid": "1340f5a43e3a421a92188835e534a777", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1340f5a43e3a421a92188835e534a777.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1340f5a43e3a421a92188835e534a777"}}, "title": "The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence.", "authors": [{"family": "Norling", "given": "Martin", "initials": "M"}, {"family": "Bishop", "given": "Richard P", "initials": "RP"}, {"family": "Pelle", "given": "Roger", "initials": "R"}, {"family": "Qi", "given": "Weihong", "initials": "W"}, {"family": "Henson", "given": "Sonal", "initials": "S"}, {"family": "Dr\u00e1bek", "given": "Elliott F", "initials": "EF"}, {"family": "Tretina", "given": "Kyle", "initials": "K"}, {"family": "Odongo", "given": "David", "initials": "D"}, {"family": "Mwaura", "given": "Stephen", "initials": "S"}, {"family": "Njoroge", "given": "Thomas", "initials": "T"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Daubenberger", "given": "Claudia A", "initials": "CA"}, {"family": "Silva", "given": "Joana C", "initials": "JC"}], "type": "journal article", "published": "2015-09-24", "journal": {"volume": "16", "issn": "1471-2164", "issue": null, "pages": "729", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "There are no commercially available vaccines against human protozoan parasitic diseases, despite the success of vaccination-induced long-term protection against infectious diseases. East Coast fever, caused by the protist Theileria parva, kills one million cattle each year in sub-Saharan Africa, and contributes significantly to hunger and poverty in the region. A highly effective, live, multi-isolate vaccine against T. parva exists, but its component isolates have not been characterized. Here we sequence and compare the three component T. parva stocks within this vaccine, the Muguga Cocktail, namely Muguga, Kiambu5 and Serengeti-transformed, aiming to identify genomic features that contribute to vaccine efficacy.\n\nWe find that Serengeti-transformed, originally isolated from the wildlife carrier, the African Cape buffalo, is remarkably and unexpectedly similar to the Muguga isolate. The 420 detectable non-synonymous SNPs were distributed among only 53 genes, primarily subtelomeric antigens and antigenic families. The Kiambu5 isolate is considerably more divergent, with close to 40,000 SNPs relative to Muguga, including >8,500 non-synonymous mutations distributed among >1,700 (42.5 %) of the predicted genes. These genetic markers of the component stocks can be used to characterize the composition of new batches of the Muguga Cocktail.\n\nDifferences among these three isolates, while extensive, represent only a small proportion of the genetic variation in the entire species. Given the efficacy of the Muguga Cocktail in inducing long-lasting protection against infections in the field, our results suggest that whole-organism vaccines against parasitic diseases can be highly efficacious despite considerable genome-wide differences relative to the isolates against which they protect.", "doi": "10.1186/s12864-015-1910-9", "pmid": "26403690", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-015-1910-9"}, {"db": "pmc", "key": "PMC4583173"}], "notes": [], "created": "2017-05-02T12:57:55.849Z", "modified": "2020-01-21T13:56:00.820Z"}, {"entity": "publication", "iuid": "027985dca2834b938bcf4996063d306b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/027985dca2834b938bcf4996063d306b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/027985dca2834b938bcf4996063d306b"}}, "title": "Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica.", "authors": [{"family": "Gkarmiri", "given": "Konstantia", "initials": "K"}, {"family": "Finlay", "given": "Roger D", "initials": "RD"}, {"family": "Alstr\u00f6m", "given": "Sadhna", "initials": "S"}, {"family": "Thomas", "given": "Elizabeth", "initials": "E"}, {"family": "Cubeta", "given": "Marc A", "initials": "MA"}, {"family": "H\u00f6gberg", "given": "Nils", "initials": "N"}], "type": "journal article", "published": "2015-08-22", "journal": {"volume": "16", "issn": "1471-2164", "issue": null, "pages": "630", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. Rhizoctonia solani is an important soil-associated fungal pathogen and its chemical treatment is not feasible or economic. The genomes of the plant-associated bacteria Serratia proteamaculans S4 and Serratia plymuthica AS13 have been sequenced, revealing genetic traits that may explain their diverse plant growth promoting activities and antagonistic interactions with R. solani. To understand the functional response of this pathogen to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq.\n\nApproximately 104,504 million clean 75-100 bp paired-end reads were obtained from three libraries, each in triplicate (AG3-Control, AG3-S4 and AG3-AS13). Transcriptome analysis revealed that approximately 10% of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had values of log2 fold-change\u2009>\u20093 and for further analyses this cut-off value was used. Functional classification of DEGs based on Gene Ontology enrichment analysis and on KEGG pathway annotations revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation.\n\nThis RNA-seq profiling generated a novel dataset describing the functional response of the phytopathogen R. solani AG3 to the plant-associated Serratia bacteria S4 and AS13. Most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere.", "doi": "10.1186/s12864-015-1758-z", "pmid": "26296338", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-015-1758-z"}, {"db": "pmc", "key": "PMC4546130"}], "notes": [], "created": "2017-05-02T12:57:06.383Z", "modified": "2020-01-21T13:56:00.515Z"}, {"entity": "publication", "iuid": "edc4228d642b4f87a72a1da844100488", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edc4228d642b4f87a72a1da844100488.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edc4228d642b4f87a72a1da844100488"}}, "title": "Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress.", "authors": [{"family": "Wallace-Salinas", "given": "Valeria", "initials": "V"}, {"family": "Brink", "given": "Daniel P", "initials": "DP"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Gorwa-Grauslund", "given": "Marie F", "initials": "MF"}], "type": "comparative study", "published": "2015-07-09", "journal": {"volume": "16", "issn": "1471-2164", "issue": null, "pages": "514", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Laboratory evolution is an important tool for developing robust yeast strains for bioethanol production since the biological basis behind combined tolerance requires complex alterations whose proper regulation is difficult to achieve by rational metabolic engineering. Previously, we reported on the evolved industrial Saccharomyces cerevisiae strain ISO12 that had acquired improved tolerance to grow and ferment in the presence of lignocellulose-derived inhibitors at high temperature (39 \u00b0C). In the current study, we used comparative genomics to uncover the extent of the genomic alterations that occurred during the evolution process and investigated possible associations between the mutations and the phenotypic traits in ISO12.\r\n\r\nThrough whole-genome sequencing and variant calling we identified a high number of strain-unique SNPs and INDELs in both ISO12 and the parental strain Ethanol Red. The variants were predicted to have 760 non-synonymous effects in both strains combined and were significantly enriched in Gene Ontology terms related to cell periphery, membranes and cell wall. Eleven genes, including MTL1, FLO9/FLO11, and CYC3 were found to be under positive selection in ISO12. Additionally, the FLO genes exhibited changes in copy number, and the alterations to this gene family were correlated with experimental results of multicellularity and invasive growth in the adapted strain. An independent lipidomic analysis revealed further differences between the strains in the content of nine lipid species. Finally, ISO12 displayed improved viability in undiluted spruce hydrolysate that was unrelated to reduction of inhibitors and changes in cell wall integrity, as shown by HPLC and lyticase assays.\r\n\r\nTogether, the results of the sequence comparison and the physiological characterisations indicate that cell-periphery proteins (e.g. extracellular sensors such as MTL1) and peripheral lipids/membranes are important evolutionary targets in the process of adaptation to the combined stresses. The capacity of ISO12 to develop complex colony formation also revealed multicellularity as a possible evolutionary strategy to improve competitiveness and tolerance to environmental stresses (also reflected by the FLO genes). Although a panel of altered genes with high relevance to the novel phenotype was detected, this study also demonstrates that the observed long-term molecular effects of thermal and inhibitor stress have polygenetic basis.", "doi": "10.1186/s12864-015-1737-4", "pmid": "26156140", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-015-1737-4"}, {"db": "pmc", "key": "PMC4496855"}], "notes": [], "created": "2017-05-02T12:58:54.149Z", "modified": "2020-01-21T13:53:21.644Z"}, {"entity": "publication", "iuid": "c43f0bab915c4d528cd487794cf3c8d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c43f0bab915c4d528cd487794cf3c8d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c43f0bab915c4d528cd487794cf3c8d2"}}, "title": "The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling.", "authors": [{"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Linn\u00e9", "given": "Jerker", "initials": "J"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Sundberg", "given": "Carl Johan", "initials": "CJ"}, {"family": "Lindholm", "given": "Malene", "initials": "M"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Choi", "given": "Howard", "initials": "H"}, {"family": "Liem", "given": "David A", "initials": "DA"}, {"family": "Ping", "given": "Peipei", "initials": "P"}, {"family": "V\u00e4remo", "given": "Leif", "initials": "L"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Larsson", "given": "Erik", "initials": "E"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2015-06-25", "journal": {"volume": "16", "issn": "1471-2164", "issue": null, "pages": "475", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "To understand cardiac and skeletal muscle function, it is important to define and explore their molecular constituents and also to identify similarities and differences in the gene expression in these two different striated muscle tissues. Here, we have investigated the genes and proteins with elevated expression in cardiac and skeletal muscle in relation to all other major human tissues and organs using a global transcriptomics analysis complemented with antibody-based profiling to localize the corresponding proteins on a single cell level.\n\nOur study identified a comprehensive list of genes expressed in cardiac and skeletal muscle. The genes with elevated expression were further stratified according to their global expression pattern across the human body as well as their precise localization in the muscle tissues. The functions of the proteins encoded by the elevated genes are well in line with the physiological functions of cardiac and skeletal muscle, such as contraction, ion transport, regulation of membrane potential and actomyosin structure organization. A large fraction of the transcripts in both cardiac and skeletal muscle correspond to mitochondrial proteins involved in energy metabolism, which demonstrates the extreme specialization of these muscle tissues to provide energy for contraction.\n\nOur results provide a comprehensive list of genes and proteins elevated in striated muscles. A number of proteins not previously characterized in cardiac and skeletal muscle were identified and localized to specific cellular subcompartments. These proteins represent an interesting starting point for further functional analysis of their role in muscle biology and disease.", "doi": "10.1186/s12864-015-1686-y", "pmid": "26109061", "labels": {"Tissue Profiling": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-015-1686-y"}, {"db": "pmc", "key": "PMC4479346"}, {"db": "GEO", "key": "GSE58387"}, {"db": "GEO", "key": "GSE58608"}], "notes": [], "created": "2017-05-02T12:57:51.478Z", "modified": "2021-07-08T13:44:33.602Z"}, {"entity": "publication", "iuid": "517ca4f80a264abc88a799d8f5e65bb1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/517ca4f80a264abc88a799d8f5e65bb1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/517ca4f80a264abc88a799d8f5e65bb1"}}, "title": "CGGBP1 mitigates cytosine methylation at repetitive DNA sequences.", "authors": [{"family": "Agarwal", "given": "Prasoon", "initials": "P"}, {"family": "Collier", "given": "Paul", "initials": "P"}, {"family": "Fritz", "given": "Markus Hsi-Yang", "initials": "MH"}, {"family": "Benes", "given": "Vladimir", "initials": "V"}, {"family": "Wiklund", "given": "Helena Jernberg", "initials": "HJ"}, {"family": "Westermark", "given": "Bengt", "initials": "B"}, {"family": "Singh", "given": "Umashankar", "initials": "U"}], "type": "journal article", "published": "2015-05-16", "journal": {"volume": "16", "issn": "1471-2164", "issue": null, "pages": "390", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "CGGBP1 is a repetitive DNA-binding transcription regulator with target sites at CpG-rich sequences such as CGG repeats and Alu-SINEs and L1-LINEs. The role of CGGBP1 as a possible mediator of CpG methylation however remains unknown. At CpG-rich sequences cytosine methylation is a major mechanism of transcriptional repression. Concordantly, gene-rich regions typically carry lower levels of CpG methylation than the repetitive elements. It is well known that at interspersed repeats Alu-SINEs and L1-LINEs high levels of CpG methylation constitute a transcriptional silencing and retrotransposon inactivating mechanism.\n\nHere, we have studied genome-wide CpG methylation with or without CGGBP1-depletion. By high throughput sequencing of bisulfite-treated genomic DNA we have identified CGGBP1 to be a negative regulator of CpG methylation at repetitive DNA sequences. In addition, we have studied CpG methylation alterations on Alu and L1 retrotransposons in CGGBP1-depleted cells using a novel bisulfite-treatment and high throughput sequencing approach.\n\nThe results clearly show that CGGBP1 is a possible bidirectional regulator of CpG methylation at Alus, and acts as a repressor of methylation at L1 retrotransposons.", "doi": "10.1186/s12864-015-1593-2", "pmid": "25981527", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-015-1593-2"}, {"db": "pmc", "key": "PMC4432828"}], "notes": [], "created": "2017-05-02T12:58:14.972Z", "modified": "2020-01-21T13:56:02.300Z"}, {"entity": "publication", "iuid": "fc128150f0c649cfb1173c27c2b6bb58", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc128150f0c649cfb1173c27c2b6bb58.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc128150f0c649cfb1173c27c2b6bb58"}}, "title": "Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis.", "authors": [{"family": "Vigil-Stenman", "given": "Theoden", "initials": "T"}, {"family": "Larsson", "given": "John", "initials": "J"}, {"family": "Nylander", "given": "Johan A A", "initials": "JA"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}], "type": "journal article", "published": "2015-03-17", "journal": {"volume": "16", "issn": "1471-2164", "issue": null, "pages": "193", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Insertion sequences (ISs) are approximately 1 kbp long \"jumping\" genes found in prokaryotes. ISs encode the protein Transposase, which facilitates the excision and reinsertion of ISs in genomes, making these sequences a type of class I (\"cut-and-paste\") Mobile Genetic Elements. ISs are proposed to be involved in the reductive evolution of symbiotic prokaryotes. Our previous sequencing of the genome of the cyanobacterium 'Nostoc azollae' 0708, living in a tight perpetual symbiotic association with a plant (the water fern Azolla), revealed the presence of an eroding genome, with a high number of insertion sequences (ISs) together with an unprecedented large proportion of pseudogenes. To investigate the role of ISs in the reductive evolution of 'Nostoc azollae' 0708, and potentially in the formation of pseudogenes, a bioinformatic investigation of the IS identities and positions in 47 cyanobacterial genomes was conducted. To widen the scope, the IS contents were analysed qualitatively and quantitatively in 20 other genomes representing both free-living and symbiotic bacteria.\n\nInsertion Sequences were not randomly distributed in the bacterial genomes and were found to transpose short distances from their original location (\"local hopping\") and pseudogenes were enriched in the vicinity of IS elements. In general, symbiotic organisms showed higher densities of IS elements and pseudogenes than non-symbiotic bacteria. A total of 1108 distinct repeated sequences over 500\u00a0bp were identified in the 67 genomes investigated. In the genome of 'Nostoc azollae' 0708, IS elements were apparent at 970 locations (14.3%), with 428 being full-length. Morphologically complex cyanobacteria with large genomes showed higher frequencies of IS elements, irrespective of life style.\n\nThe apparent co-location of IS elements and pseudogenes found in prokaryotic genomes implies earlier IS transpositions into genes. As transpositions tend to be local rather than genome wide this likely explains the proximity between IS elements and pseudogenes. These findings suggest that ISs facilitate the reductive evolution in for instance in the symbiotic cyanobacterium 'Nostoc azollae' 0708 and in other obligate prokaryotic symbionts.", "doi": "10.1186/s12864-015-1386-7", "pmid": "25885210", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-015-1386-7"}, {"db": "pmc", "key": "PMC4369082"}], "notes": [], "created": "2017-05-02T12:58:51.466Z", "modified": "2020-01-21T13:53:20.988Z"}, {"entity": "publication", "iuid": "53b5880c43c0494ba6f1db70c623fd0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53b5880c43c0494ba6f1db70c623fd0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53b5880c43c0494ba6f1db70c623fd0a"}}, "title": "High opsin diversity in a non-visual infaunal brittle star.", "authors": [{"family": "Delroisse", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Ullrich-L\u00fcter", "given": "Esther", "initials": "E"}, {"family": "Ortega-Martinez", "given": "Olga", "initials": "O"}, {"family": "Dupont", "given": "Sam", "initials": "S"}, {"family": "Arnone", "given": "Maria-Ina", "initials": "MI"}, {"family": "Mallefet", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Flammang", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2014-11-28", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "1035", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "In metazoans, opsins are photosensitive proteins involved in both vision and non-visual photoreception. Echinoderms have no well-defined eyes but several opsin genes were found in the purple sea urchin (Strongylocentrotus purpuratus) genome. Molecular data are lacking for other echinoderm classes although many species are known to be light sensitive.\n\nIn this study focused on the European brittle star Amphiura filiformis, we first highlighted a blue-green light sensitivity using a behavioural approach. We then identified 13 new putative opsin genes against eight bona fide opsin genes in the genome of S. purpuratus. Six opsins were included in the rhabdomeric opsin group (r-opsins). In addition, one putative ciliary opsin (c-opsin), showing high similarity with the c-opsin of S. purpuratus (Sp-opsin 1), one Go opsin similar to Sp-opsins 3.1 and 3.2, two basal-branch opsins similar to Sp-opsins 2 and 5, and two neuropsins similar to Sp-opsin 8, were identified. Finally, two sequences from one putative RGR opsin similar to Sp-opsin 7 were also detected. Adult arm transcriptome analysis pinpointed opsin mRNAs corresponding to one r-opsin, one neuropsin and the homologue of Sp-opsin 2. Opsin phylogeny was determined by maximum likelihood and Bayesian analyses. Using antibodies designed against c- and r-opsins from S. purpuratus, we detected putative photoreceptor cells mainly in spines and tube feet of A. filiformis, respectively. The r-opsin expression pattern is similar to the one reported in S. purpuratus with cells labelled at the tip and at the base of the tube feet. In addition, r-opsin positive cells were also identified in the radial nerve of the arm. C-opsins positive cells, expressed in pedicellariae, spines, tube feet and epidermis in S. purpuratus were observed at the level of the spine stroma in the brittle star.\n\nLight perception in A. filiformis seems to be mediated by opsins (c- and r-) in, at least, spines, tube feet and in the radial nerve cord. Other non-visual opsin types could participate to the light perception process indicating a complex expression pattern of opsins in this infaunal brittle star.", "doi": "10.1186/1471-2164-15-1035", "pmid": "25429842", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "1471-2164-15-1035"}, {"db": "pmc", "key": "PMC4289182"}], "notes": [], "created": "2017-11-01T12:55:01.631Z", "modified": "2020-01-21T13:53:21.662Z"}, {"entity": "publication", "iuid": "d027212b436046778a1d7ebf768467f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d027212b436046778a1d7ebf768467f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d027212b436046778a1d7ebf768467f8"}}, "title": "The Chironomus tentans genome sequence and the organization of the Balbiani ring genes.", "authors": [{"family": "Kutsenko", "given": "Alexey", "initials": "A"}, {"family": "Svensson", "given": "Thomas", "initials": "T", "orcid": "0000-0002-9190-2979", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc636683ece84dc4ac3e4d10df0c7a49.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Bj\u00f6rk", "given": "Petra", "initials": "P"}, {"family": "Sonnhammer", "given": "Erik", "initials": "E"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Visa", "given": "Neus", "initials": "N"}, {"family": "Wieslander", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2014-09-27", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "819", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, we report the first draft genome of Ch. tentans and characterize its gene expression machineries and genomic architecture of the BR genes.\n\nThe genome of Ch. tentans is approximately 200 Mb in size, and has a low GC content (31%) and a low repeat fraction (15%) compared to other Dipteran species. Phylogenetic inference revealed that Ch. tentans is a sister clade to mosquitoes, with a split 150-250 million years ago. To characterize the Ch. tentans gene expression machineries, we identified potential orthologus sequences to more than 600 Drosophila melanogaster (D. melanogaster) proteins involved in the expression of protein-coding genes. We report novel data on the organization of the BR gene loci, including a novel putative BR gene, and we present a model for the organization of chromatin bundles in the BR2 puff based on genic and intergenic in situ hybridizations.\n\nWe show that the molecular machineries operating in gene expression are largely conserved between Ch. tentans and D. melanogaster, and we provide enhanced insight into the organization and expression of the BR genes. Our data strengthen the generality of the BR genes as a unique model system and provide essential background for in-depth studies of the biogenesis of messenger ribonucleoprotein complexes.", "doi": "10.1186/1471-2164-15-819", "pmid": "25261295", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-819"}, {"db": "pmc", "key": "PMC4192438"}], "notes": [], "created": "2017-05-04T14:58:24.735Z", "modified": "2021-07-08T13:26:08.361Z"}, {"entity": "publication", "iuid": "aab88baf82cb4f46a382a588d0809a37", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aab88baf82cb4f46a382a588d0809a37.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aab88baf82cb4f46a382a588d0809a37"}}, "title": "Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Molin", "given": "Mikael", "initials": "M"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2014-09-01", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "749", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant selection pressures revealed by the presence of detoxification genes in marine bacteria. To capture a broad range of potential toxicants we selected detoxification protein families representing systems protecting microorganisms from a variety of stressors, such as metals, organic compounds, antibiotics and oxygen radicals.\n\nUsing a bioinformatics procedure based on comparative analysis to finished bacterial genomes we found that the amount of detoxification genes present in marine microorganisms seems surprisingly small. The underrepresentation is particularly evident for toxicant transporters and proteins involved in detoxifying metals. Exceptions are enzymes involved in oxidative stress defense where peroxidase enzymes are more abundant in marine bacteria compared to bacteria in general. In contrast, catalases are almost completely absent from the open ocean environment, suggesting that peroxidases and peroxiredoxins constitute a core line of defense against reactive oxygen species (ROS) in the marine milieu.\n\nWe found no indication that detoxification systems would be generally more abundant close to the coast compared to the open ocean. On the contrary, for several of the protein families that displayed a significant geographical distribution, like peroxidase, penicillin binding transpeptidase and divalent ion transport protein, the open ocean samples showed the highest abundance. Along the same lines, the abundance of most detoxification proteins did not increase with estimated pollution. The low level of detoxification systems in marine bacteria indicate that the majority of marine bacteria have a low capacity to adapt to increased pollution. Our study exemplifies the use of metagenomics data in ecotoxicology, and in particular how anthropogenic consequences on life in the sea can be examined.", "doi": "10.1186/1471-2164-15-749", "pmid": "25179155", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-749"}, {"db": "pmc", "key": "PMC4161860"}], "notes": [], "created": "2017-05-04T14:56:30.100Z", "modified": "2020-01-21T13:53:20.757Z"}, {"entity": "publication", "iuid": "d58d90e1b5b54964b9aa5becd6d9e2d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d58d90e1b5b54964b9aa5becd6d9e2d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d58d90e1b5b54964b9aa5becd6d9e2d6"}}, "title": "Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.", "authors": [{"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Johansson", "given": "Tomas", "initials": "T"}, {"family": "Canb\u00e4ck", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Bentzer", "given": "Johan", "initials": "J"}, {"family": "Rosenblad", "given": "Magnus Alm", "initials": "MA"}, {"family": "Johannesson", "given": "Kerstin", "initials": "K"}, {"family": "Tunlid", "given": "Anders", "initials": "A"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}], "type": "journal article", "published": "2014-08-18", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "687", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. Secondly, we performed a genome-wide comparison of four closely related Littorina species: L. fabalis, L. compressa, L. arcana and L. saxatilis and of populations of L. saxatilis found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying \"Crab\" and \"Wave\" ecotypes of L. saxatilis.\n\nWe could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of L. arcana, L. compressa and L. saxatilis could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the Littorina genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of L. saxatilis, but we did not detect any significant genome divergence associated with ecotypes of L. saxatilis.\n\nThe present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to Littorina species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of L. saxatilis ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms.", "doi": "10.1186/1471-2164-15-687", "pmid": "25135785", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-687"}, {"db": "pmc", "key": "PMC4148934"}, {"db": "GEO", "key": "GSE59825"}], "notes": [], "created": "2017-05-04T14:56:30.407Z", "modified": "2020-01-21T13:56:16.790Z"}, {"entity": "publication", "iuid": "f578abdd2dcc468fb3e0008446419448", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f578abdd2dcc468fb3e0008446419448.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f578abdd2dcc468fb3e0008446419448"}}, "title": "Analysis of stranded information using an automated procedure for strand specific RNA sequencing.", "authors": [{"family": "Sigurgeirsson", "given": "Benjam\u00edn", "initials": "B"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2014-07-28", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "631", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Strand specific RNA sequencing is rapidly replacing conventional cDNA sequencing as an approach for assessing information about the transcriptome. Alongside improved laboratory protocols the development of bioinformatical tools is steadily progressing. In the current procedure the Illumina TruSeq library preparation kit is used, along with additional reagents, to make stranded libraries in an automated fashion which are then sequenced on Illumina HiSeq 2000. By the use of freely available bioinformatical tools we show, through quality metrics, that the protocol is robust and reproducible. We further highlight the practicality of strand specific libraries by comparing expression of strand specific libraries to non-stranded libraries, by looking at known antisense transcription of pseudogenes and by identifying novel transcription. Furthermore, two ribosomal depletion kits, RiboMinus and RiboZero, are compared and two sequence aligners, Tophat2 and STAR, are also compared.\n\nThe, non-stranded, Illumina TruSeq kit can be adapted to generate strand specific libraries and can be used to access detailed information on the transcriptome. The RiboZero kit is very effective in removing ribosomal RNA from total RNA and the STAR aligner produces high mapping yield in a short time. Strand specific data gives more detailed and correct results than does non-stranded data as we show when estimating expression values and in assembling transcripts. Even well annotated genomes need improvements and corrections which can be achieved using strand specific data.\n\nResearchers in the field should strive to use strand specific data; it allows for more confidence in the data analysis and is less likely to lead to false conclusions. If faced with analysing non-stranded data, researchers should be well aware of the caveats of that approach.", "doi": "10.1186/1471-2164-15-631", "pmid": "25070246", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-631"}, {"db": "pmc", "key": "PMC4247151"}], "notes": [], "created": "2017-05-04T14:58:25.245Z", "modified": "2021-07-08T13:26:08.416Z"}, {"entity": "publication", "iuid": "803742fd3a1f42ab9c6d6bd9f029ce06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/803742fd3a1f42ab9c6d6bd9f029ce06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/803742fd3a1f42ab9c6d6bd9f029ce06"}}, "title": "Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria.", "authors": [{"family": "Ekblom", "given": "Robert", "initials": "R"}, {"family": "Smeds", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2014-06-12", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "467", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Genome and transcriptome sequencing applications that rely on variation in sequence depth can be negatively affected if there are systematic biases in coverage. We have investigated patterns of local variation in sequencing coverage by utilising ultra-deep sequencing (>100,000X) of mtDNA obtained during sequencing of two vertebrate genomes, wolverine (Gulo gulo) and collared flycatcher (Ficedula albicollis). With such extreme depth, stochastic variation in coverage should be negligible, which allows us to provide a very detailed, fine-scale picture of sequence dependent coverage variation and sequencing error rates.\n\nSequencing coverage showed up to six-fold variation across the complete mtDNA and this variation was highly repeatable in sequencing of multiple individuals of the same species. Moreover, coverage in orthologous regions was correlated between the two species and was negatively correlated with GC content. We also found a negative correlation between the site-specific sequencing error rate and coverage, with certain sequence motifs \"CCNGCC\" being particularly prone to high rates of error and low coverage.\n\nOur results demonstrate that inherent sequence characteristics govern variation in coverage and suggest that some of this variation, like GC content, should be controlled for in, for example, RNA-Seq and detection of copy number variation.", "doi": "10.1186/1471-2164-15-467", "pmid": "24923674", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-467"}, {"db": "pmc", "key": "PMC4070552"}], "notes": [], "created": "2017-05-04T15:01:33.450Z", "modified": "2020-01-21T13:56:03.342Z"}, {"entity": "publication", "iuid": "062de5b535954abc89347c8dfaaaf44b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/062de5b535954abc89347c8dfaaaf44b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/062de5b535954abc89347c8dfaaaf44b"}}, "title": "Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.", "authors": [{"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Ye", "given": "Rosa", "initials": "R"}, {"family": "Knudsen", "given": "Bjarne", "initials": "B"}, {"family": "Simonsen", "given": "Martin", "initials": "M"}, {"family": "Turner", "given": "Benjamin", "initials": "B"}, {"family": "de Jong", "given": "Pieter", "initials": "P"}, {"family": "Wu", "given": "Cheng-Cang", "initials": "CC"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2014-06-06", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "439", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Sampling genomes with Fosmid vectors and sequencing of pooled Fosmid libraries on the Illumina platform for massive parallel sequencing is a novel and promising approach to optimizing the trade-off between sequencing costs and assembly quality.\n\nIn order to sequence the genome of Norway spruce, which is of great size and complexity, we developed and applied a new technology based on the massive production, sequencing, and assembly of Fosmid pools (FP). The spruce chromosomes were sampled with ~40,000 bp Fosmid inserts to obtain around two-fold genome coverage, in parallel with traditional whole genome shotgun sequencing (WGS) of haploid and diploid genomes. Compared to the WGS results, the contiguity and quality of the FP assemblies were high, and they allowed us to fill WGS gaps resulting from repeats, low coverage, and allelic differences. The FP contig sets were further merged with WGS data using a novel software package GAM-NGS.\n\nBy exploiting FP technology, the first published assembly of a conifer genome was sequenced entirely with massively parallel sequencing. Here we provide a comprehensive report on the different features of the approach and the optimization of the process.We have made public the input data (FASTQ format) for the set of pools used in this study:ftp://congenie.org/congenie/Nystedt_2013/Assembly/ProcessedData/FosmidPools/.(alternatively accessible via http://congenie.org/downloads).The software used for running the assembly process is available at http://research.scilifelab.se/andrej_alexeyenko/downloads/fpools/.", "doi": "10.1186/1471-2164-15-439", "pmid": "24906298", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1471-2164-15-439"}, {"db": "pmc", "key": "PMC4070561"}], "notes": [], "created": "2017-05-04T14:56:29.797Z", "modified": "2021-07-08T13:26:08.069Z"}, {"entity": "publication", "iuid": "c248ff0b310d4cd5a43454d043b9745f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c248ff0b310d4cd5a43454d043b9745f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c248ff0b310d4cd5a43454d043b9745f"}}, "title": "Identification of candidate risk gene variations by whole-genome sequence analysis of four rat strains commonly used in inflammation research.", "authors": [{"family": "B\u00e4ckdahl", "given": "Liselotte", "initials": "L"}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Holmdahl", "given": "Rikard", "initials": "R"}], "type": "journal article", "published": "2014-05-21", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "391", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The DA rat strain is particularly susceptible to the induction of a number of chronic inflammatory diseases, such as models for rheumatoid arthritis and multiple sclerosis. Here we sequenced the genomes of two DA sub-strains and two disease resistant strains, E3 and PVG, previously used together with DA strains in genetically segregating crosses.\n\nThe data uncovers genomic variations, such as single nucleotide variations (SNVs) and copy number variations that underlie phenotypic differences between the strains. Comparisons of regional differences between the two DA sub-strains identified 8 genomic regions that discriminate between the strains that together cover 38 Mbp and harbor 302 genes. We analyzed 10 fine-mapped quantitative trait loci and our data implicate strong candidates for genetic variations that mediate their effects. For example we could identify a single SNV candidate in a regulatory region of the gene Il21r, which has been associated to differential expression in both rats and human MS patients. In the APLEC complex we identified two SNVs in a highly conserved region, which could affect the regulation of all APLEC encoded genes and explain the polygenic differential expression seen in the complex. Furthermore, the non-synonymous SNV modifying aa153 of the Ncf1 protein was confirmed as the sole causative factor.\n\nThis complete map of genetic differences between the most commonly used rat strains in inflammation research constitutes an important reference in understanding how genetic variations contribute to the traits of importance for inflammatory diseases.", "doi": "10.1186/1471-2164-15-391", "pmid": "24885425", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-391"}, {"db": "pmc", "key": "PMC4041999"}, {"db": "SRA", "key": "ERP0004908"}], "notes": [], "created": "2017-05-04T15:02:32.220Z", "modified": "2020-01-21T13:56:05.053Z"}, {"entity": "publication", "iuid": "b56e3defd35045d8893452a4b7863fea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b56e3defd35045d8893452a4b7863fea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b56e3defd35045d8893452a4b7863fea"}}, "title": "Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution.", "authors": [{"family": "Wang", "given": "Biao", "initials": "B"}, {"family": "Ekblom", "given": "Robert", "initials": "R"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Siitari", "given": "Heli", "initials": "H"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2014-03-06", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "180", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The different regions of a genome do not evolve at the same rate. For example, comparative genomic studies have suggested that the sex chromosomes and the regions harbouring the immune defence genes in the Major Histocompatability Complex (MHC) may evolve faster than other genomic regions. The advent of the next generation sequencing technologies has made it possible to study which genomic regions are evolutionary liable to change and which are static, as well as enabling an increasing number of genome studies of non-model species. However, de novo sequencing of the whole genome of an organism remains non-trivial. In this study, we present the draft genome of the black grouse, which was developed using a reference-guided assembly strategy.\n\nWe generated 133 Gbp of sequence data from one black grouse individual by the SOLiD platform and used a combination of de novo assembly and chicken reference genome mapping to assemble the reads into 4572 scaffolds with a total length of 1022 Mb. The draft genome well covers the main chicken chromosomes 1 ~ 28 and Z which have a total length of 1001 Mb. The draft genome is fragmented, but has a good coverage of the homologous chicken genes. Especially, 33.0% of the coding regions of the homologous genes have more than 90% proportion of their sequences covered. In addition, we identified ~1 M SNPs from the genome and identified 106 genomic regions which had a high nucleotide divergence between black grouse and chicken or between black grouse and turkey.\n\nOur results support the hypothesis that the chromosome X (Z) evolves faster than the autosomes and our data are consistent with the MHC regions being more liable to change than the genome average. Our study demonstrates how a moderate sequencing effort can be combined with existing genome references to generate a draft genome for a non-model species.", "doi": "10.1186/1471-2164-15-180", "pmid": "24602261", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-180"}, {"db": "pmc", "key": "PMC4022176"}, {"db": "SRA", "key": "SRA061602"}], "notes": [], "created": "2017-05-04T15:02:32.539Z", "modified": "2020-01-21T13:56:04.751Z"}, {"entity": "publication", "iuid": "4e0d648beb724ac882611eb7ebb736ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e0d648beb724ac882611eb7ebb736ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e0d648beb724ac882611eb7ebb736ef"}}, "title": "Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment.", "authors": [{"family": "Berglund", "given": "Eva C", "initials": "EC"}, {"family": "Lindqvist", "given": "Carl M\u00e5rten", "initials": "CM"}, {"family": "Hayat", "given": "Shahina", "initials": "S"}, {"family": "\u00d6vern\u00e4s", "given": "Elin", "initials": "E"}, {"family": "Henriksson", "given": "Niklas", "initials": "N"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Wahlberg", "given": "Per", "initials": "P"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2013-12-05", "journal": {"volume": "14", "issn": "1471-2164", "issue": null, "pages": "856", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Target enrichment and resequencing is a widely used approach for identification of cancer genes and genetic variants associated with diseases. Although cost effective compared to whole genome sequencing, analysis of many samples constitutes a significant cost, which could be reduced by pooling samples before capture. Another limitation to the number of cancer samples that can be analyzed is often the amount of available tumor DNA. We evaluated the performance of whole genome amplified DNA and the power to detect subclonal somatic single nucleotide variants in non-indexed pools of cancer samples using the HaloPlex technology for target enrichment and next generation sequencing.\n\nWe captured a set of 1528 putative somatic single nucleotide variants and germline SNPs, which were identified by whole genome sequencing, with the HaloPlex technology and sequenced to a depth of 792-1752. We found that the allele fractions of the analyzed variants are well preserved during whole genome amplification and that capture specificity or variant calling is not affected. We detected a large majority of the known single nucleotide variants present uniquely in one sample with allele fractions as low as 0.1 in non-indexed pools of up to ten samples. We also identified and experimentally validated six novel variants in the samples included in the pools.\n\nOur work demonstrates that whole genome amplified DNA can be used for target enrichment equally well as genomic DNA and that accurate variant detection is possible in non-indexed pools of cancer samples. These findings show that analysis of a large number of samples is feasible at low cost, even when only small amounts of DNA is available, and thereby significantly increases the chances of indentifying recurrent mutations in cancer samples.", "doi": "10.1186/1471-2164-14-856", "pmid": "24314227", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-14-856"}, {"db": "pmc", "key": "PMC4046713"}], "notes": [], "created": "2017-05-04T14:57:49.698Z", "modified": "2021-07-07T15:11:02.446Z"}, {"entity": "publication", "iuid": "755fd30de33c4815b37355906e7fd5f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/755fd30de33c4815b37355906e7fd5f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/755fd30de33c4815b37355906e7fd5f8"}}, "title": "Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing.", "authors": [{"family": "Jiao", "given": "Xiang", "initials": "X"}, {"family": "Hooper", "given": "Sean D", "initials": "SD"}, {"family": "Djureinovic", "given": "Tatjana", "initials": "T"}, {"family": "Larsson", "given": "Chatarina", "initials": "C"}, {"family": "W\u00e4rnberg", "given": "Fredrik", "initials": "F"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2013-03-12", "journal": {"volume": "14", "issn": "1471-2164", "issue": null, "pages": "165", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Chromosomal rearrangements in the form of deletions, insertions, inversions and translocations are frequently observed in breast cancer genomes, and a subset of these rearrangements may play a crucial role in tumorigenesis. To identify novel somatic chromosomal rearrangements, we determined the genome structures of 15 hormone-receptor negative breast tumors by long-insert mate pair massively parallel sequencing.\n\nWe identified and validated 40 somatic structural alterations, including the recurring fusion between genes DDX10 and SKA3 and translocations involving the EPHA5 gene. Other rearrangements were found to affect genes in pathways involved in epigenetic regulation, mitosis and signal transduction, underscoring their potential role in breast tumorigenesis. RNA interference-mediated suppression of five candidate genes (DDX10, SKA3, EPHA5, CLTC and TNIK) led to inhibition of breast cancer cell growth. Moreover, downregulation of DDX10 in breast cancer cells lead to an increased frequency of apoptotic nuclear morphology.\n\nUsing whole genome mate pair sequencing and RNA interference assays, we have discovered a number of novel gene rearrangements in breast cancer genomes and identified DDX10, SKA3, EPHA5, CLTC and TNIK as potential cancer genes with impact on the growth and proliferation of breast cancer cells.", "doi": "10.1186/1471-2164-14-165", "pmid": "23496902", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-14-165"}, {"db": "pmc", "key": "PMC3600027"}], "notes": [], "created": "2017-05-04T15:02:19.774Z", "modified": "2020-01-21T13:56:03.052Z"}, {"entity": "publication", "iuid": "ad2c391497fa466d8c3db143b4549e43", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad2c391497fa466d8c3db143b4549e43.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad2c391497fa466d8c3db143b4549e43"}}, "title": "Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms.", "authors": [{"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Uebbing", "given": "Severin", "initials": "S"}, {"family": "Gyllenstrand", "given": "Niclas", "initials": "N"}, {"family": "Lagercrantz", "given": "Ulf", "initials": "U"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}], "type": "comparative study", "published": "2012-11-02", "journal": {"volume": "13", "issn": "1471-2164", "issue": null, "pages": "589", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "A detailed knowledge about spatial and temporal gene expression is important for understanding both the function of genes and their evolution. For the vast majority of species, transcriptomes are still largely uncharacterized and even in those where substantial information is available it is often in the form of partially sequenced transcriptomes. With the development of next generation sequencing, a single experiment can now simultaneously identify the transcribed part of a species genome and estimate levels of gene expression.\n\nmRNA from actively growing needles of Norway spruce (Picea abies) was sequenced using next generation sequencing technology. In total, close to 70 million fragments with a length of 76 bp were sequenced resulting in 5 Gbp of raw data. A de novo assembly of these reads, together with publicly available expressed sequence tag (EST) data from Norway spruce, was used to create a reference transcriptome. Of the 38,419 PUTs (putative unique transcripts) longer than 150 bp in this reference assembly, 83.5% show similarity to ESTs from other spruce species and of the remaining PUTs, 3,704 show similarity to protein sequences from other plant species, leaving 4,167 PUTs with limited similarity to currently available plant proteins. By predicting coding frames and comparing not only the Norway spruce PUTs, but also PUTs from the close relatives Picea glauca and Picea sitchensis to both Pinus taeda and Taxus mairei, we obtained estimates of synonymous and non-synonymous divergence among conifer species. In addition, we detected close to 15,000 SNPs of high quality and estimated gene expression differences between samples collected under dark and light conditions.\n\nOur study yielded a large number of single nucleotide polymorphisms as well as estimates of gene expression on transcriptome scale. In agreement with a recent study we find that the synonymous substitution rate per year (0.6\u2009\u00d7\u200910-09 and 1.1\u2009\u00d7\u200910-09) is an order of magnitude smaller than values reported for angiosperm herbs. However, if one takes generation time into account, most of this difference disappears. The estimates of the dN/dS ratio (non-synonymous over synonymous divergence) reported here are in general much lower than 1 and only a few genes showed a ratio larger than 1.", "doi": "10.1186/1471-2164-13-589", "pmid": "23122049", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-13-589"}, {"db": "pmc", "key": "PMC3543189"}], "notes": [], "created": "2017-05-04T15:00:55.331Z", "modified": "2020-01-21T13:56:04.567Z"}, {"entity": "publication", "iuid": "4ac7c51a01b2483582546addacfcc239", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ac7c51a01b2483582546addacfcc239.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ac7c51a01b2483582546addacfcc239"}}, "title": "Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.", "authors": [{"family": "Solnestam", "given": "Beata Werne", "initials": "BW"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Akan", "given": "Pelin", "initials": "P"}], "type": "comparative study", "published": "2012-10-30", "journal": {"volume": "13", "issn": "1471-2164", "issue": null, "pages": "574", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The majority of published gene-expression studies have used RNA isolated from whole cells, overlooking the potential impact of including nuclear transcriptome in the analyses. In this study, mRNA fractions from the cytoplasm and from whole cells (total RNA) were prepared from three human cell lines and sequenced using massive parallel sequencing.\n\nFor all three cell lines, of about 15000 detected genes approximately 400 to 1400 genes were detected in different amounts in the cytoplasmic and total RNA fractions. Transcripts detected at higher levels in the total RNA fraction had longer coding sequences and higher number of miRNA target sites. Transcripts detected at higher levels in the cytoplasmic fraction were shorter or contained shorter untranslated regions. Nuclear retention of transcripts and mRNA degradation via miRNA pathway might contribute to this differential detection of genes. The consequence of the differential detection was further investigated by comparison to proteomics data. Interestingly, the expression profiles of cytoplasmic and total RNA correlated equally well with protein abundance levels indicating regulation at a higher level.\n\nWe conclude that expression levels derived from the total RNA fraction be regarded as an appropriate estimate of the amount of mRNAs present in a given cell population, independent of the coding sequence length or UTRs.", "doi": "10.1186/1471-2164-13-574", "pmid": "23110385", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "1471-2164-13-574"}, {"db": "pmc", "key": "PMC3495644"}], "notes": [], "created": "2017-05-04T14:55:09.570Z", "modified": "2021-07-08T13:26:08.160Z"}, {"entity": "publication", "iuid": "0ccfaf0b5fba4e478a018931b547b6fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ccfaf0b5fba4e478a018931b547b6fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ccfaf0b5fba4e478a018931b547b6fb"}}, "title": "Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens.", "authors": [{"family": "N\u00e4tt", "given": "Daniel", "initials": "D"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Wright", "given": "Dominic", "initials": "D"}, {"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Belt\u00e9ky", "given": "Johan", "initials": "J"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Jensen", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2012-02-04", "journal": {"volume": "13", "issn": "1471-2164", "issue": null, "pages": "59", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Variations in gene expression, mediated by epigenetic mechanisms, may cause broad phenotypic effects in animals. However, it has been debated to what extent expression variation and epigenetic modifications, such as patterns of DNA methylation, are transferred across generations, and therefore it is uncertain what role epigenetic variation may play in adaptation.\n\nIn Red Junglefowl, ancestor of domestic chickens, gene expression and methylation profiles in thalamus/hypothalamus differed substantially from that of a domesticated egg laying breed. Expression as well as methylation differences were largely maintained in the offspring, demonstrating reliable inheritance of epigenetic variation. Some of the inherited methylation differences were tissue-specific, and the differential methylation at specific loci were little changed after eight generations of intercrossing between Red Junglefowl and domesticated laying hens. There was an over-representation of differentially expressed and methylated genes in selective sweep regions associated with chicken domestication.\n\nOur results show that epigenetic variation is inherited in chickens, and we suggest that selection of favourable epigenomes, either by selection of genotypes affecting epigenetic states, or by selection of methylation states which are inherited independently of sequence differences, may have been an important aspect of chicken domestication.", "doi": "10.1186/1471-2164-13-59", "pmid": "22305654", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "1471-2164-13-59"}, {"db": "pmc", "key": "PMC3297523"}], "notes": [], "created": "2017-05-04T15:02:55.478Z", "modified": "2017-05-30T14:49:47.817Z"}, {"entity": "publication", "iuid": "b0c9cd20e86541bcbd1cc2c3211c019d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0c9cd20e86541bcbd1cc2c3211c019d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0c9cd20e86541bcbd1cc2c3211c019d"}}, "title": "Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development.", "authors": [{"family": "Bizuayehu", "given": "Teshome T", "initials": "TT"}, {"family": "Lanes", "given": "Carlos F C", "initials": "CFC"}, {"family": "Furmanek", "given": "Tomasz", "initials": "T"}, {"family": "Karlsen", "given": "B\u00e5rd O", "initials": "BO"}, {"family": "Fernandes", "given": "Jorge M O", "initials": "JMO"}, {"family": "Johansen", "given": "Steinar D", "initials": "SD"}, {"family": "Babiak", "given": "Igor", "initials": "I"}], "type": "journal article", "published": "2012-01-10", "journal": {"volume": "13", "issn": "1471-2164", "issue": null, "pages": "11", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "MicroRNAs (miRNAs) play a major role in animal ontogenesis. Size variants of miRNAs, isomiRs, are observed along with the main miRNA types, but their origin and possible biological role are uncovered yet. Developmental profiles of miRNAs have been reported in few fish species only and, to our knowledge, differential expressions of isomiRs have not yet been shown during fish development. Atlantic halibut, Hippoglossus hippoglossus L., undergoes dramatic metamorphosis during early development from symmetrical pelagic larval stage to unsymmetrical flatfish. No data exist on role of miRNAs in halibut metamorphosis.\r\n\r\nmiRNA profiling using SOLiD deep sequencing technology revealed a total of 199 conserved, one novel antisense, and one miRNA* mature form. Digital expression profiles of selected miRNAs were validated using reverse transcription quantitative PCR. We found developmental transition-specific miRNA expression. Expression of some miRNA* exceeded the guide strand miRNA. We revealed that nucleotide truncations and/or additions at the 3' end of mature miRNAs resulted in size variants showing differential expression patterns during the development in a number of miRNA families. We confirmed the presence of isomiRs by cloning and Sanger sequencing. Also, we found inverse relationship between expression levels of sense/antisense miRNAs during halibut development.\r\n\r\nDevelopmental transitions during early development of Atlantic halibut are associated with expression of certain miRNA types. IsomiRs are abundant and often show differential expression during the development.", "doi": "10.1186/1471-2164-13-11", "pmid": "22233483", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-13-11"}, {"db": "pmc", "key": "PMC3398304"}], "notes": [], "created": "2017-05-04T14:57:30.723Z", "modified": "2020-01-21T13:56:10.369Z"}, {"entity": "publication", "iuid": "4981f4e297634c109a11f7a33ef378df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4981f4e297634c109a11f7a33ef378df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4981f4e297634c109a11f7a33ef378df"}}, "title": "Muscle wasting and the temporal gene expression pattern in a novel rat intensive care unit model.", "authors": [{"family": "Llano-Diez", "given": "Monica", "initials": "M"}, {"family": "Gustafson", "given": "Ann-Marie", "initials": "AM"}, {"family": "Olsson", "given": "Carl", "initials": "C"}, {"family": "Goransson", "given": "Hanna", "initials": "H"}, {"family": "Larsson", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2011-12-13", "journal": {"volume": "12", "issn": "1471-2164", "issue": null, "pages": "602", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Acute quadriplegic myopathy (AQM) or critical illness myopathy (CIM) is frequently observed in intensive care unit (ICU) patients. To elucidate duration-dependent effects of the ICU intervention on molecular and functional networks that control the muscle wasting and weakness associated with AQM, a gene expression profile was analyzed at time points varying from 6 hours to 14 days in a unique experimental rat model mimicking ICU conditions, i.e., post-synaptically paralyzed, mechanically ventilated and extensively monitored animals.\n\nDuring the observation period, 1583 genes were significantly up- or down-regulated by factors of two or greater. A significant temporal gene expression pattern was constructed at short (6 h-4 days), intermediate (5-8 days) and long (9-14 days) durations. A striking early and maintained up-regulation (6 h-14d) of muscle atrogenes (muscle ring-finger 1/tripartite motif-containing 63 and F-box protein 32/atrogin-1) was observed, followed by an up-regulation of the proteolytic systems at intermediate and long durations (5-14d). Oxidative stress response genes and genes that take part in amino acid catabolism, cell cycle arrest, apoptosis, muscle development, and protein synthesis together with myogenic factors were significantly up-regulated from 5 to 14 days. At 9-14 d, genes involved in immune response and the caspase cascade were up-regulated. At 5-14d, genes related to contractile (myosin heavy chain and myosin binding protein C), regulatory (troponin, tropomyosin), developmental, caveolin-3, extracellular matrix, glycolysis/gluconeogenesis, cytoskeleton/sarcomere regulation and mitochondrial proteins were down-regulated. An activation of genes related to muscle growth and new muscle fiber formation (increase of myogenic factors and JunB and down-regulation of myostatin) and up-regulation of genes that code protein synthesis and translation factors were found from 5 to 14 days.\n\nNovel temporal patterns of gene expression have been uncovered, suggesting a unique, coordinated and highly complex mechanism underlying the muscle wasting associated with AQM in ICU patients and providing new target genes and avenues for intervention studies.", "doi": "10.1186/1471-2164-12-602", "pmid": "22165895", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "1471-2164-12-602"}, {"db": "pmc", "key": "PMC3266306"}], "notes": [], "created": "2017-05-04T15:02:51.187Z", "modified": "2017-05-30T14:49:24.252Z"}, {"entity": "publication", "iuid": "d80b83743fac433cbc81d4d3f3724da1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d80b83743fac433cbc81d4d3f3724da1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d80b83743fac433cbc81d4d3f3724da1"}}, "title": "Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer.", "authors": [{"family": "H\u00e5fstr\u00f6m", "given": "Therese", "initials": "T"}, {"family": "Jansson", "given": "D\u00e9sir\u00e9e S", "initials": "DS"}, {"family": "Segerman", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2011-08-04", "journal": {"volume": "12", "issn": "1471-2164", "issue": null, "pages": "395", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Brachyspira spp. colonize the intestines of some mammalian and avian species and show different degrees of enteropathogenicity. Brachyspira intermedia can cause production losses in chickens and strain PWS/AT now becomes the fourth genome to be completed in the genus Brachyspira.\n\n15 classes of unique and shared genes were analyzed in B. intermedia, B. murdochii, B. hyodysenteriae and B. pilosicoli. The largest number of unique genes was found in B. intermedia and B. murdochii. This indicates the presence of larger pan-genomes. In general, hypothetical protein annotations are overrepresented among the unique genes. A 3.2 kb plasmid was found in B. intermedia strain PWS/AT. The plasmid was also present in the B. murdochii strain but not in nine other Brachyspira isolates. Within the Brachyspira genomes, genes had been translocated and also frequently switched between leading and lagging strands, a process that can be followed by different AT-skews in the third positions of synonymous codons. We also found evidence that bacteriophages were being remodeled and genes incorporated into them.\n\nThe accessory gene pool shapes species-specific traits. It is also influenced by reductive genome evolution and horizontal gene transfer. Gene-transfer events can cross both species and genus boundaries and bacteriophages appear to play an important role in this process. A mechanism for horizontal gene transfer appears to be gene translocations leading to remodeling of bacteriophages in combination with broad tropism.", "doi": "10.1186/1471-2164-12-395", "pmid": "21816042", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-12-395"}, {"db": "pmc", "key": "PMC3163572"}], "notes": [], "created": "2017-05-04T14:57:16.486Z", "modified": "2020-01-21T13:56:05.540Z"}, {"entity": "publication", "iuid": "6020ba73a1074d6781fddb32a0955729", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6020ba73a1074d6781fddb32a0955729.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6020ba73a1074d6781fddb32a0955729"}}, "title": "Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements.", "authors": [{"family": "Skarin", "given": "Hanna", "initials": "H"}, {"family": "H\u00e5fstr\u00f6m", "given": "Therese", "initials": "T"}, {"family": "Westerberg", "given": "Josefina", "initials": "J"}, {"family": "Segerman", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2011-04-12", "journal": {"volume": "12", "issn": "1471-2164", "issue": null, "pages": "185", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Clostridium botulinum strains can be divided into four physiological groups that are sufficiently diverged to be considered as separate species. Here we present the first complete genome of a C. botulinum strain from physiological group III, causing animal botulism. We also compare the sequence to three new draft genomes from the same physiological group.\n\nThe 2.77 Mb chromosome was highly conserved between the isolates and also closely related to that of C. novyi. However, the sequence was very different from the human C. botulinum group genomes. Replication-directed translocations were rare and conservation of synteny was high. The largest difference between C. botulinum group III isolates occurred within their surprisingly large plasmidomes and in the pattern of mobile elements insertions. Five plasmids, constituting 13.5% of the total genetic material, were present in the completed genome. Interestingly, the set of plasmids differed compared to other isolates. The largest plasmid, the botulinum-neurotoxin carrying prophage, was conserved at a level similar to that of the chromosome while the medium-sized plasmids seemed to be undergoing faster genetic drift. These plasmids also contained more mobile elements than other replicons. Several toxins and resistance genes were identified, many of which were located on the plasmids.\n\nThe completion of the genome of C. botulinum group III has revealed it to be a genome with dual identity. It belongs to the pathogenic species C. botulinum, but as a genotypic species it should also include C. novyi and C. haemolyticum. The genotypic species share a conserved chromosomal core that can be transformed into various pathogenic variants by modulation of the highly plastic plasmidome.", "doi": "10.1186/1471-2164-12-185", "pmid": "21486474", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-12-185"}, {"db": "pmc", "key": "PMC3098183"}], "notes": [], "created": "2017-05-04T14:57:16.786Z", "modified": "2020-01-21T13:56:02.619Z"}, {"entity": "publication", "iuid": "bbc4aa27752846dea221f0b103fdcdbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bbc4aa27752846dea221f0b103fdcdbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bbc4aa27752846dea221f0b103fdcdbf"}}, "title": "Analysis of transcript and protein overlap in a human osteosarcoma cell line.", "authors": [{"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2010-12-02", "journal": {"volume": "11", "issn": "1471-2164", "issue": null, "pages": "684", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome scale have been improved, including the availability of the new generation sequencing instruments and high-throughput antibody-based methods to analyze the presence and localization of proteins. In this study, we used massive transcriptome sequencing (RNA-seq) to investigate the transcriptome of a human osteosarcoma cell line and compared the expression levels with in situ protein data obtained in-situ from antibody-based immunohistochemistry (IHC) and immunofluorescence microscopy (IF).\r\n\r\nA large-scale analysis based on 2749 genes was performed, corresponding to approximately 13% of the protein coding genes in the human genome. We found the presence of both RNA and proteins to a large fraction of the analyzed genes with 60% of the analyzed human genes detected by all three methods. Only 34 genes (1.2%) were not detected on the transcriptional or protein level with any method. Our data suggest that the majority of the human genes are expressed at detectable transcript or protein levels in this cell line. Since the reliability of antibodies depends on possible cross-reactivity, we compared the RNA and protein data using antibodies with different reliability scores based on various criteria, including Western blot analysis. Gene products detected in all three platforms generally have good antibody validation scores, while those detected only by antibodies, but not by RNA sequencing, generally consist of more low-scoring antibodies.\r\n\r\nThis suggests that some antibodies are staining the cells in an unspecific manner, and that assessment of transcript presence by RNA-seq can provide guidance for validation of the corresponding antibodies.", "doi": "10.1186/1471-2164-11-684", "pmid": "21126332", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-684"}, {"db": "pmc", "key": "PMC3014981"}, {"db": "BioProject", "description": "RNA-seq of human osteosarcoma cell line U2-OS", "key": "PRJNA79747"}, {"db": "SRA", "description": "RNA-seq of human osteosarcoma cell line U2-OS", "key": "SRP003405"}], "notes": [], "created": "2017-05-04T14:55:06.554Z", "modified": "2021-07-08T13:44:33.569Z"}, {"entity": "publication", "iuid": "95602e2c69144b29be43c990a4c55b8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95602e2c69144b29be43c990a4c55b8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95602e2c69144b29be43c990a4c55b8d"}}, "title": "SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools.", "authors": [{"family": "Marklund", "given": "Stefan", "initials": "S"}, {"family": "Carlborg", "given": "Orjan", "initials": "O"}], "type": "journal article", "published": "2010-11-25", "journal": {"volume": "11", "issn": "1471-2164", "issue": null, "pages": "665", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Next-generation sequencing technologies are widely used for detection of millions of Single Nucleotide Polymorphisms (SNPs) and also provide a means of assessing their variation. This information is useful for composing subsets of highly informative SNPs for region-specific or genome-wide analysis and to identify mutations regulating phenotypic differences within or between populations. In this study, we investigated the sensitivity of SNP detection and introduced the flanking SNPs value (FSV) as a novel measure for predicting SNP-variability using ~5X genome resequencing with ABI SOLID and DNA pools from two chicken lines divergently selected for juvenile bodyweight.\n\nGenotyping with a 60 K SNP chip revealed polymorphisms within or between two divergently selected chicken lines for 31 363 SNPs, 48% of which were also detected using resequencing of DNA pools. SNP detection using resequencing was more powerful for positions with larger differences in allele frequency between the lines. About 50% of the SNPs with non-reference allele frequencies in the range 0.5-0.6 and 67% of those with frequencies > 0.9 could be detected. On average, ~3.7 SNPs/kb were detected by resequencing, with about 5% lower density on microchromosomes than on macrochromosomes. There was a positive correlation between the observed between-line SNP variation from the 60 K chip analysis and our proposed FSV score computed from the genome resequencing data. The strongest correlations on macrochromosomes and microchromosomes were observed when the FSV was calculated with total flanking regions of 62 kb (correlation 0.55) and 38 kb (correlation 0.45), respectively.\n\nGenome resequencing with limited coverage (~5X) using pooled DNA samples and three non-reference reads as a threshold for SNP detection, identified 50 - 67% of the 60 K SNPs with a non-reference allele frequency larger than 0.5. The SNP density was around 5% lower on the microchromosomes, most likely because of their higher gene content. Our proposed method to estimate the SNP variation (FSV) uses additional sequence information to better predict SNP informativity. The FSV scores showed higher correlations for SNPs with a larger difference in allele frequency between the populations. The correlation was strongest on macrochromosomes, probably due to a lower recombination rate.", "doi": "10.1186/1471-2164-11-665", "pmid": "21108801", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-665"}, {"db": "pmc", "key": "PMC3091782"}], "notes": [], "created": "2017-05-04T15:01:50.437Z", "modified": "2020-01-21T13:56:03.840Z"}, {"entity": "publication", "iuid": "58f43beadb93437ea9cafbb654feb5e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58f43beadb93437ea9cafbb654feb5e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58f43beadb93437ea9cafbb654feb5e5"}}, "title": "Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles.", "authors": [{"family": "Xue-Franz\u00e9n", "given": "Yongtao", "initials": "Y"}, {"family": "Johnsson", "given": "Anna", "initials": "A"}, {"family": "Brodin", "given": "David", "initials": "D"}, {"family": "Henriksson", "given": "Johan", "initials": "J"}, {"family": "B\u00fcrglin", "given": "Thomas R", "initials": "TR"}, {"family": "Wright", "given": "Anthony P H", "initials": "AP"}], "type": "journal article", "published": "2010-03-25", "journal": {"volume": "11", "issn": "1471-2164", "issue": null, "pages": "200", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Gcn5 is a transcriptional coactivator with histone acetyltransferase activity that is conserved with regard to structure as well as its histone substrates throughout the eukaryotes. Gene regulatory networks within cells are thought to be evolutionarily diverged. The use of evolutionarily divergent yeast species, such as S. cerevisiae and S. pombe, which can be studied under similar environmental conditions, provides an opportunity to examine the interface between conserved regulatory components and their cellular applications in different organisms.\n\nWe show that Gcn5 is important for a common set of stress responses in evolutionarily diverged yeast species and that the activity of the conserved histone acetyltransferase domain is required. We define a group of KCl stress response genes in S. cerevisiae that are specifically dependent on Gcn5. Gcn5 is localised to many Gcn5-dependent genes including Gcn5 repressed targets such as FLO8. Gcn5 regulates divergent sets of KCl responsive genes in S. cerevisiae and S. pombe. Genome-wide localization studies showed a tendency for redistribution of Gcn5 during KCl stress adaptation in S. cerevisiae from short genes to the transcribed regions of long genes. An analogous redistribution was not observed in S. pombe.\n\nGcn5 is required for the regulation of divergent sets of KCl stress-response genes in S. cerevisiae and S. pombe even though it is required a common group of stress responses, including the response to KCl. Genes that are physically associated with Gcn5 require its activity for their repression or activation during stress adaptation, providing support for a role of Gcn5 as a corepressor as well as a coactivator. The tendency of Gcn5 to re-localise to the transcribed regions of long genes during KCl stress adaptation suggests that Gcn5 plays a specific role in the expression of long genes under adaptive conditions, perhaps by regulating transcriptional elongation as has been seen for Gcn5 in S. pombe. Interestingly an analogous redistribution of Gcn5 is not seen in S. pombe. The study thus provides important new insights in relation to why coregulators like Gcn5 are required for the correct expression of some genes but not others.", "doi": "10.1186/1471-2164-11-200", "pmid": "20338033", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-200"}, {"db": "pmc", "key": "PMC2861062"}], "notes": [], "created": "2017-05-04T15:03:03.327Z", "modified": "2017-05-30T14:50:16.038Z"}, {"entity": "publication", "iuid": "69b4e0a9132849dfa4d5a7cc15ddc6ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69b4e0a9132849dfa4d5a7cc15ddc6ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69b4e0a9132849dfa4d5a7cc15ddc6ac"}}, "title": "Gene-specific FACS sorting method for target selection in high-throughput amplicon sequencing.", "authors": [{"family": "Sandberg", "given": "Julia", "initials": "J"}, {"family": "Neiman", "given": "Marten", "initials": "M"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2010-02-26", "journal": {"volume": "11", "issn": "1471-2164", "issue": null, "pages": "140", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "In addition to shotgun sequencing, next generation sequencing has been shown to be suitable for deep sequencing of many specific PCR-amplified target genes in parallel. However, unspecific product formation is a common problem in amplicon sequencing since these fragments are difficult to fully remove by gel purification, and their presence inevitably reduces the number of mappable sequence reads that can be obtained in each sequencing run.\n\nWe have used a novel flow cytometric sorting approach to specifically enrich Roche/454 DNA Capture beads carrying target DNA sequences on their surface, and reject beads carrying unspecific sequences. This procedure gives a nearly three-fold increase in the fraction of informative sequences obtained. Presented results also show that there are no significant differences in the distribution or presence of different genotypes between a FACS-enriched sample and a standard-enriched control sample.\n\nTarget-specific FACS enrichment prior to Roche/454 sequencing provides a quick, inexpensive way of increasing the amount of high quality data obtained in a single sequencing run, without introducing any sequence bias.", "doi": "10.1186/1471-2164-11-140", "pmid": "20184782", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-140"}, {"db": "pmc", "key": "PMC2842249"}], "notes": [], "created": "2017-05-04T14:57:10.155Z", "modified": "2021-07-08T13:26:08.201Z"}, {"entity": "publication", "iuid": "10b55a25abea4522937f46c043a9c3f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10b55a25abea4522937f46c043a9c3f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10b55a25abea4522937f46c043a9c3f0"}}, "title": "High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus.", "authors": [{"family": "Berlin", "given": "Sofia", "initials": "S"}, {"family": "Lagercrantz", "given": "Ulf", "initials": "U"}, {"family": "von Arnold", "given": "Sara", "initials": "S"}, {"family": "Ost", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "R\u00f6nnberg-W\u00e4stljung", "given": "Ann Christin", "initials": "AC"}], "type": "journal article", "published": "2010-02-23", "journal": {"volume": "11", "issn": "1471-2164", "issue": null, "pages": "129", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Salix (willow) and Populus (poplar) are members of the Salicaceae family and they share many ecological as well as genetic and genomic characteristics. The interest of using willow for biomass production is growing, which has resulted in increased pressure on breeding of high yielding and resistant clones adapted to different environments. The main purpose of this work was to develop dense genetic linkage maps for mapping of traits related to yield and resistance in willow. We used the Populus trichocarpa genome to extract evenly spaced markers and mapped the orthologous loci in the willow genome. The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 mya.\n\nWe constructed two linkage maps covering the 19 linkage groups in willow. The most detailed consensus map, S1, contains 495 markers with a total genetic distance of 2477 cM and an average distance of 5.0 cM between the markers. The S3 consensus map contains 221 markers and has a total genetic distance of 1793 cM and an average distance of 8.1 cM between the markers. We found high degree of synteny and gene order conservation between willow and poplar. There is however evidence for two major interchromosomal rearrangements involving poplar LG I and XVI and willow LG Ib, suggesting a fission or a fusion in one of the lineages, as well as five intrachromosomal inversions. The number of silent substitutions were three times lower (median: 0.12) between orthologs than between paralogs (median: 0.37 - 0.41).\n\nThe relatively slow rates of genomic change between willow and poplar mean that the genomic resources in poplar will be most useful in genomic research in willow, such as identifying genes underlying QTLs of important traits. Our data suggest that the whole-genome duplication occurred long before the divergence of the two genera, events which have until now been regarded as contemporary. Estimated silent substitution rates were 1.28 x 10-9 and 1.68 x 10-9 per site and year, which are close to rates found in other perennials but much lower than rates in annuals.", "doi": "10.1186/1471-2164-11-129", "pmid": "20178595", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-129"}, {"db": "pmc", "key": "PMC2834636"}], "notes": [], "created": "2017-05-04T15:00:28.266Z", "modified": "2020-01-21T13:56:00.745Z"}], "created": "2017-05-09T09:12:44.789Z", "modified": "2020-11-27T13:14:03.639Z"}