{"entity": "researcher", "timestamp": "2026-05-21T04:37:46.542Z", "family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "affiliations": ["Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946"}}, "publications": [{"entity": "publication", "iuid": "99d94470f07541c2b23fad1eefd0f74b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/99d94470f07541c2b23fad1eefd0f74b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/99d94470f07541c2b23fad1eefd0f74b"}}, "title": "Genomic studies in Linum shed light on the evolution of the distyly supergene and the molecular basis of convergent floral evolution.", "authors": [{"family": "Zervakis", "given": "Panagiotis-Ioannis", "initials": "PI", "orcid": "0000-0002-5197-3502", "researcher": {"href": "https://publications.scilifelab.se/researcher/295e9debf36c4641aa6c346e915b64ef.json"}}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Losvik", "given": "Aleksandra", "initials": "A", "orcid": "0000-0001-7669-9266", "researcher": {"href": "https://publications.scilifelab.se/researcher/e85c35a0abd54a7087c94942290179be.json"}}, {"family": "Fracassetti", "given": "Marco", "initials": "M", "orcid": "0000-0002-2962-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/695213cdd1a645cbbf10d44122237b18.json"}}, {"family": "Sol\u00e9r", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E", "orcid": "0000-0003-3752-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9257ccdfc6484cd9a95f9b2f17f9a8d1.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Churcher", "given": "Allison", "initials": "A", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "247", "issue": "6", "pages": "2964-2981"}, "abstract": "Distyly, an example of convergent evolution, is governed by a supergene, the S-locus, in several species. Recent studies highlight similar genomic architectures of independently evolved S-loci, but its mode of origin and whether similar regulatory pathways underlie the convergent evolution of distyly remains unclear. We examined the evolution of supergenes and mechanisms underlying distyly in Linum species that diverged c. 33 million years ago (Ma). Using haplotype-resolved genomes and population genomics, we identified and characterized the S-loci of Linum perenne (distylous) and Linum grandiflorum (style length dimorphic), and compared them to that of Linum tenue (distylous). We then tested for a conserved hormonal mechanism regulating style length polymorphism in Linum. The S-locus supergene was consistently hemizygous in short-styled individuals across all three species, although it showed variation in size, gene content, repeat elements and extent of recombination suppression. Two S-linked candidate genes, TSS1 (style length) and WDR-44 (anther height/pollen self-incompatibility), were conserved. Consistent with a brassinosteroid-dependent role of TSS1, epibrassinolide treatment revealed a conserved, morph-specific effect on style length. S-locus structural polymorphism, candidate distyly genes and mechanisms regulating style length remain conserved > 30 Ma in Linum. In combination with findings from other systems, our results suggest that the brassinosteroid pathway frequently contributes to style length polymorphism.", "doi": "10.1111/nph.70392", "pmid": "40682296", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12371154"}], "notes": [], "created": "2025-08-19T13:25:54.698Z", "modified": "2025-11-19T10:24:41.159Z"}, {"entity": "publication", "iuid": "09b2174874b74c20886dd68920d6961e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/09b2174874b74c20886dd68920d6961e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/09b2174874b74c20886dd68920d6961e"}}, "title": "Single-cell transcriptomics reveal transcriptional programs underlying male and female cell fate during Plasmodium falciparum gametocytogenesis.", "authors": [{"family": "Mohammed", "given": "Mubasher", "initials": "M"}, {"family": "Dziedziech", "given": "Alexis", "initials": "A"}, {"family": "Macedo", "given": "Diego", "initials": "D"}, {"family": "Huppertz", "given": "Frederik", "initials": "F"}, {"family": "Veith", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-1810-8808", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e316fdf93964e89a0606e68da08c336.json"}}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Christ", "given": "Elena", "initials": "E"}, {"family": "Scheytt", "given": "Richard", "initials": "R", "orcid": "0009-0004-1405-6360", "researcher": {"href": "https://publications.scilifelab.se/researcher/3866987412724150b6af427c16dd17cf.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/44339821900646b3881d4b4dfd09e8d5.json"}}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}], "type": "journal article", "published": "2024-08-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "7177"}, "abstract": "The Plasmodium falciparum life cycle includes obligate transition between a human and mosquito host. Gametocytes are responsible for transmission from the human to the mosquito vector where gamete fusion followed by meiosis occurs. To elucidate how male and female gametocytes differentiate in the absence of sex chromosomes, we perform FACS-based cell enrichment of a P. falciparum gametocyte reporter line followed by single-cell RNA-seq. In our analyses we define the transcriptional programs and predict candidate driver genes underlying male and female development, including genes from the ApiAP2 family of transcription factors. A motif-driven, gene regulatory network analysis indicates that AP2-G5 specifically modulates male development. Additionally, genes linked to the inner membrane complex, involved in morphological changes, are uniquely expressed in the female lineage. The transcriptional programs of male and female development detailed herein allow for further exploration of the evolution of sex in eukaryotes and provide targets for future development of transmission blocking therapies.", "doi": "10.1038/s41467-024-51201-3", "pmid": "39187486", "labels": {"Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "NGI Short read": null}, "xrefs": [{"db": "pmc", "key": "PMC11347709"}, {"db": "pii", "key": "10.1038/s41467-024-51201-3"}], "notes": [], "created": "2024-11-25T10:17:42.276Z", "modified": "2025-07-18T10:45:32.069Z"}, {"entity": "publication", "iuid": "c0da1688f3a74822ac6329a2a61bbfdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0da1688f3a74822ac6329a2a61bbfdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0da1688f3a74822ac6329a2a61bbfdb"}}, "title": "Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum.", "authors": [{"family": "Guti\u00e9rrez-Valencia", "given": "Juanita", "initials": "J"}, {"family": "Zervakis", "given": "Panagiotis-Ioannis", "initials": "P"}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Fracassetti", "given": "Marco", "initials": "M"}, {"family": "Losvik", "given": "Aleksandra", "initials": "A"}, {"family": "Mehrabi", "given": "Sara", "initials": "S"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Hughes", "given": "P William", "initials": "PW"}, {"family": "D\u00e9samor\u00e9", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Abdelaziz", "given": "Mohamed", "initials": "M"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Arroyo", "given": "Juan", "initials": "J"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2024-05-03", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "41", "issue": "5", "pages": null}, "abstract": "Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility. Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly in Linum trigynum, which is closely related to distylous Linum tenue. Building on a high-quality genome assembly, we show that L. trigynum harbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles in L. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylous Primula and Fagopyrum, L. trigynum harbors no fixed loss-of-function mutations in coding sequences of S-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating the S-linked LtWDR-44 candidate gene for male self-incompatibility and/or anther height could underlie homostyly and self-compatibility in L. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate that L. trigynum is highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative to L. tenue. Our analyses shed light on the loss of distyly in L. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.", "doi": "10.1093/molbev/msae087", "pmid": "38709782", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11114476"}, {"db": "pii", "key": "7665594"}], "notes": [], "created": "2024-05-17T09:14:33.893Z", "modified": "2024-11-15T11:28:42.391Z"}, {"entity": "publication", "iuid": "7bd79b56a03d4b9681320b2232ceba02", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7bd79b56a03d4b9681320b2232ceba02.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7bd79b56a03d4b9681320b2232ceba02"}}, "title": "Mutation accumulation opposes polymorphism: supergenes and the curious case of balanced lethals.", "authors": [{"family": "Berdan", "given": "Emma L", "initials": "EL", "orcid": "0000-0002-6435-4604", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f65066e9a744b95b25ec0597b4b8e23.json"}}, {"family": "Blanckaert", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-2735-7491", "researcher": {"href": "https://publications.scilifelab.se/researcher/58b46b670d114ae1b79ad4e2fbec04bb.json"}}, {"family": "Butlin", "given": "Roger K", "initials": "RK", "orcid": "0000-0003-4736-0954", "researcher": {"href": "https://publications.scilifelab.se/researcher/e510a963ebeb4e8c8af68b10a001a326.json"}}, {"family": "Flatt", "given": "Thomas", "initials": "T", "orcid": "0000-0002-5990-1503", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce1066c17f8748c184b896d61101cca2.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Wielstra", "given": "Ben", "initials": "B", "orcid": "0000-0002-7112-5965", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3f0ef3bd8fe4ee4b6927293d4f2e19d.json"}}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "Philos. Trans. R. Soc. Lond., B, Biol. Sci.", "issn": "1471-2970", "volume": "377", "issue": "1856", "pages": "20210199", "issn-l": "0962-8436"}, "abstract": "Supergenes offer spectacular examples of long-term balancing selection in nature, but their origin and maintenance remain a mystery. Reduced recombination between arrangements, a critical aspect of many supergenes, protects adaptive multi-trait phenotypes but can lead to mutation accumulation. Mutation accumulation can stabilize the system through the emergence of associative overdominance (AOD), destabilize the system, or lead to new evolutionary outcomes. One outcome is the formation of maladaptive balanced lethal systems, where only heterozygotes remain viable and reproduce. We investigated the conditions under which these different outcomes occur, assuming a scenario of introgression after divergence. We found that AOD aided the invasion of a new supergene arrangement and the establishment of a polymorphism. However, this polymorphism was easily destabilized by further mutation accumulation, which was often asymmetric, disrupting the quasi-equilibrium state. Mechanisms that accelerated degeneration tended to amplify asymmetric mutation accumulation between the supergene arrangements and vice-versa. As the evolution of balanced lethal systems requires symmetric degeneration of both arrangements, this leaves only restricted conditions for their evolution, namely small population sizes and low rates of gene conversion. The dichotomy between the persistence of polymorphism and degeneration of supergene arrangements likely underlies the rarity of balanced lethal systems in nature. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.", "doi": "10.1098/rstb.2021.0199", "pmid": "35694750", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9189497"}], "notes": [], "created": "2023-11-27T21:54:29.401Z", "modified": "2024-01-16T13:48:35.522Z"}, {"entity": "publication", "iuid": "6afe7eb5e9a94df680b83253610f4fcf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6afe7eb5e9a94df680b83253610f4fcf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6afe7eb5e9a94df680b83253610f4fcf"}}, "title": "Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.", "authors": [{"family": "Guti\u00e9rrez-Valencia", "given": "Juanita", "initials": "J"}, {"family": "Fracassetti", "given": "Marco", "initials": "M"}, {"family": "Horvath", "given": "Robert", "initials": "R", "orcid": "0000-0002-3221-8835", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd1f411c815a49bf91ada0eac39dee8b.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "D\u00e9samore", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Drouzas", "given": "Andreas D", "initials": "AD"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Kol\u00e1\u0159", "given": "Filip", "initials": "F"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2022-01-07", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "39", "issue": "1", "pages": null}, "abstract": "Fertilization in angiosperms involves the germination of pollen on the stigma, followed by the extrusion of a pollen tube that elongates through the style and delivers two sperm cells to the embryo sac. Sexual selection could occur throughout this process when male gametophytes compete for fertilization. The strength of sexual selection during pollen competition should be affected by the number of genotypes deposited on the stigma. As increased self-fertilization reduces the number of mating partners, and the genetic diversity and heterozygosity of populations, it should thereby reduce the intensity of sexual selection during pollen competition. Despite the prevalence of mating system shifts, few studies have directly compared the molecular signatures of sexual selection during pollen competition in populations with different mating systems. Here we analyzed whole-genome sequences from natural populations of Arabis alpina, a species showing mating system variation across its distribution, to test whether shifts from cross- to self-fertilization result in molecular signatures consistent with sexual selection on genes involved in pollen competition. We found evidence for efficient purifying selection on genes expressed in vegetative pollen, and overall weaker selection on sperm-expressed genes. This pattern was robust when controlling for gene expression level and specificity. In agreement with the expectation that sexual selection intensifies under cross-fertilization, we found that the efficacy of purifying selection on male gametophyte-expressed genes was significantly stronger in genetically more diverse and outbred populations. Our results show that intra-sexual competition shapes the evolution of pollen-expressed genes, and that its strength fades with increasing self-fertilization rates.", "doi": "10.1093/molbev/msab349", "pmid": "34878144", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8788238"}, {"db": "pii", "key": "6456311"}], "notes": [], "created": "2022-02-17T12:52:26.583Z", "modified": "2024-01-16T13:48:37.803Z"}, {"entity": "publication", "iuid": "183750a1213e40eab8d3343e3823bee1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/183750a1213e40eab8d3343e3823bee1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/183750a1213e40eab8d3343e3823bee1"}}, "title": "Selection on accessible chromatin regions in Capsella grandiflora.", "authors": [{"family": "Horvath", "given": "Robert", "initials": "R", "orcid": "0000-0002-3221-8835", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd1f411c815a49bf91ada0eac39dee8b.json"}}, {"family": "Josephs", "given": "Emily B", "initials": "EB"}, {"family": "Pesquet", "given": "Edouard", "initials": "E"}, {"family": "Stinchcombe", "given": "John R", "initials": "JR"}, {"family": "Wright", "given": "Stephen I", "initials": "SI", "orcid": "0000-0001-9973-9697", "researcher": {"href": "https://publications.scilifelab.se/researcher/31879f06b29d4e919c6dbcc55a7d4318.json"}}, {"family": "Scofield", "given": "Douglas", "initials": "D"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2021-09-08", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038"}, "abstract": "Accurate estimates of genome-wide rates and fitness effects of new mutations are essential for an improved understanding of molecular evolutionary processes. Although eukaryotic genomes generally contain a large non-coding fraction, functional non-coding regions and fitness effects of mutations in such regions are still incompletely characterized. A promising approach to characterize functional non-coding regions relies on identifying accessible chromatin regions (ACRs) tightly associated with regulatory DNA. Here, we applied this approach to identify and estimate selection on ACRs in Capsella grandiflora, a crucifer species ideal for population genomic quantification of selection due to its favourable population demography. We describe a population-wide ACR distribution based on ATAC-seq data for leaf samples of 16 individuals from a natural population. We use population genomic methods to estimate fitness effects and proportions of positively selected fixations (\u03b1) in ACRs and find that intergenic ACRs harbor a considerable fraction of weakly deleterious new mutations, as well as a significantly higher proportion of strongly deleterious mutations than comparable inaccessible intergenic regions. ACRs are enriched for expression quantitative trait loci (eQTL) and depleted of transposable element (TE) insertions, as expected if intergenic ACRs are under selection because they harbor regulatory regions. By integrating empirical identification of intergenic ACRs with analyses of eQTL and population genomic analyses of selection, we demonstrate that intergenic regulatory regions are an important source of nearly neutral mutations. These results improve our understanding of selection on non-coding regions and the role of nearly neutral mutations for evolutionary processes in outcrossing Brassicaceae species.", "doi": "10.1093/molbev/msab270", "pmid": "34498072", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6366554"}], "notes": [], "created": "2021-10-01T09:09:08.357Z", "modified": "2024-01-16T13:48:38.533Z"}, {"entity": "publication", "iuid": "4adf66bcf02144de8e00d95337520efa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4adf66bcf02144de8e00d95337520efa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4adf66bcf02144de8e00d95337520efa"}}, "title": "Genome assemblies of three closely related leaf beetle species (Galerucella spp.).", "authors": [{"family": "Yang", "given": "Xuyue", "initials": "X", "orcid": "0000-0003-2084-1651", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0959fee187345d497cec63bce88d136.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA"}], "type": "journal article", "published": "2021-08-07", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "11", "issue": "8", "issn-l": "2160-1836"}, "abstract": "Galerucella (Coleoptera: Chrysomelidae) is a leaf beetle genus that has been extensively used for ecological and evolutionary studies. It has also been used as biological control agent against invading purple loosestrife in North America, with large effects on biodiversity. Here, we report genome assembly and annotation of three closely related Galerucella species: G. calmariensis, G. pusilla, and G. tenella. The three assemblies have a genome size ranging from 460 to 588 Mbp, with N50 from 31,588 to 79,674 kbp, containing 29,202 to 40,929 scaffolds. Using an ab initio evidence-driven approach, 30,302 to 33,794 protein-coding genes were identified and functionally annotated. These draft genomes will contribute to the understanding of host-parasitoid interactions, evolutionary comparisons of leaf beetle species and future population genomics studies.", "doi": "10.1093/g3journal/jkab214", "pmid": "34849825", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6307723"}, {"db": "pmc", "key": "PMC8496278"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5470650"}], "notes": [], "created": "2021-12-10T09:54:47.125Z", "modified": "2024-01-16T13:48:38.816Z"}, {"entity": "publication", "iuid": "df0dbc510b754682bfdebf127ba2393e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df0dbc510b754682bfdebf127ba2393e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df0dbc510b754682bfdebf127ba2393e"}}, "title": "Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives.", "authors": [{"family": "Bohut\u00ednsk\u00e1", "given": "Magdalena", "initials": "M"}, {"family": "Vl\u010dek", "given": "Jakub", "initials": "J", "orcid": "0000-0002-2174-9374", "researcher": {"href": "https://publications.scilifelab.se/researcher/26fabad020684e8296458cc3589813c0.json"}}, {"family": "Yair", "given": "Sivan", "initials": "S", "orcid": "0000-0001-5806-6895", "researcher": {"href": "https://publications.scilifelab.se/researcher/117c0e3537664adfbb1fbd8a3eb6ca71.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Kone\u010dn\u00e1", "given": "Veronika", "initials": "V"}, {"family": "Fracassetti", "given": "Marco", "initials": "M"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Kol\u00e1\u0159", "given": "Filip", "initials": "F", "orcid": "0000-0002-8793-7992", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bfaa4ec7256437badb1ad8c41dff51b.json"}}], "type": "journal article", "published": "2021-05-25", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "21", "issn-l": "0027-8424"}, "abstract": "Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species, which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches, we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores, and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning \u223c0.02 to 18 My of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection on the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species, and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.", "doi": "10.1073/pnas.2022713118", "pmid": "34001609", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "2022713118"}, {"db": "pmc", "key": "PMC8166048"}], "notes": [], "created": "2021-12-10T15:14:38.311Z", "modified": "2021-12-10T15:14:38.443Z"}, {"entity": "publication", "iuid": "549443ffa52c46e79ec1e23b16e1829a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/549443ffa52c46e79ec1e23b16e1829a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/549443ffa52c46e79ec1e23b16e1829a"}}, "title": "The Genomic Architecture and Evolutionary Fates of Supergenes.", "authors": [{"family": "Guti\u00e9rrez-Valencia", "given": "Juanita", "initials": "J", "orcid": "0000-0001-9725-8523", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e653c94bfe34ed2ad11adc4e39bbe20.json"}}, {"family": "Hughes", "given": "P William", "initials": "PW", "orcid": "0000-0003-4142-2579", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bf5ac057e4044f29e640c540270b893.json"}}, {"family": "Berdan", "given": "Emma L", "initials": "EL", "orcid": "0000-0002-6435-4604", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f65066e9a744b95b25ec0597b4b8e23.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2021-05-07", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "5", "issn-l": "1759-6653"}, "abstract": "Supergenes are genomic regions containing sets of tightly linked loci that control multi-trait phenotypic polymorphisms under balancing selection. Recent advances in genomics have uncovered significant variation in both the genomic architecture as well as the mode of origin of supergenes across diverse organismal systems. Although the role of genomic architecture for the origin of supergenes has been much discussed, differences in the genomic architecture also subsequently affect the evolutionary trajectory of supergenes and the rate of degeneration of supergene haplotypes. In this review, we synthesize recent genomic work and historical models of supergene evolution, highlighting how the genomic architecture of supergenes affects their evolutionary fate. We discuss how recent findings on classic supergenes involved in governing ant colony social form, mimicry in butterflies, and heterostyly in flowering plants relate to theoretical expectations. Furthermore, we use forward simulations to demonstrate that differences in genomic architecture affect the degeneration of supergenes. Finally, we discuss implications of the evolution of supergene haplotypes for the long-term fate of balanced polymorphisms governed by supergenes.", "doi": "10.1093/gbe/evab057", "pmid": "33739390", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6178796"}, {"db": "pmc", "key": "PMC8160319"}], "notes": [], "created": "2022-11-09T15:51:59.011Z", "modified": "2024-01-16T13:48:39.777Z"}, {"entity": "publication", "iuid": "5c1d6cec9af048a39ac813f6e0a4ce30", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c1d6cec9af048a39ac813f6e0a4ce30.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c1d6cec9af048a39ac813f6e0a4ce30"}}, "title": "Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm.", "authors": [{"family": "Dziasek", "given": "Katarzyna", "initials": "K", "orcid": "0000-0002-7279-1417", "researcher": {"href": "https://publications.scilifelab.se/researcher/0376b8a4203a4ffba9f688227a8632a2.json"}}, {"family": "Simon", "given": "Lauriane", "initials": "L", "orcid": "0000-0001-7285-9437", "researcher": {"href": "https://publications.scilifelab.se/researcher/08c7a8b7df834ad7b1f905986eb1a99a.json"}}, {"family": "Lafon-Placette", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0001-6634-8104", "researcher": {"href": "https://publications.scilifelab.se/researcher/63262f71f9c54f438d6f08380d799d96.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "W\u00e4rdig", "given": "Cecilia", "initials": "C"}, {"family": "Santos-Gonz\u00e1lez", "given": "Juan", "initials": "J", "orcid": "0000-0002-8712-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/d26cc8b837e64875aa2226cb9a8b8da3.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "17", "issue": "2", "pages": "e1009370", "issn-l": "1553-7390"}, "abstract": "Hybridization of closely related plant species is frequently connected to endosperm arrest and seed failure, for reasons that remain to be identified. In this study, we investigated the molecular events accompanying seed failure in hybrids of the closely related species pair Capsella rubella and C. grandiflora. Mapping of QTL for the underlying cause of hybrid incompatibility in Capsella identified three QTL that were close to pericentromeric regions. We investigated whether there are specific changes in heterochromatin associated with interspecific hybridizations and found a strong reduction of chromatin condensation in the endosperm, connected with a strong loss of CHG and CHH methylation and random loss of a single chromosome. Consistent with reduced DNA methylation in the hybrid endosperm, we found a disproportionate deregulation of genes located close to pericentromeric regions, suggesting that reduced DNA methylation allows access of transcription factors to targets located in heterochromatic regions. Since the identified QTL were also associated with pericentromeric regions, we propose that relaxation of heterochromatin in response to interspecies hybridization exposes and activates loci leading to hybrid seed failure.", "doi": "10.1371/journal.pgen.1009370", "pmid": "33571184", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-20-01346"}, {"db": "pmc", "key": "PMC7904229"}], "notes": [], "created": "2021-12-07T21:42:03.071Z", "modified": "2024-01-16T13:48:40.834Z"}, {"entity": "publication", "iuid": "e75a328b0c454c5db0f2f80fb863a92f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e75a328b0c454c5db0f2f80fb863a92f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e75a328b0c454c5db0f2f80fb863a92f"}}, "title": "HEARTBREAK Controls Post-translational Modification of INDEHISCENT to Regulate Fruit Morphology in Capsella.", "authors": [{"family": "Dong", "given": "Yang", "initials": "Y", "orcid": "0000-0003-2117-538X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2aec5d6e4f0046dfa7e101dc45bee6d7.json"}}, {"family": "Majda", "given": "Mateusz", "initials": "M", "orcid": "0000-0003-3405-2901", "researcher": {"href": "https://publications.scilifelab.se/researcher/582d7b364d4d4442a7f470e52ed031bc.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J"}, {"family": "Horvath", "given": "Robert", "initials": "R"}, {"family": "Srivastava", "given": "Anjil K", "initials": "AK", "orcid": "0000-0001-9871-5781", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f1e429f187d483e86336b2733592b2a.json"}}, {"family": "\u0141angowski", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Eldridge", "given": "Tilly", "initials": "T", "orcid": "0000-0003-1408-5001", "researcher": {"href": "https://publications.scilifelab.se/researcher/7feb9cd320e344e297bddc29826ccfd7.json"}}, {"family": "Stacey", "given": "Nicola", "initials": "N"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Sadanandom", "given": "Ari", "initials": "A"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Smith", "given": "Richard S", "initials": "RS"}, {"family": "\u00d8stergaard", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2020-10-05", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "30", "issue": "19", "pages": "3880-3888.e5", "issn-l": "0960-9822"}, "abstract": "Morphological variation is the basis of natural diversity and adaptation. For example, angiosperms (flowering plants) evolved during the Cretaceous period more than 100 mya and quickly colonized terrestrial habitats [1]. A major reason for their astonishing success was the formation of fruits, which exist in a myriad of different shapes and sizes [2]. Evolution of organ shape is fueled by variation in expression patterns of regulatory genes causing changes in anisotropic cell expansion and division patterns [3-5]. However, the molecular mechanisms that alter the polarity of growth to generate novel shapes are largely unknown. The heart-shaped fruits produced by members of the Capsella genus comprise an anatomical novelty, making it particularly well suited for studies on morphological diversification [6-8]. Here, we show that post-translational modification of regulatory proteins provides a critical step in organ-shape formation. Our data reveal that the SUMO protease, HEARTBREAK (HTB), from Capsella rubella controls the activity of the key regulator of fruit development, INDEHISCENT (CrIND in C. rubella), via de-SUMOylation. This post-translational modification initiates a transduction pathway required to ensure precisely localized auxin biosynthesis, thereby facilitating anisotropic cell expansion to ultimately form the heart-shaped Capsella fruit. Therefore, although variation in the expression of key regulatory genes is known to be a primary driver in morphological evolution, our work demonstrates how other processes-such as post-translational modification of one such regulator-affects organ morphology.", "doi": "10.1016/j.cub.2020.07.055", "pmid": "32795439", "labels": {"Swedish Metabolomics Centre": null}, "xrefs": [{"db": "pii", "key": "S0960-9822(20)31080-0"}, {"db": "pmc", "key": "PMC7544509"}], "notes": [], "created": "2020-12-11T11:56:12.239Z", "modified": "2025-10-17T13:03:16.627Z"}, {"entity": "publication", "iuid": "342bc12c089c4c7fa2ac81719202f980", "links": {"self": {"href": "https://publications.scilifelab.se/publication/342bc12c089c4c7fa2ac81719202f980.json"}, "display": {"href": "https://publications.scilifelab.se/publication/342bc12c089c4c7fa2ac81719202f980"}}, "title": "Differential Expression of Immune Genes between Two Closely Related Beetle Species with Different Immunocompetence following Attack by Asecodes parviclava.", "authors": [{"family": "Yang", "given": "Xuyue", "initials": "X", "orcid": "0000-0003-2084-1651", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0959fee187345d497cec63bce88d136.json"}}, {"family": "Fors", "given": "Lisa", "initials": "L"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Theopold", "given": "Ulrich", "initials": "U"}, {"family": "Binzer-Panchal", "given": "Mahesh", "initials": "M"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA"}], "type": "journal article", "published": "2020-05-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "12", "issue": "5", "pages": "522-534", "issn-l": "1759-6653"}, "abstract": "Endoparasitoid wasps are important natural enemies of many insect species and are major selective forces on the host immune system. Despite increased interest in insect antiparasitoid immunity, there is sparse information on the evolutionary dynamics of biological pathways and gene regulation involved in host immune defense outside Drosophila species. We de novo assembled transcriptomes from two beetle species and used time-course differential expression analysis to investigate gene expression differences in closely related species Galerucella pusilla and G. calmariensis that are, respectively, resistant and susceptible against parasitoid infection by Asecodes parviclava parasitoids. Approximately 271 million and 224 million paired-ended reads were assembled and filtered to form 52,563 and 59,781 transcripts for G. pusilla and G. calmariensis, respectively. In the whole-transcriptome level, an enrichment of functional categories related to energy production, biosynthetic process, and metabolic process was exhibited in both species. The main difference between species appears to be immune response and wound healing process mounted by G. pusilla larvae. Using reciprocal BLAST against the Drosophila melanogaster proteome, 120 and 121 immune-related genes were identified in G. pusilla and G. calmariensis, respectively. More immune genes were differentially expressed in G. pusilla than in G. calmariensis, in particular genes involved in signaling, hematopoiesis, and melanization. In contrast, only one gene was differentially expressed in G. calmariensis. Our study characterizes important genes and pathways involved in different immune functions after parasitoid infection and supports the role of signaling and hematopoiesis genes as key players in host immunity in Galerucella against parasitoid wasps.", "doi": "10.1093/gbe/evaa075", "pmid": "32282901", "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": "5819554"}, {"db": "pmc", "key": "PMC7211424"}], "notes": [], "created": "2020-07-08T13:04:36.500Z", "modified": "2024-01-16T13:48:42.522Z"}, {"entity": "publication", "iuid": "e0e653f6b4f54d8584da0f7e3225d6ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0e653f6b4f54d8584da0f7e3225d6ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0e653f6b4f54d8584da0f7e3225d6ab"}}, "title": "Genetic basis and timing of a major mating system shift in Capsella.", "authors": [{"family": "Bachmann", "given": "J\u00f6rg A", "initials": "JA"}, {"family": "Tedder", "given": "Andrew", "initials": "A", "orcid": "0000-0002-7378-4673", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a29b3c1160f46bf8b21e331268eb4b1.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Fracassetti", "given": "Marco", "initials": "M", "orcid": "0000-0002-2962-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/695213cdd1a645cbbf10d44122237b18.json"}}, {"family": "D\u00e9samor\u00e9", "given": "Aur\u00e9lie", "initials": "A", "orcid": "0000-0003-1922-3557", "researcher": {"href": "https://publications.scilifelab.se/researcher/e117d822871c4a38960b526e3d0dcd0a.json"}}, {"family": "Lafon-Placette", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0001-6634-8104", "researcher": {"href": "https://publications.scilifelab.se/researcher/63262f71f9c54f438d6f08380d799d96.json"}}, {"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Callot", "given": "Caroline", "initials": "C"}, {"family": "Marande", "given": "William", "initials": "W"}, {"family": "Neuffer", "given": "Barbara", "initials": "B"}, {"family": "Berg\u00e8s", "given": "H\u00e9l\u00e8ne", "initials": "H", "orcid": "0000-0002-5492-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/728be2338bd2407980d11b8850d85d9c.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}, {"family": "Castric", "given": "Vincent", "initials": "V", "orcid": "0000-0002-4461-4915", "researcher": {"href": "https://publications.scilifelab.se/researcher/f891128567d64aaba03bdd9f4bc5d458.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2019-10-00", "journal": {"volume": "224", "issn": "1469-8137", "issue": "1", "pages": "505-517", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self-incompatibility locus (S-locus). Theory predicts that S-linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long-read sequencing of complete S-haplotypes, gene expression analyses and controlled crosses. We show that loss of SI in C. orientalis occurred < 2.6 Mya and maps as a dominant trait to the S-locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S-linked small RNA that is predicted to cause dominance of self-compatibility. Our results agree with predictions on the contribution of dominant S-linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions.", "doi": "10.1111/nph.16035", "pmid": "31254395", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "GENBANK", "key": "PRJEB32122"}, {"db": "GENBANK", "key": "KJ772374.1"}], "notes": [], "created": "2019-12-03T10:47:11.816Z", "modified": "2024-01-16T13:48:43.769Z"}, {"entity": "publication", "iuid": "7e4ab87cd1154a83990d12f76cad4ee8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e4ab87cd1154a83990d12f76cad4ee8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e4ab87cd1154a83990d12f76cad4ee8"}}, "title": "Impact of demography on linked selection in two outcrossing Brassicaceae species.", "authors": [{"family": "Mattila", "given": "Tiina M", "initials": "TM", "orcid": "0000-0002-1298-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dbb4f417ab0440fb02a305aaf81b3d5.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Horvath", "given": "Robert", "initials": "R"}, {"family": "H\u00e4m\u00e4l\u00e4", "given": "Tuomas", "initials": "T", "orcid": "0000-0001-8306-3397", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac9fe6733a03417fbd5f6ca780c5589f.json"}}, {"family": "Savolainen", "given": "Outi", "initials": "O"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2019-09-00", "journal": {"volume": "9", "issn": "2045-7758", "issue": "17", "pages": "9532-9545", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": "Genetic diversity is shaped by mutation, genetic drift, gene flow, recombination, and selection. The dynamics and interactions of these forces shape genetic diversity across different parts of the genome, between populations and species. Here, we have studied the effects of linked selection on nucleotide diversity in outcrossing populations of two Brassicaceae species, Arabidopsis lyrata and Capsella grandiflora, with contrasting demographic history. In agreement with previous estimates, we found evidence for a modest population size expansion thousands of generations ago, as well as efficient purifying selection in C. grandiflora. In contrast, the A. lyrata population exhibited evidence for very recent strong population size decline and weaker efficacy of purifying selection. Using multiple regression analyses with recombination rate and other genomic covariates as explanatory variables, we can explain 47% of the variance in neutral diversity in the C. grandiflora population, while in the A. lyrata population, only 11% of the variance was explained by the model. Recombination rate had a significant positive effect on neutral diversity in both species, suggesting that selection at linked sites has an effect on patterns of neutral variation. In line with this finding, we also found reduced neutral diversity in the vicinity of genes in the C. grandiflora population. However, in A. lyrata no such reduction in diversity was evident, a finding that is consistent with expectations of the impact of a recent bottleneck on patterns of neutral diversity near genes. This study thus empirically demonstrates how differences in demographic history modulate the impact of selection at linked sites in natural populations.", "doi": "10.1002/ece3.5463", "pmid": "31534673", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ECE35463"}, {"db": "pmc", "key": "PMC6745670"}], "notes": [], "created": "2019-12-03T13:10:35.648Z", "modified": "2024-01-16T13:48:43.958Z"}, {"entity": "publication", "iuid": "f02be0b28f3a44ca8d96ffa0d34f7a1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f02be0b28f3a44ca8d96ffa0d34f7a1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f02be0b28f3a44ca8d96ffa0d34f7a1e"}}, "title": "Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA", "authors": [{"family": "Ahmed", "given": "Engy", "initials": "E"}, {"family": "Parducci", "given": "Laura", "initials": "L"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "\u00c5gren", "given": "Rasmus", "initials": "R"}, {"family": "Schenk", "given": "Frederik", "initials": "F", "orcid": "0000-0002-4768-9832", "researcher": {"href": "https://publications.scilifelab.se/researcher/a279f1342a264d16ba1007115ef6cf83.json"}}, {"family": "Rattray", "given": "Jayne E", "initials": "JE"}, {"family": "Han", "given": "Lu", "initials": "L"}, {"family": "Muschitiello", "given": "Francesco", "initials": "F"}, {"family": "Pedersen", "given": "Mikkel W", "initials": "MW"}, {"family": "Smittenberg", "given": "Rienk H", "initials": "RH"}, {"family": "Yamoah", "given": "Kweku Afrifa", "initials": "KA"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Wohlfarth", "given": "Barbara", "initials": "B"}], "type": "journal-article", "published": "2018-02-00", "journal": {"volume": "181", "issn": "0277-3791", "issue": null, "pages": "19-29", "title": "Quaternary Science Reviews", "issn-l": null}, "abstract": null, "doi": "10.1016/j.quascirev.2017.11.037", "pmid": null, "labels": {"Systems Biology": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-01-09T08:41:14.286Z", "modified": "2024-01-16T13:48:47.029Z"}, {"entity": "publication", "iuid": "1c039b8df777464b9dabb5e4dc900c99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c039b8df777464b9dabb5e4dc900c99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c039b8df777464b9dabb5e4dc900c99"}}, "title": "Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina.", "authors": [{"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Tedder", "given": "Andrew", "initials": "A"}, {"family": "Nowak", "given": "Michael D", "initials": "MD"}, {"family": "Tor\u00e4ng", "given": "Per", "initials": "P"}, {"family": "Wunder", "given": "J\u00f6rg", "initials": "J"}, {"family": "W\u00f6tzel", "given": "Stefan", "initials": "S"}, {"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Kourmpetis", "given": "Yiannis", "initials": "Y"}, {"family": "Odong", "given": "Thomas", "initials": "T"}, {"family": "Drouzas", "given": "Andreas D", "initials": "AD"}, {"family": "Bink", "given": "Marco C A M", "initials": "MCAM"}, {"family": "\u00c5gren", "given": "Jon", "initials": "J"}, {"family": "Coupland", "given": "George", "initials": "G"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2018-01-23", "journal": {"volume": "115", "issn": "1091-6490", "issue": "4", "pages": "816-821", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Plant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population-genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles, whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, mating system and demography shape the impact of purifying selection on genomic variation in A. alpina These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.", "doi": "10.1073/pnas.1707492115", "pmid": "29301967", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "1707492115"}, {"db": "pmc", "key": "PMC5789905"}], "notes": [], "created": "2019-01-07T22:21:08.774Z", "modified": "2021-06-21T14:35:07.593Z"}, {"entity": "publication", "iuid": "a606501cd092464a84df30e0303ff7ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a606501cd092464a84df30e0303ff7ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a606501cd092464a84df30e0303ff7ad"}}, "title": "Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora.", "authors": [{"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG", "orcid": "0000-0001-5235-6461", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a8063a48a446a7947d55f9900894a6.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2017-01-31", "journal": {"volume": "114", "issn": "1091-6490", "issue": "5", "pages": "1087-1092", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are under weaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species.", "doi": "10.1073/pnas.1612561114", "pmid": "28096395", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1612561114"}, {"db": "pmc", "key": "PMC5293047"}], "notes": [], "created": "2017-08-23T14:19:03.168Z", "modified": "2024-01-16T13:48:48.655Z"}, {"entity": "publication", "iuid": "4147e731341943eaaba69bd08e720934", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4147e731341943eaaba69bd08e720934.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4147e731341943eaaba69bd08e720934"}}, "title": "The role of transposable elements for gene expression in Capsella hybrids and allopolyploids", "authors": [{"family": "Steige", "given": "Kim", "initials": "K"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Rebernig", "given": "Carolin A", "initials": "CA"}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "posted-content", "published": "2016-03-16", "journal": {"volume": null, "issn": null, "issue": null, "pages": null, "title": "bioRxiv", "issn-l": null}, "abstract": null, "doi": "10.1101/044016", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:58:38.375Z", "modified": "2021-06-21T15:59:25.495Z"}]}