{"entity": "journal", "iuid": "3e0628365d304e89b7fd3d390c3549d5", "timestamp": "2026-07-20T03:27:26.408Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Genome%20Biol%20Evol.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Genome%20Biol%20Evol"}}, "title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "publications_count": 55, "publications": [{"entity": "publication", "iuid": "053ef45f515a4c6d94ba0ee3a1b5a74a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/053ef45f515a4c6d94ba0ee3a1b5a74a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/053ef45f515a4c6d94ba0ee3a1b5a74a"}}, "title": "Genome Shows no Recent Inbreeding in Near-Extinction Woolly Rhinoceros Sample Found in Ancient Wolf's Stomach.", "authors": [{"family": "Gu\u00f0j\u00f3nsd\u00f3ttir", "given": "S\u00f3lveig M", "initials": "SM", "orcid": "0009-0002-6435-4409", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d580e28f1f4e9ea90b46b330b6dcff.json"}}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Leme\u017e", "given": "\u0160pela", "initials": "\u0160", "orcid": "0000-0002-0387-1421", "researcher": {"href": "https://publications.scilifelab.se/researcher/381dee4d331a43369d747adc51275fea.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Stanton", "given": "David W G", "initials": "DWG", "orcid": "0000-0002-9753-3166", "researcher": {"href": "https://publications.scilifelab.se/researcher/2732b89a34b54967bcb87811cdc3fb1c.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Fedorov", "given": "Sergey", "initials": "S", "orcid": "0000-0001-8179-740X", "researcher": {"href": "https://publications.scilifelab.se/researcher/856215bb926b471c9d74e7408715f8e6.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}], "type": "journal article", "published": "2026-01-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "18", "issue": "1", "issn-l": "1759-6653"}, "abstract": "Using temporarily spaced high-coverage ancient genomes, we can assess population decline prior to extinction. However, finding suitable ancient remains for recovering this type of data is challenging. Here, we sequenced a high-coverage genome from muscle tissue of a 14,400-year-old woolly rhinoceros (Coelodonta antiquitatis)-a cold-adapted herbivore that went extinct \u223c14,000-years ago-found inside a permafrost-preserved wolf's stomach. We compared genome-wide diversity, inbreeding, genetic load, and population size changes in this sample with two other Late Pleistocene Siberian woolly rhinoceros. We found no evidence of population size decline, nor any genomic erosion, shortly prior to the species' demise. Given the few long homozygous segments, typically indicative of recent inbreeding, we infer a stable population size only a few centuries before extinction. Thus, the woolly rhinoceros' extinction likely happened rapidly, during the B\u00f8lling-Aller\u00f8d interstadial. This study demonstrates the ability to recover high-quality DNA from unlikely sources to elucidate species' extinction dynamics.", "doi": "10.1093/gbe/evaf239", "pmid": "41530912", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12799484"}, {"db": "pii", "key": "8414728"}], "notes": [], "created": "2026-01-22T13:27:26.594Z", "modified": "2026-01-22T13:27:27.263Z"}, {"entity": "publication", "iuid": "ea181adcfb564b289434e673fccd07a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea181adcfb564b289434e673fccd07a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea181adcfb564b289434e673fccd07a3"}}, "title": "Paleogenomics Reveals a Loss of Bovine Lineages in Mid-latitude Asia Over the Last 200,000 Years.", "authors": [{"family": "Gilardet", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-4851-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f507b07ed934c73988dfd0537254485.json"}}, {"family": "Oppenheimer", "given": "Jonas", "initials": "J", "orcid": "0000-0001-7973-6173", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8b1165126184cb980f8bc7e9b9c0fdd.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G", "orcid": "0000-0002-0957-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/62bbfad753a943ea94eb9a0384713a17.json"}}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6929-4869", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0d428a542d44a829e17924e94a3f6dc.json"}}, {"family": "Kosintsev", "given": "Pavel", "initials": "P"}, {"family": "Southon", "given": "John", "initials": "J"}, {"family": "Vasiliev", "given": "Sergey K", "initials": "SK"}, {"family": "Shunkov", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-1388-2308", "researcher": {"href": "https://publications.scilifelab.se/researcher/c43a1135a5804441b6ab9680f7cbd2b3.json"}}, {"family": "Kozlikin", "given": "Maxim B", "initials": "MB", "orcid": "0000-0001-5082-3345", "researcher": {"href": "https://publications.scilifelab.se/researcher/da2a8523fc1c42178159bbd3e8b64ecc.json"}}, {"family": "Douka", "given": "Katerina", "initials": "K", "orcid": "0000-0002-0558-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a6efe4f6db44f6b85ed2653d2a3342f.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2025-10-29", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "17", "issue": "11", "issn-l": "1759-6653"}, "abstract": "Bovines have a complex yet poorly understood evolutionary history that is characterized by admixture and diversity loss during the Late Pleistocene. Unraveling this history is challenging in part because deep-time and geographically widespread genetic data are currently limited. In mid-latitude Asia, Denisova Cave, located in the Altai, Siberia, and nearby paleontological sites have yielded a large collection of remains spanning the Middle to Late Pleistocene, many of which are identifiable as bovines via morphology or paleoproteomics. In this study, we screened these bovine bones for ancient DNA and generated mitogenomes, to refine knowledge of Pleistocene bovine diversity in the region. We found that bovines carrying a yak-like mitogenome were common residents of the Altai mountains, along with bison belonging to the clade X mitochondrial lineage and, more rarely, aurochs. The yak-like mitochondrial lineage identified in this study represents a previously unknown lineage sister to present-day yak mitogenome diversity. This yak-like mitochondrial lineage, termed yak X, was identified at several sites, and survived in mid-latitude Asia across climatic transitions for around 200,000 years. Our findings suggest that all three bovine taxa harbored diversity no longer present in extant populations, thus mirroring archaic hominin findings at Denisova Cave. The Altai mountains therefore appear to have been a hotspot of both bovine and hominin diversity.", "doi": "10.1093/gbe/evaf206", "pmid": "41206445", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12628791"}, {"db": "pii", "key": "8315343"}], "notes": [], "created": "2025-11-21T17:51:54.435Z", "modified": "2025-11-21T17:51:56.168Z"}, {"entity": "publication", "iuid": "a2b369b29d704e429e7d6fc25ebcdee7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2b369b29d704e429e7d6fc25ebcdee7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2b369b29d704e429e7d6fc25ebcdee7"}}, "title": "Genetic Origins of the Kiritimati Population from Central-Eastern Micronesia.", "authors": [{"family": "Larena", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-8799-7645", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d580f1f3e584c809f5f22d7355f154f.json"}}, {"family": "Chowdhury", "given": "Afifa Enam", "initials": "AE", "orcid": "0009-0000-8509-0276", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d3db9785b2f47fd93c5d4a23d8b2ced.json"}}, {"family": "Kels", "given": "Ma Junaliah Tuazon", "initials": "MJT", "orcid": "0000-0002-8730-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/083b0316d97f4be3a43126d01f9a173e.json"}}, {"family": "T\u00e4tte", "given": "Kai", "initials": "K", "orcid": "0000-0002-4753-8954", "researcher": {"href": "https://publications.scilifelab.se/researcher/d44e6836c0144dac85f38f1054520e44.json"}}, {"family": "Metspalu", "given": "Mait", "initials": "M", "orcid": "0000-0003-3099-9161", "researcher": {"href": "https://publications.scilifelab.se/researcher/0557a5b67af948ee8e47473a8ee621d7.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Garcia-Bertrand", "given": "Ralph", "initials": "R", "orcid": "0000-0003-3011-9822", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e0cd4c1175c444c912c1a6db7f44665.json"}}, {"family": "Herrera", "given": "Rene J", "initials": "RJ", "orcid": "0000-0002-5119-4381", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cd8305c817e4adabe92faeebb02fe6e.json"}}], "type": "journal article", "published": "2025-03-06", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "17", "issue": "3", "issn-l": "1759-6653"}, "abstract": "The migration of Austronesian-speaking populations through Oceania has intrigued researchers for decades. The Kiribati islands, situated along the boundaries of Micronesia and Polynesia, provide a crucial link in this migration. We analyzed the genome-wide data of the Kiritimati population of Kiribati to uncover their genetic origins and connections with other Oceanian groups. Our study reveals that the Kiritimati population primarily exhibits Remote Oceanian-related ancestry associated with ancient Lapita and present-day Polynesian populations. In addition, our identity-by-descent analysis identifies populations from the coastal southern Philippines as their closest relatives in Island Southeast Asia. The genetic links between Kiritimati, ancient Lapita, and modern Polynesians underscore the shared ancestry and continuous gene flow across these regions. This genetic continuity and ongoing links are supported by linguistic and cultural evidence, illustrating a complex history of migration and admixture in Oceania.", "doi": "10.1093/gbe/evaf046", "pmid": "40065639", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11937891"}, {"db": "pii", "key": "8069057"}], "notes": [], "created": "2025-09-08T07:15:27.954Z", "modified": "2025-11-14T11:07:53.391Z"}, {"entity": "publication", "iuid": "0477d212635a4177b3e68b39e3fa2f20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0477d212635a4177b3e68b39e3fa2f20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0477d212635a4177b3e68b39e3fa2f20"}}, "title": "Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring.", "authors": [{"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Quintela", "given": "Mar\u00eda", "initials": "M"}, {"family": "Besnier", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Deng", "given": "Qiaoling", "initials": "Q"}, {"family": "Berg", "given": "Florian", "initials": "F", "orcid": "0000-0003-1543-8112", "researcher": {"href": "https://publications.scilifelab.se/researcher/902b6c39c4f5463ea25888c17732fc3e.json"}}, {"family": "Kvamme", "given": "Cecilie", "initials": "C"}, {"family": "Bekkevold", "given": "Dorte", "initials": "D", "orcid": "0000-0002-5297-032X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c62afa02e94554ba1c3afcfc622555.json"}}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "MB"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Lille-Lang\u00f8y", "given": "Roger", "initials": "R"}, {"family": "Leonori", "given": "Iole", "initials": "I", "orcid": "0000-0001-7673-1684", "researcher": {"href": "https://publications.scilifelab.se/researcher/abf52b64cdde43838c36347af47ea670.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications.scilifelab.se/researcher/b67a52aca631482d8b8f58e525a82d14.json"}}, {"family": "Glover", "given": "Kevin A", "initials": "KA"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2024-07-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "16", "issue": "7", "pages": null}, "abstract": "The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors.", "doi": "10.1093/gbe/evae133", "pmid": "38918882", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11226789"}, {"db": "pii", "key": "7699122"}], "notes": [], "created": "2024-11-04T20:50:27.197Z", "modified": "2024-11-25T10:24:21.553Z"}, {"entity": "publication", "iuid": "c8247c4a542e4c94ae4a3ee22db83900", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8247c4a542e4c94ae4a3ee22db83900.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8247c4a542e4c94ae4a3ee22db83900"}}, "title": "Comparative Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles.", "authors": [{"family": "Papachristos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0002-4777-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf7a545a218455fa134b3dd8bb1b895.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A", "orcid": "0000-0002-5662-9145", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f74f301499b4f888e0ac7c5161ae161.json"}}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}], "type": "journal article", "published": "2024-07-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "16", "issue": "7", "pages": null}, "abstract": "Male seminal fluid proteins often show signs of positive selection and divergent evolution, believed to reflect male-female coevolution. Yet, our understanding of the predicted concerted evolution of seminal fluid proteins and female reproductive proteins is limited. We sequenced, assembled, and annotated the genome of two species of seed beetles allowing a comparative analysis of four closely related species of these herbivorous insects. We compare the general pattern of evolution in genes encoding seminal fluid proteins and female reproductive proteins with those in digestive protein genes and well-conserved reference genes. We found that female reproductive proteins showed an overall ratio of nonsynonymous to synonymous substitutions (\u03c9) similar to that of conserved genes, while seminal fluid proteins and digestive proteins exhibited higher overall \u03c9 values. Further, seminal fluid proteins and digestive proteins showed a higher proportion of sites putatively under positive selection, and explicit tests showed no difference in relaxed selection between protein types. Evolutionary rate covariation analyses showed that evolutionary rates among seminal fluid proteins were on average more closely correlated with those in female reproductive proteins than with either digestive or conserved genes. Gene expression showed the expected negative covariation with \u03c9 values, except for male-biased genes where this negative relationship was reversed. In conclusion, seminal fluid proteins showed relatively rapid evolution and signs of positive selection. In contrast, female reproductive proteins evolved at a lower rate under selective constraints, on par with genes known to be well conserved. Although our findings provide support for concerted evolution of seminal fluid proteins and female reproductive proteins, they also suggest that these two classes of proteins evolve under partly distinct selective regimes.", "doi": "10.1093/gbe/evae143", "pmid": "38941482", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11251426"}, {"db": "pii", "key": "7701342"}], "notes": [], "created": "2024-11-12T10:52:28.961Z", "modified": "2024-11-25T10:24:28.390Z"}, {"entity": "publication", "iuid": "85509550f8a04133b34f785895ed87e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85509550f8a04133b34f785895ed87e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85509550f8a04133b34f785895ed87e7"}}, "title": "Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region.", "authors": [{"family": "Larsson", "given": "Martin N A", "initials": "MNA"}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P"}, {"family": "Pan", "given": "Li", "initials": "L"}, {"family": "Ba\u015fak Vural", "given": "K\u0131v\u0131lc\u0131m", "initials": "K"}, {"family": "Kaptan", "given": "Damla", "initials": "D"}, {"family": "Rodrigues Soares", "given": "Andr\u00e9 Elias", "initials": "AE"}, {"family": "Kivikero", "given": "Hanna", "initials": "H"}, {"family": "Kantanen", "given": "Juha", "initials": "J", "orcid": "0000-0001-6350-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd2d0b84728048f39df9c1153300252a.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}], "type": "journal article", "published": "2024-06-04", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "6", "issn-l": "1759-6653"}, "abstract": "Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and \u00c5land, dating from the Late Neolithic (\u223c4,100 cal BP) to historical times (\u223c1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.", "doi": "10.1093/gbe/evae114", "pmid": "38795367", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Ancient DNA": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11162877"}, {"db": "pii", "key": "7682331"}], "notes": [], "created": "2024-07-01T06:11:08.407Z", "modified": "2025-02-28T14:18:19.091Z"}, {"entity": "publication", "iuid": "b25e3b7b87f74800833f5282c1e78098", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b25e3b7b87f74800833f5282c1e78098.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b25e3b7b87f74800833f5282c1e78098"}}, "title": "Experimental Evaluation of a Direct Fitness Effect of the De Novo Evolved Mouse Gene Pldi.", "authors": [{"family": "Linnenbrink", "given": "Miriam", "initials": "M", "orcid": "0000-0003-0163-3056", "researcher": {"href": "https://publications.scilifelab.se/researcher/bea3667ac83f4d72a7603ec75362c157.json"}}, {"family": "Breton", "given": "Gwenna", "initials": "G", "orcid": "0000-0002-4100-9963", "researcher": {"href": "https://publications.scilifelab.se/researcher/757353d5314b4c20ac2ef4833dd207d9.json"}}, {"family": "Misra", "given": "Pallavi", "initials": "P", "orcid": "0000-0001-8547-793X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd215131b4e2465085afb3659f1967f0.json"}}, {"family": "Pfeifle", "given": "Christine", "initials": "C", "orcid": "0009-0003-4762-0602", "researcher": {"href": "https://publications.scilifelab.se/researcher/a49e120682a2434da8da8c984fa53e62.json"}}, {"family": "Dutheil", "given": "Julien Y", "initials": "JY", "orcid": "0000-0001-7753-4121", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e10ad188dac4206949942827ec0dea6.json"}}, {"family": "Tautz", "given": "Diethard", "initials": "D", "orcid": "0000-0002-0460-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec0e6229b6a461c841ebe304cac80c5.json"}}], "type": "journal article", "published": "2024-05-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "5", "issn-l": "1759-6653"}, "abstract": "De novo evolved genes emerge from random parts of noncoding sequences and have, therefore, no homologs from which a function could be inferred. While expression analysis and knockout experiments can provide insights into the function, they do not directly test whether the gene is beneficial for its carrier. Here, we have used a seminatural environment experiment to test the fitness of the previously identified de novo evolved mouse gene Pldi, which has been implicated to have a role in sperm differentiation. We used a knockout mouse strain for this gene and competed it against its parental wildtype strain for several generations of free reproduction. We found that the knockout (ko) allele frequency decreased consistently across three replicates of the experiment. Using an approximate Bayesian computation framework that simulated the data under a demographic scenario mimicking the experiment's demography, we could estimate a selection coefficient ranging between 0.21 and 0.61 for the wildtype allele compared to the ko allele in males, under various models. This implies a relatively strong selective advantage, which would fix the new gene in less than hundred generations after its emergence.", "doi": "10.1093/gbe/evae084", "pmid": "38742287", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11091481"}, {"db": "pii", "key": "7668359"}], "notes": [], "created": "2024-11-01T08:24:59.306Z", "modified": "2024-11-01T08:24:59.606Z"}, {"entity": "publication", "iuid": "4c8011797b384556b77dc6f719cf9763", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c8011797b384556b77dc6f719cf9763.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c8011797b384556b77dc6f719cf9763"}}, "title": "Population genomic history of the endangered Anatolian and Cyprian mouflons in relation to worldwide wild, feral and domestic sheep lineages.", "authors": [{"family": "Ata\u011f", "given": "G\u00f6zde", "initials": "G", "orcid": "0000-0001-6173-3126", "researcher": {"href": "https://publications.scilifelab.se/researcher/e478e5f000ce44a090ccd7fad904bf36.json"}}, {"family": "Kaptan", "given": "Damla", "initials": "D"}, {"family": "Y\u00fcnc\u00fc", "given": "Eren", "initials": "E"}, {"family": "Ba\u015fak Vural", "given": "K\u0131v\u0131lc\u0131m", "initials": "K"}, {"family": "Mereu", "given": "Paolo", "initials": "P"}, {"family": "Pirastru", "given": "Monica", "initials": "M"}, {"family": "Barbato", "given": "Mario", "initials": "M"}, {"family": "Leoni", "given": "Giovanni Giuseppe", "initials": "GG"}, {"family": "G\u00fcler", "given": "Merve N", "initials": "MN"}, {"family": "Er", "given": "Tu\u011f\u00e7e", "initials": "T"}, {"family": "Eker", "given": "Elifnaz", "initials": "E"}, {"family": "Yaz\u0131c\u0131", "given": "Tunca Deniz", "initials": "TD"}, {"family": "K\u0131l\u0131\u00e7", "given": "Muhammed S\u0131dd\u0131k", "initials": "MS"}, {"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE"}, {"family": "\u00c7elik", "given": "Ecem Ay\u015fe", "initials": "EA"}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Floridia", "given": "Viviana", "initials": "V"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Bilgin", "given": "C Can", "initials": "CC"}, {"family": "Togan", "given": "\u0130nci", "initials": "\u0130"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "Hadjisterkotis", "given": "Eleftherios", "initials": "E"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}], "type": "journal article", "published": "2024-04-27", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653"}, "abstract": "Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the IUCN. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them to eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (Ovis gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity (ROH) blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne as well as mutation load estimates are lower in Cyprian compared to Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages, and a limited consistency between viability metrics and IUCN conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.", "doi": "10.1093/gbe/evae090", "pmid": "38670119", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "7658889"}], "notes": [], "created": "2024-05-17T09:15:15.975Z", "modified": "2024-05-17T09:15:16.133Z"}, {"entity": "publication", "iuid": "1d736b8b72eb494b9bb389cec88fafc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d736b8b72eb494b9bb389cec88fafc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d736b8b72eb494b9bb389cec88fafc6"}}, "title": "Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.", "authors": [{"family": "David", "given": "Gabriel", "initials": "G", "orcid": "0009-0007-2935-3335", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b3c0232a812453cb58532f946233fad.json"}}, {"family": "Bertolotti", "given": "Alicia", "initials": "A"}, {"family": "Layer", "given": "Ryan", "initials": "R", "orcid": "0000-0002-5823-3232", "researcher": {"href": "https://publications.scilifelab.se/researcher/e448323eee2b4098a3fc8b7e4e610524.json"}}, {"family": "Scofield", "given": "Douglas", "initials": "D"}, {"family": "Hayward", "given": "Alexander", "initials": "A", "orcid": "0000-0001-7413-718X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5472a9b21fa405eaef0dba5323746ad.json"}}, {"family": "Baril", "given": "Tobias", "initials": "T", "orcid": "0000-0002-5936-7531", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf3dffb6823e4a56af5d7f5760a73bd4.json"}}, {"family": "Burnett", "given": "Hamish A", "initials": "HA"}, {"family": "Gudmunds", "given": "Erik", "initials": "E"}, {"family": "Jensen", "given": "Henrik", "initials": "H", "orcid": "0000-0001-7804-1564", "researcher": {"href": "https://publications.scilifelab.se/researcher/27e3fe8ca67c4bfea44b8bff1f996f8c.json"}}, {"family": "Husby", "given": "Arild", "initials": "A", "orcid": "0000-0003-1911-8351", "researcher": {"href": "https://publications.scilifelab.se/researcher/a30bcb02f8a44229815afcf33cd62d23.json"}}], "type": "journal article", "published": "2024-04-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "4", "issn-l": "1759-6653"}, "abstract": "Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.", "doi": "10.1093/gbe/evae049", "pmid": "38489588", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11018544"}, {"db": "pii", "key": "7630036"}], "notes": [], "created": "2024-11-12T19:38:46.847Z", "modified": "2024-11-25T10:24:06.035Z"}, {"entity": "publication", "iuid": "21b05c7704a44023bd01b0eb68f84123", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21b05c7704a44023bd01b0eb68f84123.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21b05c7704a44023bd01b0eb68f84123"}}, "title": "Chromosome-scale Genome Assembly of the Rough Periwinkle Littorina saxatilis.", "authors": [{"family": "De Jode", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0003-0428-439X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1ff392d2a03435795aa8a8a1ee8dd65.json"}}, {"family": "Faria", "given": "Rui", "initials": "R"}, {"family": "Formenti", "given": "Giulio", "initials": "G", "orcid": "0000-0002-7554-5991", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdf78195993a481483d7cbbf1a6d64ed.json"}}, {"family": "Sims", "given": "Ying", "initials": "Y"}, {"family": "Smith", "given": "Timothy P", "initials": "TP"}, {"family": "Tracey", "given": "Alan", "initials": "A"}, {"family": "Wood", "given": "Jonathan M D", "initials": "JMD", "orcid": "0000-0002-7545-2162", "researcher": {"href": "https://publications.scilifelab.se/researcher/c255ed6ec2f246028326f9fece911f74.json"}}, {"family": "Zagrodzka", "given": "Zuzanna B", "initials": "ZB"}, {"family": "Johannesson", "given": "Kerstin", "initials": "K"}, {"family": "Butlin", "given": "Roger K", "initials": "RK"}, {"family": "Leder", "given": "Erica H", "initials": "EH", "orcid": "0000-0002-7160-2290", "researcher": {"href": "https://publications.scilifelab.se/researcher/116c4b0c7c7940efa9d080c613a05275.json"}}], "type": "journal article", "published": "2024-04-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "4", "issn-l": "1759-6653"}, "abstract": "The intertidal gastropod Littorina saxatilis is a model system to study speciation and local adaptation. The repeated occurrence of distinct ecotypes showing different levels of genetic divergence makes L. saxatilis particularly suited to study different stages of the speciation continuum in the same lineage. A major finding is the presence of several large chromosomal inversions associated with the divergence of ecotypes and, specifically, the species offers a system to study the role of inversions in this divergence. The genome of L. saxatilis is 1.35 Gb and composed of 17 chromosomes. The first reference genome of the species was assembled using Illumina data, was highly fragmented (N50 of 44 kb), and was quite incomplete, with a BUSCO completeness of 80.1% on the Metazoan dataset. A linkage map of one full-sibling family enabled the placement of 587 Mbp of the genome into 17 linkage groups corresponding to the haploid number of chromosomes, but the fragmented nature of this reference genome limited the understanding of the interplay between divergent selection and gene flow during ecotype formation. Here, we present a newly generated reference genome that is highly contiguous, with a N50 of 67 Mb and 90.4% of the total assembly length placed in 17 super-scaffolds. It is also highly complete with a BUSCO completeness of 94.1% of the Metazoa dataset. This new reference will allow for investigations into the genomic regions implicated in ecotype formation as well as better characterization of the inversions and their role in speciation.", "doi": "10.1093/gbe/evae076", "pmid": "38584387", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11050657"}, {"db": "pii", "key": "7641934"}], "notes": [], "created": "2024-11-25T10:24:11.202Z", "modified": "2025-02-28T14:18:13.878Z"}, {"entity": "publication", "iuid": "6dad922586f84341baf632ac55a61367", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6dad922586f84341baf632ac55a61367.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6dad922586f84341baf632ac55a61367"}}, "title": "High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex.", "authors": [{"family": "Ament-Vel\u00e1squez", "given": "S Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Vogan", "given": "Aaron A", "initials": "AA", "orcid": "0000-0003-2013-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/71c6d460e3b44712a1a9dc19066211a4.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Hartmann", "given": "Fanny E", "initials": "FE", "orcid": "0000-0002-9365-4008", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac8e717031aa4621925ab90684adecdc.json"}}, {"family": "Gautier", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Silar", "given": "Philippe", "initials": "P", "orcid": "0000-0003-0104-987X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a40756e83bc493ebc1d98d8c5c374da.json"}}, {"family": "Giraud", "given": "Tatiana", "initials": "T"}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2024-03-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "3", "issn-l": "1759-6653"}, "abstract": "The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of 7 closely related species. In addition to P. anserina, high-quality genomic resources are available for 2 of these taxa. Here, we provide chromosome-level annotated assemblies of the 4 remaining species of the complex, as well as a comprehensive data set of annotated assemblies from a total of 28 Podospora genomes. We find that all 7 species have genomes of around 35 Mb arranged in 7 chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification.", "doi": "10.1093/gbe/evae034", "pmid": "38386982", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10936905"}, {"db": "pii", "key": "7612620"}], "notes": [], "created": "2024-08-02T12:17:18.611Z", "modified": "2025-02-28T14:18:08.086Z"}, {"entity": "publication", "iuid": "fa3ec7c6d57645dca27002bd711dd76c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa3ec7c6d57645dca27002bd711dd76c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa3ec7c6d57645dca27002bd711dd76c"}}, "title": "A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern.", "authors": [{"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Dias", "given": "Guilherme", "initials": "G"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Soares", "given": "Andr\u00e9", "initials": "A"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Talla", "given": "Venkat", "initials": "V", "orcid": "0000-0003-2653-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/703518ce5a1f4e5ea04719016173a867.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2024-02-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "2", "issn-l": "1759-6653"}, "abstract": "The clouded apollo (Parnassius mnemosyne) is a palearctic butterfly distributed over a large part of western Eurasia, but population declines and fragmentation have been observed in many parts of the range. The development of genomic tools can help to shed light on the genetic consequences of the decline and to make informed decisions about direct conservation actions. Here, we present a high-contiguity, chromosome-level genome assembly of a female clouded apollo butterfly and provide detailed annotations of genes and transposable elements. We find that the large genome (1.5 Gb) of the clouded apollo is extraordinarily repeat rich (73%). Despite that, the combination of sequencing techniques allowed us to assemble all chromosomes (nc = 29) to a high degree of completeness. The annotation resulted in a relatively high number of protein-coding genes (22,854) compared with other Lepidoptera, of which a large proportion (21,635) could be assigned functions based on homology with other species. A comparative analysis indicates that overall genome structure has been largely conserved, both within the genus and compared with the ancestral lepidopteran karyotype. The high-quality genome assembly and detailed annotation presented here will constitute an important tool for forthcoming efforts aimed at understanding the genetic consequences of fragmentation and decline, as well as for assessments of genetic diversity, population structure, inbreeding, and genetic load in the clouded apollo butterfly.", "doi": "10.1093/gbe/evae031", "pmid": "38368625", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10901555"}, {"db": "pii", "key": "7610114"}], "notes": [], "created": "2024-02-29T15:15:06.133Z", "modified": "2025-02-28T14:18:02.771Z"}, {"entity": "publication", "iuid": "edb9aa23ac704f2384a042691edc79e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edb9aa23ac704f2384a042691edc79e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edb9aa23ac704f2384a042691edc79e2"}}, "title": "Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite.", "authors": [{"family": "C\u012brulis", "given": "Aivars", "initials": "A", "orcid": "0000-0003-3472-865X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed7cd12abf3e450288217a8acaa2190d.json"}}, {"family": "Nord\u00e9n", "given": "Anna K", "initials": "AK"}, {"family": "Churcher", "given": "Allison M", "initials": "AM"}, {"family": "Ramm", "given": "Steven A", "initials": "SA"}, {"family": "Zadesenets", "given": "Kira S", "initials": "KS"}, {"family": "Abbott", "given": "Jessica K", "initials": "JK", "orcid": "0000-0002-8743-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/7be37bf315f34e18b7ad8714da1381b8.json"}}], "type": "journal article", "published": "2024-01-05", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "16", "issue": "1", "pages": null}, "abstract": "The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical models or comparative studies of already old sex chromosomes. We therefore investigated changes in gene expression under 3 different selection regimes for the simultaneous hermaphrodite Macrostomum lignano subjected to sex-limited experimental evolution (i.e. selection for fitness via eggs, sperm, or a control regime allowing both). After 21 and 22 generations of selection for male-specific or female-specific fitness, we characterized changes in whole-organism gene expression. We found that female-selected lines had changed the most in their gene expression. Although annotation for this species is limited, gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggest that metabolic changes (e.g. biosynthesis of amino acids and carbon metabolism) are an important adaptive component. As predicted, we found that the expression of genes previously identified as testis-biased candidates tended to be downregulated in the female-selected lines. We did not find any significant expression differences for previously identified candidates of other sex-specific organs, but this may simply reflect that few transcripts have been characterized in this way. In conclusion, our experiment suggests that changes in testis-biased gene expression are important in the early evolution of sex chromosomes and gonochorism.", "doi": "10.1093/gbe/evad235", "pmid": "38155579", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10786194"}, {"db": "pii", "key": "7503504"}], "notes": [], "created": "2024-01-09T14:09:35.198Z", "modified": "2025-02-28T14:17:57.633Z"}, {"entity": "publication", "iuid": "f361c17689bc48929bd23e7d629f9f1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f361c17689bc48929bd23e7d629f9f1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f361c17689bc48929bd23e7d629f9f1b"}}, "title": "Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird.", "authors": [{"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Tarka", "given": "Maja", "initials": "M", "orcid": "0000-0001-9651-1101", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a0abfbfc5bb4d5fb77f356c6ad80a34.json"}}, {"family": "Hasselquist", "given": "Dennis", "initials": "D", "orcid": "0000-0002-0056-6616", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a24d358af64f22b81735f577c33bbb.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": "2023-11-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "15", "issue": "11", "issn-l": "1759-6653"}, "abstract": "Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 \u00d7 10-9 mutations per site per generation (m/s/g) for the autosomes and 5.10 \u00d7 10-9 m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions predating the last glacial period (LGP) and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.", "doi": "10.1093/gbe/evad180", "pmid": "37793164", "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": "PMC10627410"}, {"db": "pii", "key": "7289221"}], "notes": [], "created": "2023-11-29T10:54:38.925Z", "modified": "2024-01-16T13:48:31.754Z"}, {"entity": "publication", "iuid": "27e5410cdd1f47228b9aa1c4b75dea54", "links": {"self": {"href": "https://publications.scilifelab.se/publication/27e5410cdd1f47228b9aa1c4b75dea54.json"}, "display": {"href": "https://publications.scilifelab.se/publication/27e5410cdd1f47228b9aa1c4b75dea54"}}, "title": "The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees.", "authors": [{"family": "Everitt", "given": "Turid", "initials": "T"}, {"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Hoffmann", "given": "Wolfgang", "initials": "W"}, {"family": "Neumann", "given": "Peter", "initials": "P"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2023-09-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "15", "issue": "9", "issn-l": "1759-6653"}, "abstract": "A range of different genetic architectures underpin local adaptation in nature. Honey bees (Apis mellifera) in the Eastern African Mountains harbor high frequencies of two chromosomal inversions that likely govern adaptation to this high-elevation habitat. In the Americas, honey bees are hybrids of European and African ancestries and adaptation to latitudinal variation in climate correlates with the proportion of these ancestries across the genome. It is unknown which, if either, of these forms of genetic variation governs adaptation in honey bees living at high elevations in the Americas. Here, we performed whole-genome sequencing of 29 honey bees from both high- and low-elevation populations in Colombia. Analysis of genetic ancestry indicated that both populations were predominantly of African ancestry, but the East African inversions were not detected. However, individuals in the higher elevation population had significantly higher proportions of European ancestry, likely reflecting local adaptation. Several genomic regions exhibited particularly high differentiation between highland and lowland bees, containing candidate loci for local adaptation. Genes that were highly differentiated between highland and lowland populations were enriched for functions related to reproduction and sperm competition. Furthermore, variation in levels of European ancestry across the genome was correlated between populations of honey bees in the highland population and populations at higher latitudes in South America. The results are consistent with the hypothesis that adaptation to both latitude and elevation in these hybrid honey bees are mediated by variation in ancestry at many loci across the genome.", "doi": "10.1093/gbe/evad157", "pmid": "37625795", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10484329"}, {"db": "pii", "key": "7251443"}], "notes": [], "created": "2023-10-11T09:08:46.279Z", "modified": "2024-01-16T13:48:32.323Z"}, {"entity": "publication", "iuid": "5f11a08653594e8c886a55b8c87b663d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f11a08653594e8c886a55b8c87b663d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f11a08653594e8c886a55b8c87b663d"}}, "title": "Base Composition, Codon Usage, and Patterns of Gene Sequence Evolution in Butterflies.", "authors": [{"family": "N\u00e4svall", "given": "Karin", "initials": "K", "orcid": "0000-0002-2970-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/9173164aadbe47b0b4132d2c6e654cf3.json"}}, {"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "Talla", "given": "Venkat", "initials": "V", "orcid": "0000-0003-2653-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/703518ce5a1f4e5ea04719016173a867.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2023-08-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "15", "issue": "8", "issn-l": "1759-6653"}, "abstract": "Coding sequence evolution is influenced by both natural selection and neutral evolutionary forces. In many species, the effects of mutation bias, codon usage, and GC-biased gene conversion (gBGC) on gene sequence evolution have not been detailed. Quantification of how these forces shape substitution patterns is therefore necessary to understand the strength and direction of natural selection. Here, we used comparative genomics to investigate the association between base composition and codon usage bias on gene sequence evolution in butterflies and moths (Lepidoptera), including an in-depth analysis of underlying patterns and processes in one species, Leptidea sinapis. The data revealed significant G/C to A/T substitution bias at third codon position with some variation in the strength among different butterfly lineages. However, the substitution bias was lower than expected from previously estimated mutation rate ratios, partly due to the influence of gBGC. We found that A/T-ending codons were overrepresented in most species, but there was a positive association between the magnitude of codon usage bias and GC-content in third codon positions. In addition, the tRNA-gene population in L. sinapis showed higher GC-content at third codon positions compared to coding sequences in general and less overrepresentation of A/T-ending codons. There was an inverse relationship between synonymous substitutions and codon usage bias indicating selection on synonymous sites. We conclude that the evolutionary rate in Lepidoptera is affected by a complex interaction between underlying G/C -> A/T mutation bias and partly counteracting fixation biases, predominantly conferred by overall purifying selection, gBGC, and selection on codon usage.", "doi": "10.1093/gbe/evad150", "pmid": "37565492", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10462419"}, {"db": "pii", "key": "7241093"}], "notes": [], "created": "2023-10-11T09:12:00.794Z", "modified": "2024-01-16T13:48:32.669Z"}, {"entity": "publication", "iuid": "4deb700f9a5d4e66bb1ede6b222c2a2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4deb700f9a5d4e66bb1ede6b222c2a2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4deb700f9a5d4e66bb1ede6b222c2a2d"}}, "title": "A Long-Standing Hybrid Population Between Pacific and Atlantic Herring in a Subarctic Fjord of Norway.", "authors": [{"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Fuentes-Pardo", "given": "Angela P", "initials": "AP"}, {"family": "Rochus", "given": "Christina M", "initials": "CM"}, {"family": "Enbody", "given": "Erik D", "initials": "ED"}, {"family": "Bi", "given": "Huijuan", "initials": "H"}, {"family": "V\u00e4in\u00f6l\u00e4", "given": "Risto", "initials": "R"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-05-05", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "15", "issue": "5", "pages": null}, "abstract": "Atlantic herring (Clupea harengus) and Pacific herring (C. pallasii) are sister species that split from a common ancestor about 2 million years ago. Balsfjord, a subarctic fjord in Northern Norway, harbors an outpost population of Pacific herring within the range of the Atlantic herring. We used whole genome sequencing to show that gene flow from Atlantic herring into the Balsfjord population has generated a stable hybrid population that has persisted for thousands of generations. The Atlantic herring ancestry in Balsfjord was estimated in the range 25-26%. The old age and large proportion of introgressed regions suggest there are no obvious genetic incompatibilities between species. Introgressed regions were widespread in the genome and large, with some in excess of 1 Mb, and they were overrepresented in low-recombination regions. We show that the distribution of introgressed material is non-random; introgressed sequence blocks in different individuals are shared more often than expected by chance. Furthermore, introgressed regions tend to show elevated divergence (FST) between Atlantic and Pacific herring. Together, our results suggest that introgression of genetic material has facilitated adaptation in the Balsfjord population. The Balsfjord population provides a rare example of a stable interspecies hybrid population that has persisted over thousands of years.", "doi": "10.1093/gbe/evad069", "pmid": "37120751", "labels": {"NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10182735"}, {"db": "pii", "key": "7147330"}], "notes": [], "created": "2023-10-30T09:48:24.059Z", "modified": "2024-01-16T13:48:33.434Z"}, {"entity": "publication", "iuid": "53fbc4d093de4ad3b1e17fcca31fca04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53fbc4d093de4ad3b1e17fcca31fca04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53fbc4d093de4ad3b1e17fcca31fca04"}}, "title": "A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea).", "authors": [{"family": "Onu\u021b-Br\u00e4nnstr\u00f6m", "given": "Ioana", "initials": "I", "orcid": "0000-0002-7723-8629", "researcher": {"href": "https://publications.scilifelab.se/researcher/e51e62ab66244945889efc4669d2d853.json"}}, {"family": "Stairs", "given": "Courtney W", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}, {"family": "Campos", "given": "Karla Iveth Aguilera", "initials": "KIA"}, {"family": "Thor\u00e9n", "given": "Markus Hiltunen", "initials": "MH", "orcid": "0000-0002-8880-872X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b54361528b4c7c8f5122d91d58b36d.json"}}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}, {"family": "Keeling", "given": "Patrick J", "initials": "PJ"}, {"family": "Bass", "given": "David", "initials": "D"}, {"family": "Burki", "given": "Fabien", "initials": "F", "orcid": "0000-0002-8248-8462", "researcher": {"href": "https://publications.scilifelab.se/researcher/c386a8e440344f25bea35d570450b09b.json"}}], "type": "journal article", "published": "2023-03-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "15", "issue": "3", "issn-l": "1759-6653"}, "abstract": "Ascetosporea are endoparasites of marine invertebrates that include economically important pathogens of aquaculture species. Owing to their often-minuscule cell sizes, strict intracellular lifestyle, lack of cultured representatives and minimal availability of molecular data, these unicellular parasites remain poorly studied. Here, we sequenced and assembled the genome and transcriptome of Paramikrocytos canceri, an endoparasite isolated from the European edible crab Cancer pagurus. Using bioinformatic predictions, we show that P. canceri likely possesses a mitochondrion-related organelle (MRO) with highly reduced metabolism, resembling the mitosomes of other parasites but with key differences. Like other mitosomes, this MRO is predicted to have reduced metabolic capacity and lack an organellar genome and function in iron-sulfur cluster (ISC) pathway-mediated Fe-S cluster biosynthesis. However, the MRO in P. canceri is uniquely predicted to produce ATP via a partial glycolytic pathway and synthesize phospholipids de novo through the CDP-DAG pathway. Heterologous gene expression confirmed that proteins from the ISC and CDP-DAG pathways retain mitochondrial targeting sequences that are recognized by yeast mitochondria. This represents a unique combination of metabolic pathways in an MRO, including the first reported case of a mitosome-like organelle able to synthesize phospholipids de novo. Some of these phospholipids, such as phosphatidylserine, are vital in other protist endoparasites that invade their host through apoptotic mimicry.", "doi": "10.1093/gbe/evad022", "pmid": "36790104", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9998036"}, {"db": "pii", "key": "7039708"}, {"db": "figshare", "key": "10.6084/m9.figshare.21206669.v1"}, {"db": "figshare", "key": "10.6084/m9.figshare.21206807.v1"}, {"db": "figshare", "key": "10.6084/m9.figshare.21770576.v1"}], "notes": [], "created": "2023-11-27T21:52:34.646Z", "modified": "2024-01-16T13:48:33.882Z"}, {"entity": "publication", "iuid": "18d1940c083c4e4780bea26c0c4df967", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18d1940c083c4e4780bea26c0c4df967.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18d1940c083c4e4780bea26c0c4df967"}}, "title": "Experimental Life History Evolution Results in Sex-specific Evolution of Gene Expression in Seed Beetles.", "authors": [{"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c9af5588c64dfdacba192b65524d43.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Stojkovi\u0107", "given": "Biljana", "initials": "B"}, {"family": "Savkovi\u0107", "given": "Uro\u0161", "initials": "U"}, {"family": "\u0110or\u0111evi\u0107", "given": "Mirko", "initials": "M"}, {"family": "Liljestrand-R\u00f6nn", "given": "Johanna", "initials": "J"}, {"family": "Wiberg", "given": "R Axel W", "initials": "RAW"}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}], "type": "journal article", "published": "2023-01-04", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "15", "issue": "1", "pages": null}, "abstract": "The patterns of reproductive timing and senescence vary within and across species owing to differences in reproductive strategies, but our understanding of the molecular underpinnings of such variation is incomplete. This is perhaps particularly true for sex differences. We investigated the evolution of sex-specific gene expression associated with life history divergence in replicated populations of the seed beetle Acanthoscelides obtectus, experimentally evolving under (E)arly or (L)ate life reproduction for >200 generations which has resulted in strongly divergent life histories. We detected 1,646 genes that were differentially expressed in E and L lines, consistent with a highly polygenic basis of life history evolution. Only 30% of differentially expressed genes were similarly affected in males and females. The evolution of long life was associated with significantly reduced sex differences in expression, especially in non-reproductive tissues. The expression differences were overall more pronounced in females, in accordance with their greater phenotypic divergence in lifespan. Functional enrichment analysis revealed differences between E and L beetles in gene categories previously implicated in aging, such as mitochondrial function and defense response. The results show that divergent life history evolution can be associated with profound changes in gene expression that alter the transcriptome in a sex-specific way, highlighting the importance of understanding the mechanisms of aging in each sex.", "doi": "10.1093/gbe/evac177", "pmid": "36542472", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9830990"}, {"db": "pii", "key": "6948356"}], "notes": [], "created": "2023-12-01T12:26:26.019Z", "modified": "2024-07-01T06:04:47.982Z"}, {"entity": "publication", "iuid": "52b6011191b94c74b6f4baaea4ff448c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52b6011191b94c74b6f4baaea4ff448c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52b6011191b94c74b6f4baaea4ff448c"}}, "title": "Genome Evolution of a Symbiont Population for Pathogen Defense in Honeybees.", "authors": [{"family": "Dyrhage", "given": "Karl", "initials": "K"}, {"family": "Garcia-Montaner", "given": "Andrea", "initials": "A"}, {"family": "Tamarit", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4940-719X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b6e6e8715ff4f76985f2e09972e1013.json"}}, {"family": "Seeger", "given": "Christian", "initials": "C"}, {"family": "N\u00e4slund", "given": "Kristina", "initials": "K"}, {"family": "Olofsson", "given": "Tobias C", "initials": "TC"}, {"family": "Vasquez", "given": "Alejandra", "initials": "A"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Andersson", "given": "Siv G E", "initials": "SGE"}], "type": "journal article", "published": "2022-11-04", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "14", "issue": "11", "issn-l": "1759-6653"}, "abstract": "The honeybee gut microbiome is thought to be important for bee health, but the role of the individual members is poorly understood. Here, we present closed genomes and associated mobilomes of 102 Apilactobacillus kunkeei isolates obtained from the honey crop (foregut) of honeybees sampled from beehives in Helsingborg in the south of Sweden and from the islands Gotland and \u00c5land in the Baltic Sea. Each beehive contained a unique composition of isolates and repeated sampling of similar isolates from two beehives in Helsingborg suggests that the bacterial community is stably maintained across bee generations during the summer months. The sampled bacterial population contained an open pan-genome structure with a high genomic density of transposons. A subset of strains affiliated with phylogroup A inhibited growth of the bee pathogen Melissococcus plutonius, all of which contained a 19.5 kb plasmid for the synthesis of the antimicrobial compound kunkecin A, while a subset of phylogroups B and C strains contained a 32.9 kb plasmid for the synthesis of a putative polyketide antibiotic. This study suggests that the mobile gene pool of A. kunkeei plays a key role in pathogen defense in honeybees, providing new insights into the evolutionary dynamics of defensive symbiont populations.", "doi": "10.1093/gbe/evac153", "pmid": "36263788", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9648514"}, {"db": "pii", "key": "6764223"}], "notes": [], "created": "2022-11-21T10:10:14.246Z", "modified": "2024-01-16T13:48:34.499Z"}, {"entity": "publication", "iuid": "9d6ef0ad3fbc4458add397850c87d9d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d6ef0ad3fbc4458add397850c87d9d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d6ef0ad3fbc4458add397850c87d9d8"}}, "title": "A Genome for Edith's Checkerspot Butterfly: An Insect with Complex Host-Adaptive Suites and Rapid Evolutionary Responses to Environmental Changes.", "authors": [{"family": "Tunstrom", "given": "Kalle", "initials": "K", "orcid": "0000-0002-5285-1531", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd0ddb97d724542b6e7c46f782f3bbd.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "Parmesan", "given": "Camille", "initials": "C"}, {"family": "Singer", "given": "Michael C", "initials": "MC"}, {"family": "Mikheyev", "given": "Alexander S", "initials": "AS"}], "type": "journal article", "published": "2022-08-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "14", "issue": "8", "pages": null}, "abstract": "Insects have been key players in the assessments of biodiversity impacts of anthropogenically driven environmental change, including the evolutionary and ecological impacts of climate change. Populations of Edith's Checkerspot Butterfly (Euphydryas editha) adapt rapidly to diverse environmental conditions, with numerous high-impact studies documenting these dynamics over several decades. However, studies of the underlying genetic bases of these responses have been hampered by missing genomic resources, limiting the ability to connect genomic responses to environmental change. Using a combination of Oxford Nanopore long reads, haplotype merging, HiC scaffolding followed by Illumina polishing, we generated a highly contiguous and complete assembly (contigs n = 142, N50 = 21.2 Mb, total length = 607.8 Mb; BUSCOs n = 5,286, single copy complete = 97.8%, duplicated = 0.9%, fragmented = 0.3%, missing = 1.0%). A total of 98% of the assembled genome was placed into 31 chromosomes, which displayed large-scale synteny with other well-characterized lepidopteran genomes. The E. editha genome, annotation, and functional descriptions now fill a missing gap for one of the leading field-based ecological model systems in North America.", "doi": "10.1093/gbe/evac113", "pmid": "35876165", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9348621"}, {"db": "pii", "key": "6649524"}], "notes": [], "created": "2022-08-19T08:38:20.953Z", "modified": "2024-01-16T13:48:35.474Z"}, {"entity": "publication", "iuid": "6adf5f1180a14b25afaeb95640385448", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6adf5f1180a14b25afaeb95640385448.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6adf5f1180a14b25afaeb95640385448"}}, "title": "The Assembled and Annotated Genome of the Fairy-Ring Fungus Marasmius oreades.", "authors": [{"family": "Hiltunen", "given": "Markus", "initials": "M", "orcid": "0000-0002-8880-872X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b54361528b4c7c8f5122d91d58b36d.json"}}, {"family": "Ament-Vel\u00e1squez", "given": "Sandra Lorena", "initials": "SL"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}], "type": "journal article", "published": "2021-07-06", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "7", "issn-l": "1759-6653"}, "abstract": "Marasmius oreades is a basidiomycete fungus that grows in so called \"fairy rings,\" which are circular, underground mycelia common in lawns across temperate areas of the world. Fairy rings can be thought of as natural, long-term evolutionary experiments. As each ring has a common origin and expands radially outwards over many years, different sectors will independently accumulate mutations during growth. The genotype can be followed to the next generation, as mushrooms producing the sexual spores are formed seasonally at the edge of the ring. Here, we present new genomic data from 95 single-spore isolates of the species, which we used to construct a genetic linkage map and an updated version of the genome assembly. The 44-Mb assembly was anchored to 11 linkage groups, producing chromosome-length scaffolds. Gene annotation revealed 13,891 genes, 55% of which contained a pfam domain. The repetitive fraction of the genome was 22%, and dominated by retrotransposons and DNA elements of the KDZ and Plavaka groups. The level of assembly contiguity we present is so far rare in mushroom-forming fungi, and we expect studies of genomics, transposons, phylogenetics, and evolution to be facilitated by the data we present here of the iconic fairy-ring mushroom.", "doi": "10.1093/gbe/evab126", "pmid": "34051082", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6288491"}, {"db": "pmc", "key": "PMC8290104"}, {"db": "Dryad", "key": "10.5061/dryad.000000034"}], "notes": [], "created": "2022-11-09T15:48:09.737Z", "modified": "2024-01-16T13:48:39.144Z"}, {"entity": "publication", "iuid": "b4b7cd80fc134196bac1013b8e838d13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4b7cd80fc134196bac1013b8e838d13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4b7cd80fc134196bac1013b8e838d13"}}, "title": "Comparative Genomics Reveals Factors Associated with Phenotypic Expression of Wolbachia.", "authors": [{"family": "Bai\u00e3o", "given": "Guilherme Costa", "initials": "GC"}, {"family": "Janice", "given": "Jessin", "initials": "J"}, {"family": "Galinou", "given": "Maria", "initials": "M"}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications.scilifelab.se/researcher/409de77af489419db6d2b599b590d02f.json"}}], "type": "journal article", "published": "2021-07-06", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "7", "issn-l": "1759-6653"}, "abstract": "Wolbachia is a widespread, vertically transmitted bacterial endosymbiont known for manipulating arthropod reproduction. Its most common form of reproductive manipulation is cytoplasmic incompatibility (CI), observed when a modification in the male sperm leads to embryonic lethality unless a compatible rescue factor is present in the female egg. CI attracts scientific attention due to its implications for host speciation and in the use of Wolbachia for controlling vector-borne diseases. However, our understanding of CI is complicated by the complexity of the phenotype, whose expression depends on both symbiont and host factors. In the present study, we perform a comparative analysis of nine complete Wolbachia genomes with known CI properties in the same genetic host background, Drosophila simulans STC. We describe genetic differences between closely related strains and uncover evidence that phages and other mobile elements contribute to the rapid evolution of both genomes and phenotypes of Wolbachia. Additionally, we identify both known and novel genes associated with the modification and rescue functions of CI. We combine our observations with published phenotypic information and discuss how variability in cif genes, novel CI-associated genes, and Wolbachia titer might contribute to poorly understood aspects of CI such as strength and bidirectional incompatibility. We speculate that high titer CI strains could be better at invading new hosts already infected with a CI Wolbachia, due to a higher rescue potential, and suggest that titer might thus be a relevant parameter to consider for future strategies using CI Wolbachia in biological control.", "doi": "10.1093/gbe/evab111", "pmid": "34003269", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6277727"}, {"db": "pmc", "key": "PMC8290115"}], "notes": [], "created": "2022-11-09T15:49:14.203Z", "modified": "2024-01-16T13:48:39.158Z"}, {"entity": "publication", "iuid": "cd197346a3404e49b2b51b03e1b7f753", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd197346a3404e49b2b51b03e1b7f753.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd197346a3404e49b2b51b03e1b7f753"}}, "title": "High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui.", "authors": [{"family": "Zhang", "given": "Linlin", "initials": "L", "orcid": "0000-0003-0247-7710", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a9f542614414a63a2435f1e0790be58.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Reed", "given": "Robert D", "initials": "RD"}], "type": "journal article", "published": "2021-07-06", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "7", "issn-l": "1759-6653"}, "abstract": "The painted lady butterfly, Vanessa cardui, has the longest migration routes, the widest hostplant diversity, and one of the most complex wing patterns of any insect. Due to minimal culturing requirements, easily characterized wing pattern elements, and technical feasibility of CRISPR/Cas9 genome editing, V. cardui is emerging as a functional genomics model for diverse research programs. Here, we report a high-quality, annotated genome assembly of the V. cardui genome, generated using 84\u00d7 coverage of PacBio long-read data, which we assembled into 205 contigs with a total length of 425.4 Mb (N50 = 10.3 Mb). The genome was very complete (single-copy complete Benchmarking Universal Single-Copy Orthologs [BUSCO] 97%), with contigs assembled into presumptive chromosomes using synteny analyses. Our annotation used embryonic, larval, and pupal transcriptomes, and 20 transcriptomes across five different wing developmental stages. Gene annotations showed a high level of accuracy and completeness, with 14,437 predicted protein-coding genes. This annotated genome assembly constitutes an important resource for diverse functional genomic studies ranging from the developmental genetic basis of butterfly color pattern, to coevolution with diverse hostplants.", "doi": "10.1093/gbe/evab145", "pmid": "34282459", "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": "6310739"}, {"db": "pmc", "key": "PMC8290113"}], "notes": [], "created": "2021-10-01T09:02:33.146Z", "modified": "2024-01-16T13:48:39.151Z"}, {"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": "7a887e2d751543cda0fd97112b70afe0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a887e2d751543cda0fd97112b70afe0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a887e2d751543cda0fd97112b70afe0"}}, "title": "Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album).", "authors": [{"family": "Celorio-Mancera", "given": "Maria de la Paz", "initials": "MP", "orcid": "0000-0003-0296-0577", "researcher": {"href": "https://publications.scilifelab.se/researcher/2abfa65f99b44f1ba6f8f0e6f3d7d8a4.json"}}, {"family": "Rastas", "given": "Pasi", "initials": "P", "orcid": "0000-0003-2768-1339", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a8f5f2160154bdfa0b21dfc132d4871.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Nylin", "given": "Soren", "initials": "S", "orcid": "0000-0003-4195-8920", "researcher": {"href": "https://publications.scilifelab.se/researcher/68d7f780ed30472eb2af408b0762c14d.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.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": "The comma butterfly (Polygonia c-album, Nymphalidae, Lepidoptera) is a model insect species, most notably in the study of phenotypic plasticity and plant-insect coevolutionary interactions. In order to facilitate the integration of genomic tools with a diverse body of ecological and evolutionary research, we assembled the genome of a Swedish comma using 10X sequencing, scaffolding with matepair data, genome polishing, and assignment to linkage groups using a high-density linkage map. The resulting genome is 373 Mb in size, with a scaffold N50 of 11.7 Mb and contig N50 of 11,2Mb. The genome contained 90.1% of single-copy Lepidopteran orthologs in a BUSCO analysis of 5,286 genes. A total of 21,004 gene-models were annotated on the genome using RNA-Seq data from larval and adult tissue in combination with proteins from the Arthropoda database, resulting in a high-quality annotation for which functional annotations were generated. We further documented the quality of the chromosomal assembly via synteny assessment with Melitaea cinxia. The resulting annotated, chromosome-level genome will provide an important resource for investigating coevolutionary dynamics and comparative analyses in Lepidoptera.", "doi": "10.1093/gbe/evab054", "pmid": "33749729", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6179806"}, {"db": "pmc", "key": "PMC8140205"}], "notes": [], "created": "2021-06-09T12:14:35.404Z", "modified": "2024-01-16T13:48:39.799Z"}, {"entity": "publication", "iuid": "84ed076056f343a9bbd9ab0dfa94e830", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84ed076056f343a9bbd9ab0dfa94e830.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84ed076056f343a9bbd9ab0dfa94e830"}}, "title": "The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes.", "authors": [{"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "Mugal", "given": "Carina F", "initials": "CF"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2021-05-07", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "13", "issue": "5", "pages": null}, "abstract": "Recombination reshuffles the alleles of a population through crossover and gene conversion. These mechanisms have considerable consequences on the evolution and maintenance of genetic diversity. Crossover, for example, can increase genetic diversity by breaking the linkage between selected and nearby neutral variants. Bias in favor of G or C alleles during gene conversion may instead promote the fixation of one allele over the other, thus decreasing diversity. Mutation bias from G or C to A and T opposes GC-biased gene conversion (gBGC). Less recognized is that these two processes may-when balanced-promote genetic diversity. Here, we investigate how gBGC and mutation bias shape genetic diversity patterns in wood white butterflies (Leptidea sp.). This constitutes the first in-depth investigation of gBGC in butterflies. Using 60 resequenced genomes from six populations of three species, we find substantial variation in the strength of gBGC across lineages. When modeling the balance of gBGC and mutation bias and comparing analytical results with empirical data, we reject gBGC as the main determinant of genetic diversity in these butterfly species. As alternatives, we consider linked selection and GC content. We find evidence that high values of both reduce diversity. We also show that the joint effects of gBGC and mutation bias can give rise to a diversity pattern which resembles the signature of linked selection. Consequently, gBGC should be considered when interpreting the effects of linked selection on levels of genetic diversity.", "doi": "10.1093/gbe/evab064", "pmid": "33760095", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "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": "6184863"}, {"db": "pmc", "key": "PMC8175052"}, {"db": "Dryad", "key": "10.5061/dryad.fj6q573tr"}], "notes": [], "created": "2021-10-01T09:00:15.619Z", "modified": "2024-01-16T13:48:39.792Z"}, {"entity": "publication", "iuid": "a2d13b3a7d06427ca07ff4187f6fcba5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2d13b3a7d06427ca07ff4187f6fcba5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2d13b3a7d06427ca07ff4187f6fcba5"}}, "title": "The Genetic Variation of Lactase Persistence Alleles in Sudan and South Sudan.", "authors": [{"family": "Hollfelder", "given": "Nina", "initials": "N", "orcid": "0000-0002-1567-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f81a63833c146999d73fa38f588ea06.json"}}, {"family": "Babiker", "given": "Hiba", "initials": "H"}, {"family": "Graneh\u00e4ll", "given": "Lena", "initials": "L"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2021-05-07", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "5", "issn-l": "1759-6653"}, "abstract": "Lactase persistence (LP) is a well-studied example of a Mendelian trait under selection in some human groups due to gene-culture coevolution. We investigated the frequencies of genetic variants linked to LP in Sudanese and South Sudanese populations. These populations have diverse subsistence patterns, and some are dependent on milk to various extents, not only from cows but also from other livestock such as camels and goats. We sequenced a 316-bp region involved in regulating the expression of the LCT gene on chromosome 2, which encompasses five polymorphisms that have been associated with LP. Pastoralist populations showed a higher frequency of LP-associated alleles compared with nonpastoralist groups, hinting at positive selection also among northeast African pastoralists. Among the LP variants, the -14009:G variant occurs at the highest frequency among the investigated populations, followed by the -13915:G variant, which is likely of Middle Eastern origin, consistent with Middle Eastern gene flow to the Sudanese populations. There was no incidence of the \"East African\" LP allele (-14010:C) in the Sudanese and South Sudanese groups, and only one heterozygous individual for the \"European\" LP allele (-13910:T), suggesting limited recent admixture from these geographic regions. The Beja population of the Beni Amer show three different LP variants at substantial and similar levels, resulting in one of the greatest aggregation of LP variants among all populations across the world.", "doi": "10.1093/gbe/evab065", "pmid": "33760047", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6184864"}, {"db": "pmc", "key": "PMC8175049"}], "notes": [], "created": "2021-11-24T13:28:47.376Z", "modified": "2024-01-16T13:48:39.785Z"}, {"entity": "publication", "iuid": "16f5fafc79fd4f70bc29ffa58e7359c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16f5fafc79fd4f70bc29ffa58e7359c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16f5fafc79fd4f70bc29ffa58e7359c2"}}, "title": "Genome Size Reduction and Transposon Activity Impact tRNA Gene Diversity While Ensuring Translational Stability in Birds.", "authors": [{"family": "Ottenburghs", "given": "Jente", "initials": "J"}, {"family": "Geng", "given": "Keyi", "initials": "K"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Kutter", "given": "Claudia", "initials": "C"}], "type": "journal article", "published": "2021-04-05", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "4", "issn-l": "1759-6653"}, "abstract": "As a highly diverse vertebrate class, bird species have adapted to various ecological systems. How this phenotypic diversity can be explained genetically is intensively debated and is likely grounded in differences in the genome content. Larger and more complex genomes could allow for greater genetic regulation that results in more phenotypic variety. Surprisingly, avian genomes are much smaller compared to other vertebrates but contain as many protein-coding genes as other vertebrates. This supports the notion that the phenotypic diversity is largely determined by selection on non-coding gene sequences. Transfer RNAs (tRNAs) represent a group of non-coding genes. However, the characteristics of tRNA genes across bird genomes have remained largely unexplored. Here, we exhaustively investigated the evolution and functional consequences of these crucial translational regulators within bird species and across vertebrates. Our dense sampling of 55 avian genomes representing each bird order revealed an average of 169 tRNA genes with at least 31% being actively used. Unlike other vertebrates, avian tRNA genes are reduced in number and complexity but are still in line with vertebrate wobble pairing strategies and mutation-driven codon usage. Our detailed phylogenetic analyses further uncovered that new tRNA genes can emerge through multiplication by transposable elements. Together, this study provides the first comprehensive avian and cross-vertebrate tRNA gene analyses and demonstrates that tRNA gene evolution is flexible albeit constrained within functional boundaries of general mechanisms in protein translation.", "doi": "10.1093/gbe/evab016", "pmid": "33533905", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6127176"}, {"db": "pmc", "key": "PMC8044555"}], "notes": [], "created": "2022-11-09T15:43:36.588Z", "modified": "2024-01-16T13:48:40.125Z"}, {"entity": "publication", "iuid": "23a4dd2d16fc4cdbab714f9680296e55", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23a4dd2d16fc4cdbab714f9680296e55.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23a4dd2d16fc4cdbab714f9680296e55"}}, "title": "Variants That Differentiate Wolf and Dog Populations Are Enriched in Regulatory Elements.", "authors": [{"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P"}, {"family": "Yanhu", "given": "Liu", "initials": "L"}, {"family": "Xu", "given": "Jinrui", "initials": "J"}, {"family": "Kubinyi", "given": "Eniko", "initials": "E"}, {"family": "Wang", "given": "Guo-Dong", "initials": "GD"}, {"family": "Savolainen", "given": "Peter", "initials": "P"}], "type": "letter", "published": "2021-04-05", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "4", "issn-l": "1759-6653"}, "abstract": "Research on the genetics of domestication most often focuses on the protein-coding exons. However, exons cover only a minor part (1-2%) of the canine genome, whereas functional mutations may be located also in regions beyond the exome, in regulatory regions. Therefore, a large proportion of phenotypical differences between dogs and wolves may remain genetically unexplained. In this study, we identified variants that have high allelic frequency differences (i.e., highly differentiated variants) between wolves and dogs across the canine genome and investigated the potential functionality. We found that the enrichment of highly differentiated variants was substantially higher in promoters than in exons and that such variants were enriched also in enhancers. Several enriched pathways were identified including oxytocin signaling, carbohydrate digestion and absorption, cancer risk, and facial and body features, many of which reflect phenotypes of potential importance during domestication, including phenotypes of the domestication syndrome. The results highlight the importance of regulatory mutations during dog domestication and motivate the functional annotation of the noncoding part of the canine genome.", "doi": "10.1093/gbe/evab076", "pmid": "33929504", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6261009"}, {"db": "pmc", "key": "PMC8086526"}], "notes": [], "created": "2022-11-09T15:45:59.324Z", "modified": "2024-01-16T13:48:40.113Z"}, {"entity": "publication", "iuid": "f9024c2fa0084cab8c1823079ad4453e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9024c2fa0084cab8c1823079ad4453e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9024c2fa0084cab8c1823079ad4453e"}}, "title": "Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species.", "authors": [{"family": "Zhong", "given": "Xiuqin", "initials": "X"}, {"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "R\u00e5berg", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2021-03-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "3", "issn-l": "1759-6653"}, "abstract": "Differences in immune function between species could be a result of interspecific divergence in coding sequence and/or expression of immune genes. Here, we investigate how the degree of divergence in coding sequence and expression differs between functional categories of immune genes, and if differences between categories occur independently of other factors (expression level, pleiotropy). To this end, we compared spleen transcriptomes of wild-caught yellow-necked mice and bank voles. Immune genes expressed in the spleen were divided into four categories depending on the function of the encoded protein: pattern recognition receptors (PRR); signal transduction proteins; transcription factors; and cyto- and chemokines and their receptors. Genes encoding PRR and cyto-/chemokines had higher sequence divergence than genes encoding signal transduction proteins and transcription factors, even when controlling for potentially confounding factors. Genes encoding PRR also had higher expression divergence than genes encoding signal transduction proteins and transcription factors. There was a positive correlation between expression divergence and coding sequence divergence, in particular for PRR genes. We propose that this is a result of that divergence in PRR coding sequence leads to divergence in PRR expression through positive feedback of PRR ligand binding on PRR expression. When controlling for sequence divergence, expression divergence of PRR genes did not differ from other categories. Taken together, the results indicate that coding sequence divergence of PRR genes is a major cause of differences in immune function between species.", "doi": "10.1093/gbe/evab023", "pmid": "33565592", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6132239"}, {"db": "pmc", "key": "PMC7936018"}, {"db": "Dryad", "key": "10.5061/dryad.ncjsxkss3"}], "notes": [], "created": "2021-06-09T12:15:43.130Z", "modified": "2024-01-16T13:48:40.554Z"}, {"entity": "publication", "iuid": "8c725797e27b4b119d9673fe03884c05", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c725797e27b4b119d9673fe03884c05.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c725797e27b4b119d9673fe03884c05"}}, "title": "Genomic Evidence of an Ancient East Asian Divergence Event in Wild Saccharomyces cerevisiae.", "authors": [{"family": "Bendixsen", "given": "Devin P", "initials": "DP", "orcid": "0000-0003-0831-7646", "researcher": {"href": "https://publications.scilifelab.se/researcher/533f0c534a214ee68a037b243a63a028.json"}}, {"family": "Gettle", "given": "Noah", "initials": "N"}, {"family": "Gilchrist", "given": "Ciaran", "initials": "C"}, {"family": "Zhang", "given": "Zebin", "initials": "Z"}, {"family": "Stelkens", "given": "Rike", "initials": "R", "orcid": "0000-0002-8530-0656", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b3449c244a4c13b8610e401f4cbef4.json"}}], "type": "journal article", "published": "2021-02-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "2", "pages": null, "issn-l": "1759-6653"}, "abstract": "Comparative genome analyses have suggested East Asia to be the cradle of the domesticated microbe Brewer's yeast (Saccharomyces cerevisiae), used in the food and biotechnology industry worldwide. Here, we provide seven new, high-quality long-read genomes of nondomesticated yeast strains isolated from primeval forests and other natural environments in China and Taiwan. In a comprehensive analysis of our new genome assemblies, along with other long-read Saccharomycetes genomes available, we show that the newly sequenced East Asian strains are among the closest living relatives of the ancestors of the global diversity of Brewer's yeast, confirming predictions made from short-read genomic data. Three of these strains (termed the East Asian Clade IX Complex here) share a recent ancestry and evolutionary history suggesting an early divergence from other S. cerevisiae strains before the larger radiation of the species, and prior to its domestication. Our genomic analyses reveal that the wild East Asian strains contain elevated levels of structural variations. The new genomic resources provided here contribute to our understanding of the natural diversity of S. cerevisiae, expand the intraspecific genetic variation found in this heavily domesticated microbe, and provide a foundation for understanding its origin and global colonization history.", "doi": "10.1093/gbe/evab001", "pmid": "33432360", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6081032"}, {"db": "pmc", "key": "PMC7874999"}], "notes": [], "created": "2021-02-17T19:22:12.576Z", "modified": "2024-01-16T13:48:40.778Z"}, {"entity": "publication", "iuid": "da5d0305f08e461393fa1eb8676813d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da5d0305f08e461393fa1eb8676813d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da5d0305f08e461393fa1eb8676813d0"}}, "title": "From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps.", "authors": [{"family": "Gobbo", "given": "Erik", "initials": "E", "orcid": "0000-0001-9897-8610", "researcher": {"href": "https://publications.scilifelab.se/researcher/107736ba83dc4131b9b1f2033ce85d18.json"}}, {"family": "Lartillot", "given": "Nicolas", "initials": "N"}, {"family": "Hearn", "given": "Jack", "initials": "J", "orcid": "0000-0003-3358-4949", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fac223647864b76a5a7783ed7c19138.json"}}, {"family": "Stone", "given": "Graham N", "initials": "GN"}, {"family": "Abe", "given": "Yoshihisa", "initials": "Y"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Ide", "given": "Tatsuya", "initials": "T"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F"}], "type": "comparative study", "published": "2020-11-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "12", "issue": "11", "pages": "2060-2073", "issn-l": "1759-6653"}, "abstract": "Gall wasps (Hymenoptera: Cynipidae) induce complex galls on oaks, roses, and other plants, but the mechanism of gall induction is still unknown. Here, we take a comparative genomic approach to revealing the genetic basis of gall induction. We focus on Synergus itoensis, a species that induces galls inside oak acorns. Previous studies suggested that this species evolved the ability to initiate gall formation recently, as it is deeply nested within the genus Synergus, whose members are mostly inquilines that develop inside the galls of other species. We compared the genome of S. itoensis with that of three related Synergus inquilines to identify genomic changes associated with the origin of gall induction. We used a novel Bayesian selection analysis, which accounts for branch-specific and gene-specific selection effects, to search for signatures of selection in 7,600 single-copy orthologous genes shared by the four Synergus species. We found that the terminal branch leading to S. itoensis had more genes with a significantly elevated dN/dS ratio (positive signature genes) than the other terminal branches in the tree; the S. itoensis branch also had more genes with a significantly decreased dN/dS ratio. Gene set enrichment analysis showed that the positive signature gene set of S. itoensis, unlike those of the inquiline species, is enriched in several biological process Gene Ontology terms, the most prominent of which is \"Ovarian Follicle Cell Development.\" Our results indicate that the origin of gall induction is associated with distinct genomic changes, and provide a good starting point for further characterization of the genes involved.", "doi": "10.1093/gbe/evaa204", "pmid": "32986797", "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": "5912529"}, {"db": "pmc", "key": "PMC7674688"}], "notes": [], "created": "2020-12-07T16:28:56.741Z", "modified": "2024-01-16T13:48:41.438Z"}, {"entity": "publication", "iuid": "146c61589294400ca507989d19c6b16a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/146c61589294400ca507989d19c6b16a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/146c61589294400ca507989d19c6b16a"}}, "title": "A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes.", "authors": [{"family": "Cauz-Santos", "given": "Luiz Augusto", "initials": "LA"}, {"family": "da Costa", "given": "Zirlane Portugal", "initials": "ZP"}, {"family": "Callot", "given": "Caroline", "initials": "C"}, {"family": "Cauet", "given": "St\u00e9phane", "initials": "S"}, {"family": "Zucchi", "given": "Maria Imaculada", "initials": "MI"}, {"family": "Berg\u00e8s", "given": "H\u00e9l\u00e8ne", "initials": "H"}, {"family": "van den Berg", "given": "C\u00e1ssio", "initials": "C"}, {"family": "Vieira", "given": "Maria Lucia Carneiro", "initials": "MLC", "orcid": "0000-0003-0341-5714", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb37815cd9e4577b677fd053bf6e15c.json"}}], "type": "comparative study", "published": "2020-10-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "12", "issue": "10", "pages": "1841-1857", "issn-l": "1759-6653"}, "abstract": "Chloroplast genomes (cpDNA) in angiosperms are usually highly conserved. Although rearrangements have been observed in some lineages, such as Passiflora, the mechanisms that lead to rearrangements are still poorly elucidated. In the present study, we obtained 20 new chloroplast genomes (18 species from the genus Passiflora, and Dilkea retusa and Mitostemma brevifilis from the family Passifloraceae) in order to investigate cpDNA evolutionary history in this group. Passiflora cpDNAs vary in size considerably, with \u223c50 kb between shortest and longest. Large inverted repeat (IR) expansions were identified, and at the extreme opposite, the loss of an IR was detected for the first time in Passiflora, a rare event in angiosperms. The loss of an IR region was detected in Passiflora capsularis and Passiflora costaricensis, a species in which occasional biparental chloroplast inheritance has previously been reported. A repertory of rearrangements such as inversions and gene losses were detected, making Passiflora one of the few groups with complex chloroplast genome evolution. We also performed a phylogenomic study based on all the available cp genomes and our analysis implies that there is a need to reconsider the taxonomic classifications of some species in the group.", "doi": "10.1093/gbe/evaa155", "pmid": "32722748", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pii", "key": "5877432"}, {"db": "pmc", "key": "PMC7586853"}], "notes": [], "created": "2020-08-25T13:00:50.882Z", "modified": "2021-11-10T12:46:41.641Z"}, {"entity": "publication", "iuid": "154532dd2cc14c359aedcbc68f77a29c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/154532dd2cc14c359aedcbc68f77a29c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/154532dd2cc14c359aedcbc68f77a29c"}}, "title": "Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness.", "authors": [{"family": "Sato", "given": "Daiki X", "initials": "DX", "orcid": "0000-0002-9527-8253", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad2eafb0bce4d2ba7c4f9cf7ed05eac.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N", "orcid": "0000-0002-3687-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b5c32bab72f430a80485c0312ca0e21.json"}}, {"family": "Ring", "given": "Henrik", "initials": "H"}, {"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Feng", "given": "Chungang", "initials": "C"}, {"family": "Blanco-Aguiar", "given": "Jos\u00e9 A", "initials": "JA"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Villafuerte", "given": "Rafael", "initials": "R"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F", "orcid": "0000-0001-7552-187X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd6bad55b67431c82e2e54e5b007917.json"}}, {"family": "Carneiro", "given": "Miguel", "initials": "M"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "comparative study", "published": "2020-10-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "12", "issue": "10", "pages": "1918-1928", "issn-l": "1759-6653"}, "abstract": "Domestication has resulted in immense phenotypic changes in animals despite their relatively short evolutionary history. The European rabbit is one of the most recently domesticated animals, but exhibits distinct morphological, physiological, and behavioral differences from their wild conspecifics. A previous study revealed that sequence variants with striking allele frequency differences between wild and domestic rabbits were enriched in conserved noncoding regions, in the vicinity of genes involved in nervous system development. This suggests that a large proportion of the genetic changes targeted by selection during domestication might affect gene regulation. Here, we generated RNA-sequencing data for four brain regions (amygdala, hypothalamus, hippocampus, and parietal/temporal cortex) sampled at birth and revealed hundreds of differentially expressed genes (DEGs) between wild and domestic rabbits. DEGs in amygdala were significantly enriched for genes associated with dopaminergic function and all 12 DEGs in this category showed higher expression in domestic rabbits. DEGs in hippocampus were enriched for genes associated with ciliary function, all 21 genes in this category showed lower expression in domestic rabbits. These results indicate an important role of dopamine signaling and ciliary function in the evolution of tameness during rabbit domestication. Our study shows that gene expression in specific pathways has been profoundly altered during domestication, but that the majority of genes showing differential expression in this study have not been the direct targets of selection.", "doi": "10.1093/gbe/evaa158", "pmid": "32835359", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5896528"}, {"db": "pmc", "key": "PMC7594241"}], "notes": [], "created": "2020-09-15T07:00:59.512Z", "modified": "2024-01-16T13:48:41.617Z"}, {"entity": "publication", "iuid": "554b086169b84ddfbfcf49c9d41e38a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/554b086169b84ddfbfcf49c9d41e38a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/554b086169b84ddfbfcf49c9d41e38a1"}}, "title": "Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum.", "authors": [{"family": "Mahajan", "given": "Mayank", "initials": "M"}, {"family": "Seeger", "given": "Christian", "initials": "C"}, {"family": "Yee", "given": "Benjamin", "initials": "B"}, {"family": "Andersson", "given": "Siv G E", "initials": "SGE", "orcid": "0000-0003-0864-0259", "researcher": {"href": "https://publications.scilifelab.se/researcher/7884a5058383428ea3cbe7fc4505f36a.json"}}], "type": "journal article", "published": "2020-09-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "12", "issue": "9", "pages": "1528-1548"}, "abstract": "Bacteria of the Planctomycetes phylum have many unique cellular features, such as extensive membrane invaginations and the ability to import macromolecules. These features raise intriguing questions about the composition of their cell envelopes. In this study, we have used microscopy, phylogenomics, and proteomics to examine the composition and evolution of cell envelope proteins in Tuwongella immobilis and other members of the Planctomycetes. Cryo-electron tomography data indicated a distance of 45 nm between the inner and outer membranes in T. immobilis. Consistent with the wide periplasmic space, our bioinformatics studies showed that the periplasmic segments of outer-membrane proteins in type II secretion systems are extended in bacteria of the order Planctomycetales. Homologs of two highly abundant cysteine-rich cell wall proteins in T. immobilis were identified in all members of the Planctomycetales, whereas genes for peptidoglycan biosynthesis and cell elongation have been lost in many members of this bacterial group. The cell wall proteins contain multiple copies of the YTV motif, which is the only domain that is conserved and unique to the Planctomycetales. Earlier diverging taxa in the Planctomycetes phylum contain genes for peptidoglycan biosynthesis but no homologs to the YTV cell wall proteins. The major remodeling of the cell envelope in the ancestor of the Planctomycetales coincided with the emergence of budding and other unique cellular phenotypes. The results have implications for hypotheses about the process whereby complex cellular features evolve in bacteria.", "doi": "10.1093/gbe/evaa159", "pmid": "32761170", "labels": {"Cryo-EM": "Service", "Integrated Microscopy Technologies Ume\u00e5": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5882020"}, {"db": "pmc", "key": "PMC7533069"}], "notes": [], "created": "2020-12-10T11:22:52.445Z", "modified": "2024-01-16T13:48:41.787Z"}, {"entity": "publication", "iuid": "55dcf41e17e8459fb3c49cd79e48f71c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55dcf41e17e8459fb3c49cd79e48f71c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55dcf41e17e8459fb3c49cd79e48f71c"}}, "title": "Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences.", "authors": [{"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "Xu", "given": "Jingzi", "initials": "J"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "comparative study", "published": "2020-07-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "12", "issue": "7", "pages": "1031-1039"}, "abstract": "Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and allowed for the discovery of thousands of new variants for use in improving the Y-chromosome phylogeny and computing estimates that are more accurate. Here, we describe the high-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparison with existing whole Y-chromosome sequence data. Due to the increased resolution, we potentially resolve the source of haplogroup B-P70 in the Khoe-San, and reconcile recently published haplogroup A-M51 data with the most recent version of the ISOGG Y-chromosome phylogeny. Our results also improve the positioning of tentatively placed new branches of the ISOGG Y-chromosome phylogeny. The distribution of major Y-chromosome haplogroups in the Khoe-San and other African groups coincide with the emerging picture of African demographic history; with E-M2 linked to the agriculturalist Bantu expansion, E-M35 linked to pastoralist eastern African migrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestry with central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San.", "doi": "10.1093/gbe/evaa098", "pmid": "32697300", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5874966"}, {"db": "pmc", "key": "PMC7375190"}], "notes": [], "created": "2020-12-08T23:25:49.670Z", "modified": "2024-01-16T13:48:42.238Z"}, {"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": "2f662c22fce1474b9d17ade9e0181ceb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f662c22fce1474b9d17ade9e0181ceb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f662c22fce1474b9d17ade9e0181ceb"}}, "title": "Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies).", "authors": [{"family": "Wang", "given": "Xi", "initials": "X"}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK", "orcid": "0000-0001-9225-7521", "researcher": {"href": "https://publications.scilifelab.se/researcher/52a2c210ff754465a69f839b40fe8312.json"}}], "type": "journal article", "published": "2020-02-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "12", "issue": "2", "pages": "3803-3817", "issn-l": "1759-6653"}, "abstract": "Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin's paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (\u03c0 = 0.0049 in Central-Europe, \u03c0 = 0.0063 in Sweden-Norway, \u03c0 = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.", "doi": "10.1093/gbe/evaa005", "pmid": "31958121", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5709816"}, {"db": "pmc", "key": "PMC7046165"}], "notes": [], "created": "2021-01-08T16:29:08.731Z", "modified": "2024-01-16T13:48:42.975Z"}, {"entity": "publication", "iuid": "a6bc07a0f8a546cfa3841bdb3032ec2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6bc07a0f8a546cfa3841bdb3032ec2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6bc07a0f8a546cfa3841bdb3032ec2e"}}, "title": "The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants.", "authors": [{"family": "Sullivan", "given": "Alexis R", "initials": "AR", "orcid": "0000-0003-2182-911X", "researcher": {"href": "https://publications.scilifelab.se/researcher/82ef3b1f7aec4a99864cd60cad55507e.json"}}, {"family": "Eldfjell", "given": "Yrin", "initials": "Y"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B", "orcid": "0000-0002-9771-467X", "researcher": {"href": "https://publications.scilifelab.se/researcher/12527c57f62e4a46b758e061ba3f80b1.json"}}, {"family": "Delhomme", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3053-0796", "researcher": {"href": "https://publications.scilifelab.se/researcher/107fbbd40f1444fb838ad4c0365738fa.json"}}, {"family": "Asp", "given": "Torben", "initials": "T", "orcid": "0000-0002-6470-2410", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcb35e5ec7f644848c5bfabc5ed79bc3.json"}}, {"family": "Hebelstrup", "given": "Kim H", "initials": "KH", "orcid": "0000-0002-3984-3633", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfc2c2091d4d4ab0998f76118ae2bbf6.json"}}, {"family": "Keech", "given": "Olivier", "initials": "O", "orcid": "0000-0002-0546-7721", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbfa829eb0b74b67aed7865dda0e15d3.json"}}, {"family": "\u00d6berg", "given": "Lisa", "initials": "L"}, {"family": "M\u00f8ller", "given": "Ian Max", "initials": "IM", "orcid": "0000-0002-7919-7787", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0f45488d984c95b7c37b57d9b559cb.json"}}, {"family": "Arvestad", "given": "Lars", "initials": "L", "orcid": "0000-0001-5341-1733", "researcher": {"href": "https://publications.scilifelab.se/researcher/27184c3c97f2457893e5232544efee24.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.json"}}, {"family": "Wang", "given": "Xiao-Ru", "initials": "XR", "orcid": "0000-0002-6150-7046", "researcher": {"href": "https://publications.scilifelab.se/researcher/186f7b1871404673a12544f5bbf7409f.json"}}], "type": "journal article", "published": "2020-01-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "12", "issue": "1", "pages": "3586-3598", "issn-l": "1759-6653"}, "abstract": "Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.", "doi": "10.1093/gbe/evz263", "pmid": "31774499", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5644343"}, {"db": "pmc", "key": "PMC6944214"}], "notes": [], "created": "2020-09-15T06:47:15.995Z", "modified": "2024-01-16T13:48:43.093Z"}, {"entity": "publication", "iuid": "5bf650cb4a7f4b749b28c33ca56fdda5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5bf650cb4a7f4b749b28c33ca56fdda5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5bf650cb4a7f4b749b28c33ca56fdda5"}}, "title": "Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.", "authors": [{"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Dinc\u0103", "given": "Vlad", "initials": "V"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2019-10-01", "journal": {"volume": "11", "issn": "1759-6653", "issue": "10", "pages": "2875-2886", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.", "doi": "10.1093/gbe/evz212", "pmid": "31580421", "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": "5580498"}, {"db": "pmc", "key": "PMC6795238"}], "notes": [], "created": "2019-12-02T17:20:06.547Z", "modified": "2024-01-16T13:48:43.736Z"}, {"entity": "publication", "iuid": "23c6366116a74e7aa39971ef231b62b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23c6366116a74e7aa39971ef231b62b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23c6366116a74e7aa39971ef231b62b0"}}, "title": "Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly.", "authors": [{"family": "H\u00f6\u00f6k", "given": "Lars", "initials": "L"}, {"family": "Leal", "given": "Luis", "initials": "L"}, {"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2019-09-01", "journal": {"volume": "11", "issn": "1759-6653", "issue": "9", "pages": "2633-2652", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "In species with genetic sex determination, dosage compensation can evolve to equal expression levels of sex-linked and autosomal genes. Current knowledge about dosage compensation has mainly been derived from male-heterogametic (XX/XY) model organisms, whereas less is understood about the process in female-heterogametic systems (ZZ/ZW). In moths and butterflies, downregulation of Z-linked expression in males (ZZ) to match the expression level in females (ZW) is often observed. However, little is known about the underlying regulatory mechanisms, or if dosage compensation patterns vary across ontogenetic stages. In this study, we assessed dynamics of Z-linked and autosomal expression levels across developmental stages in the wood white (Leptidea sinapis). We found that although expression of Z-linked genes in general was reduced compared with autosomal genes, dosage compensation was actually complete for some categories of genes, in particular sex-biased genes, but equalization in females was constrained to a narrower gene set. We also observed a noticeable convergence in Z-linked expression between males and females after correcting for sex-biased genes. Sex-biased expression increased successively across developmental stages, and male-biased genes were enriched on the Z-chromosome. Finally, all five core genes associated with the ribonucleoprotein dosage compensation complex male-specific lethal were detected in adult females, in correspondence with a reduction in the expression difference between autosomes and the single Z-chromosome. We show that tuning of gene dosage is multilayered in Lepidoptera and argue that expression balance across chromosomal classes may predominantly be driven by enrichment of male-biased genes on the Z-chromosome and cooption of available dosage regulators.", "doi": "10.1093/gbe/evz176", "pmid": "31400207", "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": "5545957"}, {"db": "pmc", "key": "PMC6761951"}], "notes": [], "created": "2019-12-02T17:20:07.341Z", "modified": "2024-01-16T13:48:43.918Z"}, {"entity": "publication", "iuid": "ea231e9b47b0493a9cbb3de5d7dcb992", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea231e9b47b0493a9cbb3de5d7dcb992.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea231e9b47b0493a9cbb3de5d7dcb992"}}, "title": "Gene Flow in the M\u00fcllerian Mimicry Ring of a Poisonous Papuan Songbird Clade (Pitohui; Aves).", "authors": [{"family": "Garg", "given": "Kritika M", "initials": "KM"}, {"family": "Sam", "given": "Katerina", "initials": "K"}, {"family": "Chattopadhyay", "given": "Balaji", "initials": "B"}, {"family": "Sadanandan", "given": "Keren R", "initials": "KR"}, {"family": "Koane", "given": "Bonny", "initials": "B"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Rheindt", "given": "Frank E", "initials": "FE"}], "type": "journal article", "published": "2019-08-01", "journal": {"volume": "11", "issn": "1759-6653", "issue": "8", "pages": "2332-2343", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "M\u00fcllerian mimicry rings are remarkable symbiotic species assemblages in which multiple members share a similar phenotype. However, their evolutionary origin remains poorly understood. Although gene flow among species has been shown to generate mimetic patterns in some Heliconius butterflies, mimicry is believed to be due to true convergence without gene flow in many other cases. We investigated the evolutionary history of multiple members of a passerine mimicry ring in the poisonous Papuan pitohuis. Previous phylogenetic evidence indicates that the aposematic coloration shared by many, but not all, members of this genus is ancestral and has only been retained by members of the mimicry ring. Using a newly assembled genome and thousands of genomic DNA markers, we demonstrate gene flow from the hooded pitohui (Pitohui dichrous) into the southern variable pitohui (Pitohui uropygialis), consistent with shared patterns of aposematic coloration. The vicinity of putatively introgressed loci is significantly enriched for genes that are important in melanin pigment expression and toxin resistance, suggesting that gene flow may have been instrumental in the sharing of plumage patterns and toxicity. These results indicate that interspecies gene flow may be a more general mechanism in generating mimicry rings than hitherto appreciated.", "doi": "10.1093/gbe/evz168", "pmid": "31418795", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "5550337"}, {"db": "pmc", "key": "PMC6735254"}], "notes": [], "created": "2019-12-02T17:20:02.909Z", "modified": "2020-01-21T13:56:15.637Z"}, {"entity": "publication", "iuid": "19f23c88f5d44289a4ff88982fe8a86d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19f23c88f5d44289a4ff88982fe8a86d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19f23c88f5d44289a4ff88982fe8a86d"}}, "title": "Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.", "authors": [{"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Tripathy", "given": "Sucheta", "initials": "S"}, {"family": "Malar C", "given": "Mathu", "initials": "M"}, {"family": "Panda", "given": "Arijit", "initials": "A"}, {"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Andreasson", "given": "Erik", "initials": "E"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}, {"family": "Whisson", "given": "Stephen C", "initials": "SC"}], "type": "journal article", "published": "2018-09-01", "journal": {"volume": "10", "issn": "1759-6653", "issue": "9", "pages": "2432-2442", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Species from the genus Phytophthora are well represented among organisms causing serious diseases on trees. Phytophthora plurivora has been implicated in long-term decline of woodland trees across Europe. Here we present a draft genome sequence of P. plurivora, originally isolated from diseased European beech (Fagus sylvatica) in Malm\u00f6, Sweden. When compared with other sequenced Phytophthora species, the P. plurivora genome assembly is relatively compact, spanning 41\u2009Mb. This is organized in 1,919 contigs and 1,898 scaffolds, encompassing 11,741 predicted genes, and has a repeat content of approximately 15%. Comparison of allele frequencies revealed evidence for tetraploidy in the sequenced isolate. As in other sequenced Phytophthora species, P. plurivora possesses genes for pathogenicity-associated RXLR and Crinkle and Necrosis effectors, predominantly located in gene-sparse genomic regions. Comparison of the P. plurivora RXLR effectors with orthologs in other sequenced species in the same clade (Phytophthora multivora and Phytophthora capsici) revealed that the orthologs were likely to be under neutral or purifying selection.", "doi": "10.1093/gbe/evy162", "pmid": "30060094", "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": "5061551"}, {"db": "pmc", "key": "PMC6152947"}], "notes": [], "created": "2018-10-31T19:48:03.537Z", "modified": "2024-01-16T13:48:45.560Z"}, {"entity": "publication", "iuid": "64721e82902c46b0826f678881b284b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64721e82902c46b0826f678881b284b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64721e82902c46b0826f678881b284b5"}}, "title": "Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids", "authors": [{"family": "Narrowe", "given": "Adrienne B", "initials": "AB"}, {"family": "Spang", "given": "Anja", "initials": "A"}, {"family": "Stairs", "given": "Courtney W", "initials": "CW"}, {"family": "Caceres", "given": "Eva F", "initials": "EF"}, {"family": "Baker", "given": "Brett J", "initials": "BJ"}, {"family": "Miller", "given": "Christopher S", "initials": "CS"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}], "type": "journal-article", "published": "2018-09-01", "journal": {"volume": "10", "issn": "1759-6653", "issue": "9", "pages": "2380-2393", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": null, "doi": "10.1093/gbe/evy154", "pmid": "30060184", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-12-10T06:26:59.627Z", "modified": "2020-01-21T13:56:12.125Z"}, {"entity": "publication", "iuid": "77bb5a125912473b99cbdc00c8121a2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/77bb5a125912473b99cbdc00c8121a2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/77bb5a125912473b99cbdc00c8121a2d"}}, "title": "A genetic map of ostrich Z chromosome and the role of inversions in avian sex chromosome evolution.", "authors": [{"family": "Papoli Yazdi", "given": "Homa", "initials": "H"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2018-08-07", "journal": {"volume": null, "issn": "1759-6653", "issue": null, "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Recombination arrest is a necessary step for the evolution of distinct sex chromosomes. Structural changes, such as inversions, may represent the mechanistic basis for recombination suppression and comparisons of the structural organization of chromosomes as given by chromosome-level assemblies offer the possibility to infer inversions across species at some detail. In birds, deduction of the process of sex chromosome evolution has been hampered by the lack of a validated chromosome-level assembly from a representative of one of the two basal clades of modern birds, Paleognathae. We therefore developed a high-density genetic linkage map of the ostrich Z chromosome and used this to correct an existing assembly, including correction of a large chimeric superscaffold and the order and orientation of other superscaffolds. We identified the pseudoautosomal region (PAR) as a 52\u2009Mb segment (\u224860% of the Z chromosome) where recombination occurred in both sexes. By comparing the order and location of genes on the ostrich Z chromosome with that of six bird species from the other major clade of birds (Neognathae), and of reptilian outgroup species, 25 Z-linked inversions were inferred in the avian lineages. We defined Z chromosome organization in an early avian ancestor and identified inversions spanning the candidate sex-determining DMRT1 gene in this ancestor, which could potentially have triggered the onset of avian sex chromosome evolution. We conclude that avian sex chromosome evolution has been characterized by a complex process of probably both Z-linked and W-linked inversions (and/or other processes). This study illustrates the need for validated chromosome-level assemblies for inference of genome evolution.", "doi": "10.1093/gbe/evy163", "pmid": "30099482", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5067707"}], "notes": [], "created": "2018-08-16T15:30:10.251Z", "modified": "2024-01-16T13:48:45.796Z"}, {"entity": "publication", "iuid": "7288c350f11e45b4986bd6fa6331f24d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7288c350f11e45b4986bd6fa6331f24d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7288c350f11e45b4986bd6fa6331f24d"}}, "title": "Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies.", "authors": [{"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Kalsoom", "given": "Faheema", "initials": "F"}, {"family": "Dinca", "given": "Vlad", "initials": "V"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2017-10-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "10", "pages": "2491-2505", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643\u2009Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72\u2009Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths.", "doi": "10.1093/gbe/evx163", "pmid": "28981642", "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": "4091610"}, {"db": "BioProject", "description": "Rapid increase in genome size as a consequence of transposable element hyperactivity in wood-white (Leptidea) butterflies.", "key": "PRJEB21838"}, {"db": "GENBANK", "description": "Leptidea sinapis, whole genome shotgun sequencing project", "key": "FZQP00000000"}], "notes": [], "created": "2017-10-30T09:27:46.367Z", "modified": "2024-01-16T13:48:47.456Z"}, {"entity": "publication", "iuid": "dbef244a97744185a5325c6bdeaf9b13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbef244a97744185a5325c6bdeaf9b13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbef244a97744185a5325c6bdeaf9b13"}}, "title": "The Evolution of Dark Matter in the Mitogenome of Seed Beetles", "authors": [{"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Immonen", "given": "Elina", "initials": "E"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G"}], "type": "journal-article", "published": "2017-10-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "10", "pages": "2697-2706", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": null, "doi": "10.1093/gbe/evx205", "pmid": "29048527", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "GENBANK", "description": "Callosobruchus maculatus from India mitochondrion, complete genome", "key": "KY856743"}, {"db": "GENBANK", "description": "Callosobruchus chinensis mitochondrion, complete genome", "key": "KY856744"}, {"db": "GENBANK", "description": "Callosobruchus analis mitochondrion, complete genome", "key": "KY856745"}, {"db": "GENBANK", "description": "Callosobruchus maculatus from Brazil mitochondrion, complete genome", "key": "KY942060"}, {"db": "GENBANK", "description": "Callosobruchus maculatus from USA mitochondrion, complete genome", "key": "KY942061"}, {"db": "GENBANK", "description": "Callosobruchus maculatus from Yemen mitochondrion, complete genome", "key": "KY942062"}, {"db": "GENBANK", "description": "Acanthoscelides obtectus mitochondrion, complete genome", "key": "MF925724"}], "notes": [], "created": "2017-10-13T08:02:37.993Z", "modified": "2024-01-16T13:48:47.441Z"}, {"entity": "publication", "iuid": "f57321685c0b4169a4414640c3787e7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f57321685c0b4169a4414640c3787e7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f57321685c0b4169a4414640c3787e7f"}}, "title": "The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.", "authors": [{"family": "Evkaikina", "given": "Anastasiia I", "initials": "AI"}, {"family": "Berke", "given": "Lidija", "initials": "L"}, {"family": "Romanova", "given": "Marina A", "initials": "MA"}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E"}, {"family": "Ivanova", "given": "Alexandra N", "initials": "AN"}, {"family": "Rydin", "given": "Catarina", "initials": "C"}, {"family": "Pawlowski", "given": "Katharina", "initials": "K"}, {"family": "Voitsekhovskaja", "given": "Olga V", "initials": "OV"}], "type": "journal article", "published": "2017-09-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "9", "pages": "2444-2460", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Lycopodiophyta-consisting of three orders, Lycopodiales, Isoetales and Selaginellales, with different types of shoot apical meristems (SAMs)-form the earliest branch among the extant vascular plants. They represent a sister group to all other vascular plants, from which they differ in that their leaves are microphylls-that is, leaves with a single, unbranched vein, emerging from the protostele without a leaf gap-not megaphylls. All leaves represent determinate organs originating on the flanks of indeterminate SAMs. Thus, leaf formation requires the suppression of indeterminacy, that is, of KNOX transcription factors. In seed plants, this is mediated by different groups of transcription factors including ARP and YABBY.We generated a shoot tip transcriptome of Huperzia selago (Lycopodiales) to examine the genes involved in leaf formation. Our H. selago transcriptome does not contain any ARP homolog, although transcriptomes of Selaginella spp. do. Surprisingly, we discovered a YABBY homolog, although these transcription factors were assumed to have evolved only in seed plants.The existence of a YABBY homolog in H. selago suggests that YABBY evolved already in the common ancestor of the vascular plants, and subsequently was lost in some lineages like Selaginellales, whereas ARP may have been lost in Lycopodiales. The presence of YABBY in the common ancestor of vascular plants would also support the hypothesis that this common ancestor had a simplex SAM. Furthermore, a comparison of the expression patterns of ARP in shoot tips of Selaginella kraussiana (Harrison CJ, etal. 2005. Independent recruitment of a conserved developmental mechanism during leaf evolution. Nature 434(7032):509-514.) and YABBY in shoot tips of H. selago implies that the development of microphylls, unlike megaphylls, does not seem to depend on the combined activities of ARP and YABBY. Altogether, our data show that Lycopodiophyta are a diverse group; so, in order to understand the role of Lycopodiophyta in evolution, representatives of Lycopodiales, Selaginellales, as well as of Isoetales, have to be examined.", "doi": "10.1093/gbe/evx169", "pmid": "28957460", "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": "4097580"}, {"db": "pmc", "key": "PMC5622374"}, {"db": "BioProject", "description": "DNA sequencing data", "key": "PRJNA281995"}], "notes": [], "created": "2017-11-03T16:20:59.430Z", "modified": "2024-01-16T13:48:47.550Z"}, {"entity": "publication", "iuid": "728551f2381b43668a2a2516d07437aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/728551f2381b43668a2a2516d07437aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/728551f2381b43668a2a2516d07437aa"}}, "title": "Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations", "authors": [{"family": "Wang", "given": "Mi", "initials": "M"}, {"family": "Uebbing", "given": "Severin", "initials": "S"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2017-05-00", "journal": {"volume": "9", "issn": "1759-6653", "issue": "5", "pages": "1266-1279", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": null, "doi": "10.1093/gbe/evx080", "pmid": "28453623", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:57:46.835Z", "modified": "2020-01-21T13:56:11.723Z"}, {"entity": "publication", "iuid": "6bc70b0130924ae9bc7190acaeb79387", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6bc70b0130924ae9bc7190acaeb79387.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6bc70b0130924ae9bc7190acaeb79387"}}, "title": "Mating Changes Sexually Dimorphic Gene Expression in the Seed Beetle Callosobruchus maculatus.", "authors": [{"family": "Immonen", "given": "Elina", "initials": "E"}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Bayram", "given": "Helen", "initials": "H"}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2017-03-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "3", "pages": "677-699", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Sexually dimorphic phenotypes arise largely from sex-specific gene expression, which has mainly been characterized in sexually na\u00efve adults. However, we expect sexual dimorphism in transcription to be dynamic and dependent on factors such as reproductive status. Mating induces many behavioral and physiological changes distinct to each sex and is therefore expected to activate regulatory changes in many sex-biased genes. Here, we first characterized sexual dimorphism in gene expression in Callosobruchus maculatus seed beetles. We then examined how females and males respond to mating and how it affects sex-biased expression, both in sex-limited (abdomen) and sex-shared (head and thorax) tissues. Mating responses were largely sex-specific and, as expected, females showed more genes responding compared with males (\u223c2,000 vs. \u223c300 genes in the abdomen, \u223c500 vs. \u223c400 in the head and thorax, respectively). Of the sex-biased genes present in virgins, 16% (1,041 genes) in the abdomen and 17% (243 genes) in the head and thorax altered their relative expression between the sexes as a result of mating. Sex-bias status changed in 2% of the genes in the abdomen and 4% in the head and thorax following mating. Mating responses involved de-feminization of females and, to a lesser extent, de-masculinization of males relative to their virgin state: mating decreased rather than increased dimorphic expression of sex-biased genes. The fact that regulatory changes of both types of sex-biased genes occurred in both sexes suggests that male- and female-specific selection is not restricted to male- and female-biased genes, respectively, as is sometimes assumed.", "doi": "10.1093/gbe/evx029", "pmid": "28391318", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "3039479"}], "notes": [], "created": "2017-10-17T09:27:20.453Z", "modified": "2024-01-16T13:48:48.324Z"}, {"entity": "publication", "iuid": "cc6d03a2e6e0461bb7362c42487fbec8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc6d03a2e6e0461bb7362c42487fbec8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc6d03a2e6e0461bb7362c42487fbec8"}}, "title": "The Mycobacterium phlei Genome: Expectations and Surprises.", "authors": [{"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BM"}, {"family": "Behra", "given": "Phani Rama Krishna", "initials": "PR"}, {"family": "Ramesh", "given": "Malavika", "initials": "M"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Bhattacharya", "given": "Alok", "initials": "A"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal article", "published": "2016-04-08", "journal": {"volume": "8", "issn": "1759-6653", "issue": "4", "pages": "975-985", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 1898-1899. We present the complete genome sequence for theM. phlei CCUG21000(T)type strain and the draft genomes for four additional strains. The genome size for all five is 5.3 Mb with 69.4% Guanine-Cytosine content. This is \u22480.35 Mbp smaller than the previously reported M. phlei RIVM draft genome. The size difference is attributed partly to large bacteriophage sequence fragments in theM. phlei RIVM genome. Comparative analysis revealed the following: 1) A CRISPR system similar to Type 1E (cas3) in M. phlei RIVM; 2) genes involved in polyamine metabolism and transport (potAD,potF) that are absent in other mycobacteria, and 3) strain-specific variations in the number of \u03c3-factor genes. Moreover,M. phlei has as many as 82 mce(mammalian cell entry) homologs and many of the horizontally acquired genes in M. phlei are present in other environmental bacteria including mycobacteria that share similar habitat. Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and Mycobacterium rhodesiae NBB3, while it is more distant toM. smegmatis mc2 155.", "doi": "10.1093/gbe/evw049", "pmid": "26941228", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "evw049"}, {"db": "pmc", "key": "PMC4860684"}], "notes": [], "created": "2017-05-03T13:00:07.141Z", "modified": "2024-01-16T13:48:50.258Z"}, {"entity": "publication", "iuid": "4680e1040115478da3cb86be8836b882", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4680e1040115478da3cb86be8836b882.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4680e1040115478da3cb86be8836b882"}}, "title": "Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics.", "authors": [{"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BM"}, {"family": "Behra", "given": "Phani Rama Krishna", "initials": "PR"}, {"family": "Ramesh", "given": "Malavika", "initials": "M"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Bhattacharya", "given": "Alok", "initials": "A"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal article", "published": "2015-06-16", "journal": {"volume": "7", "issn": "1759-6653", "issue": "7", "pages": "1871-1886", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "We provide the genome sequences of the type strains of the polychlorophenol-degrading Mycobacterium chlorophenolicum (DSM43826), the degrader of chlorinated aliphatics Mycobacterium chubuense (DSM44219) and Mycobacterium obuense (DSM44075) that has been tested for use in cancer immunotherapy. The genome sizes of M. chlorophenolicum, M. chubuense, and M. obuense are 6.93, 5.95, and 5.58 Mb with GC-contents of 68.4%, 69.2%, and 67.9%, respectively. Comparative genomic analysis revealed that 3,254 genes are common and we predicted approximately 250 genes acquired through horizontal gene transfer from different sources including proteobacteria. The data also showed that the biodegrading Mycobacterium spp. NBB4, also referred to as M. chubuense NBB4, is distantly related to the M. chubuense type strain and should be considered as a separate species, we suggest it to be named Mycobacterium ethylenense NBB4. Among different categories we identified genes with potential roles in: biodegradation of aromatic compounds and copper homeostasis. These are the first nonpathogenic Mycobacterium spp. found harboring genes involved in copper homeostasis. These findings would therefore provide insight into the role of this group of Mycobacterium spp. in bioremediation as well as the evolution of copper homeostasis within the Mycobacterium genus.", "doi": "10.1093/gbe/evv111", "pmid": "26079817", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "evv111"}, {"db": "pmc", "key": "PMC4524478"}, {"db": "GENBANK", "key": "JYNL00000000"}, {"db": "GENBANK", "key": "JYNU00000000"}, {"db": "GENBANK", "key": "JYNX00000000"}], "notes": [], "created": "2017-05-02T12:56:49.388Z", "modified": "2021-06-16T14:51:44.591Z"}, {"entity": "publication", "iuid": "43b919f1199143c8b5d00d839afbd037", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43b919f1199143c8b5d00d839afbd037.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43b919f1199143c8b5d00d839afbd037"}}, "title": "Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea.", "authors": [{"family": "Karlsson", "given": "Magnus", "initials": "M"}, {"family": "Durling", "given": "Mikael Brandstr\u00f6m", "initials": "MB"}, {"family": "Choi", "given": "Jaeyoung", "initials": "J"}, {"family": "Kosawang", "given": "Chatchai", "initials": "C"}, {"family": "Lackner", "given": "Gerald", "initials": "G"}, {"family": "Tzelepis", "given": "Georgios D", "initials": "GD"}, {"family": "Nygren", "given": "Kristiina", "initials": "K"}, {"family": "Dubey", "given": "Mukesh K", "initials": "MK"}, {"family": "Kamou", "given": "Nathalie", "initials": "N"}, {"family": "Levasseur", "given": "Anthony", "initials": "A"}, {"family": "Zapparata", "given": "Antonio", "initials": "A"}, {"family": "Wang", "given": "Jinhui", "initials": "J"}, {"family": "Amby", "given": "Daniel Buchvaldt", "initials": "DB"}, {"family": "Jensen", "given": "Birgit", "initials": "B"}, {"family": "Sarrocco", "given": "Sabrina", "initials": "S"}, {"family": "Panteris", "given": "Emmanuel", "initials": "E"}, {"family": "Lagopodi", "given": "Anastasia L", "initials": "AL"}, {"family": "P\u00f6ggeler", "given": "Stefanie", "initials": "S"}, {"family": "Vannacci", "given": "Giovanni", "initials": "G"}, {"family": "Collinge", "given": "David B", "initials": "DB"}, {"family": "Hoffmeister", "given": "Dirk", "initials": "D"}, {"family": "Henrissat", "given": "Bernard", "initials": "B"}, {"family": "Lee", "given": "Yong-Hwan", "initials": "YH"}, {"family": "Jensen", "given": "Dan Funck", "initials": "DF"}], "type": "journal article", "published": "2015-01-08", "journal": {"volume": "7", "issn": "1759-6653", "issue": "2", "pages": "465-480", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Clonostachys rosea is a mycoparasitic fungus that can control several important plant diseases. Here, we report on the genome sequencing of C. rosea and a comparative genome analysis, in order to resolve the phylogenetic placement of C. rosea and to study the evolution of mycoparasitism as a fungal lifestyle. The genome of C. rosea is estimated to 58.3 Mb, and contains 14,268 predicted genes. A phylogenomic analysis shows that C. rosea clusters as sister taxon to plant pathogenic Fusarium species, with mycoparasitic/saprotrophic Trichoderma species in an ancestral position. A comparative analysis of gene family evolution reveals several distinct differences between the included mycoparasites. Clonostachys rosea contains significantly more ATP-binding cassette (ABC) transporters, polyketide synthases, cytochrome P450 monooxygenases, pectin lyases, glucose-methanol-choline oxidoreductases, and lytic polysaccharide monooxygenases compared with other fungi in the Hypocreales. Interestingly, the increase of ABC transporter gene number in C. rosea is associated with phylogenetic subgroups B (multidrug resistance proteins) and G (pleiotropic drug resistance transporters), whereas an increase in subgroup C (multidrug resistance-associated proteins) is evident in Trichoderma virens. In contrast with mycoparasitic Trichoderma species, C. rosea contains very few chitinases. Expression of six group B and group G ABC transporter genes was induced in C. rosea during exposure to the Fusarium mycotoxin zearalenone, the fungicide Boscalid or metabolites from the biocontrol bacterium Pseudomonas chlororaphis. The data suggest that tolerance toward secondary metabolites is a prominent feature in the biology of C. rosea.", "doi": "10.1093/gbe/evu292", "pmid": "25575496", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "evu292"}, {"db": "pmc", "key": "PMC4350171"}, {"db": "SRA", "key": "PRJEB4200"}], "notes": [], "created": "2017-05-02T12:57:35.477Z", "modified": "2020-01-21T13:56:01.904Z"}, {"entity": "publication", "iuid": "5d7e79e4e57f4e7c968bc7ea2dfe7126", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d7e79e4e57f4e7c968bc7ea2dfe7126.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d7e79e4e57f4e7c968bc7ea2dfe7126"}}, "title": "Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA.", "authors": [{"family": "Fu", "given": "Cheng-Jie", "initials": "CJ"}, {"family": "Sheikh", "given": "Sanea", "initials": "S"}, {"family": "Miao", "given": "Wei", "initials": "W"}, {"family": "Andersson", "given": "Siv G E", "initials": "SG"}, {"family": "Baldauf", "given": "Sandra L", "initials": "SL"}], "type": "journal article", "published": "2014-08-21", "journal": {"volume": "6", "issn": "1759-6653", "issue": "9", "pages": "2240-2257", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Discoba (Excavata) is an ancient group of eukaryotes with great morphological and ecological diversity. Unlike the other major divisions of Discoba (Jakobida and Euglenozoa), little is known about the mitochondrial DNAs (mtDNAs) of Heterolobosea. We have assembled a complete mtDNA genome from the aggregating heterolobosean amoeba, Acrasis kona, which consists of a single circular highly AT-rich (83.3%) molecule of 51.5 kb. Unexpectedly, A. kona mtDNA is missing roughly 40% of the protein-coding genes and nearly half of the transfer RNAs found in the only other sequenced heterolobosean mtDNAs, those of Naegleria spp. Instead, over a quarter of A. kona mtDNA consists of novel open reading frames. Eleven of the 16 protein-coding genes missing from A. kona mtDNA were identified in its nuclear DNA and polyA RNA, and phylogenetic analyses indicate that at least 10 of these 11 putative nuclear-encoded mitochondrial (NcMt) proteins arose by direct transfer from the mitochondrion. Acrasis kona mtDNA also employs C-to-U type RNA editing, and 12 homologs of DYW-type pentatricopeptide repeat (PPR) proteins implicated in plant organellar RNA editing are found in A. kona nuclear DNA. A mapping of mitochondrial gene content onto a consensus phylogeny reveals a sporadic pattern of relative stasis and rampant gene loss in Discoba. Rampant loss occurred independently in the unique common lineage leading to Heterolobosea + Tsukubamonadida and later in the unique lineage leading to Acrasis. Meanwhile, mtDNA gene content appears to be remarkably stable in the Acrasis sister lineage leading to Naegleria and in their distant relatives Jakobida.", "doi": "10.1093/gbe/evu180", "pmid": "25146648", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "evu180"}, {"db": "pmc", "key": "PMC4202320"}, {"db": "GENBANK", "key": "KJ679272"}], "notes": [], "created": "2017-05-04T14:58:37.241Z", "modified": "2021-06-16T15:16:43.365Z"}], "created": "2017-05-09T09:12:36.753Z", "modified": "2020-11-27T13:14:07.008Z"}