{"entity": "researcher", "timestamp": "2026-07-11T14:34:32.795Z", "family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275"}}, "publications": [{"entity": "publication", "iuid": "c27764ed4c514f2592c156cc59d23608", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c27764ed4c514f2592c156cc59d23608.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c27764ed4c514f2592c156cc59d23608"}}, "title": "Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.", "authors": [{"family": "Hill", "given": "Jason", "initials": "J", "orcid": "0000-0002-0151-8931", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2cb6f3cce5f4919959e18074d51256d.json"}}, {"family": "Lillie", "given": "Mette", "initials": "M", "orcid": "0000-0001-8714-0812", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce02b2116c0417e8a4dcd578f45983b.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}], "type": "journal article", "published": "2022-10-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "6033"}, "abstract": "Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin's finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin's finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin's finches' radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin's finches.", "doi": "10.1038/s41467-022-33723-w", "pmid": "36229469", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-33723-w"}, {"db": "pmc", "key": "PMC9562234"}], "notes": [], "created": "2022-11-09T16:00:11.231Z", "modified": "2024-01-16T13:48:34.742Z"}, {"entity": "publication", "iuid": "47a4b84cdcfc498c8e898c032a1c6b57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47a4b84cdcfc498c8e898c032a1c6b57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47a4b84cdcfc498c8e898c032a1c6b57"}}, "title": "Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut.", "authors": [{"family": "Edvardsen", "given": "Rolf Brudvik", "initials": "RB", "orcid": "0000-0001-8430-8042", "researcher": {"href": "https://publications.scilifelab.se/researcher/07efd6f7e7b04bbd8af5221f78e982c7.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O", "orcid": "0000-0003-1037-7904", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b32e1cfd3084b10a4c220416a6bc589.json"}}, {"family": "Furmanek", "given": "Tomasz", "initials": "T", "orcid": "0000-0001-8577-9604", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a02b990970e46409613ca730ced5914.json"}}, {"family": "Kleppe", "given": "Lene", "initials": "L"}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications.scilifelab.se/researcher/b67a52aca631482d8b8f58e525a82d14.json"}}, {"family": "Kj\u00e6rner-Semb", "given": "Erik", "initials": "E", "orcid": "0000-0001-7160-6710", "researcher": {"href": "https://publications.scilifelab.se/researcher/44013d14287f43a29ca482f5dcdc988a.json"}}, {"family": "M\u00e6hle", "given": "Stig", "initials": "S"}, {"family": "Olausson", "given": "Sara Karolina", "initials": "SK"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E", "orcid": "0000-0001-9526-8541", "researcher": {"href": "https://publications.scilifelab.se/researcher/20f87b64e71b4a00a9474ec4d898601d.json"}}, {"family": "Harboe", "given": "Torstein", "initials": "T"}, {"family": "Mangor-Jensen", "given": "Ragnfrid", "initials": "R"}, {"family": "M\u00f8gster", "given": "Margareth", "initials": "M"}, {"family": "Perrichon", "given": "Prescilla", "initials": "P", "orcid": "0000-0002-1410-878X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd8005cb7ec44f569ffc2d457d6e8bf9.json"}}, {"family": "Norberg", "given": "Birgitta", "initials": "B", "orcid": "0000-0003-1550-5725", "researcher": {"href": "https://publications.scilifelab.se/researcher/c178dcf0ef364f14b6cdb7661540070f.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "18", "issue": "2", "pages": "e1010011", "issn-l": "1553-7390"}, "abstract": "Atlantic Halibut (Hippoglossus hippoglossus) has a X/Y genetic sex determination system, but the sex determining factor is not known. We produced a high-quality genome assembly from a male and identified parts of chromosome 13 as the Y chromosome due to sequence divergence between sexes and segregation of sex genotypes in pedigrees. Linkage analysis revealed that all chromosomes exhibit heterochiasmy, i.e. male-only and female-only meiotic recombination regions (MRR/FRR). We show that FRR/MRR intervals differ in nucleotide diversity and repeat class content and that this is true also for other Pleuronectidae species. We further show that remnants of a Gypsy-like transposable element insertion on chr13 promotes early male specific expression of gonadal somatic cell derived factor (gsdf). Less than 4.5 MYA, this male-determining element evolved on an autosomal FRR segment featuring pre-existing male meiotic recombination barriers, thereby creating a Y chromosome. Our findings indicate that heterochiasmy may facilitate the evolution of genetic sex determination systems relying on linkage of sexually antagonistic loci to a sex-determining factor.", "doi": "10.1371/journal.pgen.1010011", "pmid": "35134055", "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": "PMC8824383"}, {"db": "pii", "key": "PGENETICS-D-21-00885"}], "notes": [], "created": "2022-11-29T09:16:18.063Z", "modified": "2024-01-16T13:48:37.634Z"}, {"entity": "publication", "iuid": "6f70e1a8af3e47a5a3fa4fba74483b35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f70e1a8af3e47a5a3fa4fba74483b35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f70e1a8af3e47a5a3fa4fba74483b35"}}, "title": "The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities.", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}, {"family": "Blommaert", "given": "Julie", "initials": "J", "orcid": "0000-0003-1411-2313", "researcher": {"href": "https://publications.scilifelab.se/researcher/761067515ad240c9b82f0ea7625b1320.json"}}, {"family": "Liu", "given": "Jing", "initials": "J"}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69266aa587d4126a23aa91c5bedfff8.json"}}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}], "type": "journal article", "published": "2021-09-13", "journal": {"title": "Philos. Trans. R. Soc. Lond., B, Biol. Sci.", "issn": "1471-2970", "issn-l": "0962-8436", "volume": "376", "issue": "1833", "pages": "20200186"}, "abstract": "It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.", "doi": "10.1098/rstb.2020.0186", "pmid": "34304594", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8310711"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5450746"}], "notes": [], "created": "2021-10-01T09:03:22.481Z", "modified": "2024-01-16T13:48:38.503Z"}, {"entity": "publication", "iuid": "47e2059a8c6d4ea5aefb39c53bc5c234", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47e2059a8c6d4ea5aefb39c53bc5c234.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47e2059a8c6d4ea5aefb39c53bc5c234"}}, "title": "Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring.", "authors": [{"family": "Chen", "given": "Junfeng", "initials": "J", "orcid": "0000-0001-6155-411X", "researcher": {"href": "https://publications.scilifelab.se/researcher/270488419b56484993472f518ba1d286.json"}}, {"family": "Bi", "given": "Huijuan", "initials": "H"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Sato", "given": "Daiki X", "initials": "DX", "orcid": "0000-0002-9527-8253", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad2eafb0bce4d2ba7c4f9cf7ed05eac.json"}}, {"family": "Fuentes-Pardo", "given": "Angela P", "initials": "AP", "orcid": "0000-0002-5734-9030", "researcher": {"href": "https://publications.scilifelab.se/researcher/f08a3b9b781b4ef9971a667a40b62d93.json"}}, {"family": "Mo", "given": "Chunheng", "initials": "C"}, {"family": "Younis", "given": "Shady", "initials": "S", "orcid": "0000-0002-4319-1738", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b77c6e3ed14b9ba2e10132f89ef781.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Mol\u00e9s", "given": "Gregorio", "initials": "G", "orcid": "0000-0001-5762-6993", "researcher": {"href": "https://publications.scilifelab.se/researcher/26c43e28a3fa49ccad6c77ae61f87777.json"}}, {"family": "G\u00f3mez", "given": "Ana", "initials": "A"}, {"family": "Kleinau", "given": "Gunnar", "initials": "G"}, {"family": "Scheerer", "given": "Patrick", "initials": "P", "orcid": "0000-0001-5028-2075", "researcher": {"href": "https://publications.scilifelab.se/researcher/50350a6ed93442f38ea62edb86eaa99b.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2021-06-25", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "795", "issn-l": "2399-3642"}, "abstract": "The underlying molecular mechanisms that determine long day versus short day breeders remain unknown in any organism. Atlantic herring provides a unique opportunity to examine the molecular mechanisms involved in reproduction timing, because both spring and autumn spawners exist within the same species. Although our previous whole genome comparisons revealed a strong association of TSHR alleles with spawning seasons, the functional consequences of these variants remain unknown. Here we examined the functional significance of six candidate TSHR mutations strongly associated with herring reproductive seasonality. We show that the L471M missense mutation in the spring-allele causes enhanced cAMP signaling. The best candidate non-coding mutation is a 5.2 kb retrotransposon insertion upstream of the TSHR transcription start site, near an open chromatin region, which is likely to affect TSHR expression. The insertion occurred prior to the split between Pacific and Atlantic herring and was lost in the autumn-allele. Our study shows that strongly associated coding and non-coding variants at the TSHR locus may both contribute to the regulation of seasonal reproduction in herring.", "doi": "10.1038/s42003-021-02307-7", "pmid": "34172814", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02307-7"}, {"db": "pmc", "key": "PMC8233318"}, {"db": "Dryad", "key": "10.5061/dryad.pnvx0k6kr"}], "notes": [], "created": "2021-12-07T21:41:02.372Z", "modified": "2024-01-16T13:48:39.437Z"}, {"entity": "publication", "iuid": "049e8f91b93c493bb74b43dc7d8105bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/049e8f91b93c493bb74b43dc7d8105bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/049e8f91b93c493bb74b43dc7d8105bc"}}, "title": "Activation of endogenous retroviruses during brain development causes an inflammatory response.", "authors": [{"family": "J\u00f6nsson", "given": "Marie E", "initials": "ME", "orcid": "0000-0002-1184-6269", "researcher": {"href": "https://publications.scilifelab.se/researcher/73ddc70ea52e4bfc82f97a3fc35c09cd.json"}}, {"family": "Garza", "given": "Raquel", "initials": "R", "orcid": "0000-0002-2524-3055", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d53399af304283ba62e0646acdc612.json"}}, {"family": "Sharma", "given": "Yogita", "initials": "Y"}, {"family": "Petri", "given": "Rebecca", "initials": "R", "orcid": "0000-0002-4921-2894", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dea65b928e0486cb750d7966d917c6f.json"}}, {"family": "S\u00f6dersten", "given": "Erik", "initials": "E"}, {"family": "Johansson", "given": "Jenny G", "initials": "JG"}, {"family": "Johansson", "given": "Pia A", "initials": "PA", "orcid": "0000-0002-6938-4060", "researcher": {"href": "https://publications.scilifelab.se/researcher/28206ae896f34a2c85c2ed863d4eb53e.json"}}, {"family": "Atacho", "given": "Diahann Am", "initials": "DA"}, {"family": "Pircs", "given": "Karolina", "initials": "K", "orcid": "0000-0001-8281-4785", "researcher": {"href": "https://publications.scilifelab.se/researcher/070f9eb7abde403697f7e8ba0f9ac40e.json"}}, {"family": "Madsen", "given": "Sofia", "initials": "S"}, {"family": "Yudovich", "given": "David", "initials": "D"}, {"family": "Ramakrishnan", "given": "Ramprasad", "initials": "R"}, {"family": "Holmberg", "given": "Johan", "initials": "J"}, {"family": "Larsson", "given": "Jonas", "initials": "J"}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Jakobsson", "given": "Johan", "initials": "J", "orcid": "0000-0003-0669-7673", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b08f33ec79b4a36a5f62223d7174201.json"}}], "type": "journal article", "published": "2021-05-03", "journal": {"title": "EMBO J.", "issn": "1460-2075", "volume": "40", "issue": "9", "pages": "e106423", "issn-l": "0261-4189"}, "abstract": "Endogenous retroviruses (ERVs) make up a large fraction of mammalian genomes and are thought to contribute to human disease, including brain disorders. In the brain, aberrant activation of ERVs is a potential trigger for an inflammatory response, but mechanistic insight into this phenomenon remains lacking. Using CRISPR/Cas9-based gene disruption of the epigenetic co-repressor protein Trim28, we found a dynamic H3K9me3-dependent regulation of ERVs in proliferating neural progenitor cells (NPCs), but not in adult neurons. In vivo deletion of Trim28 in cortical NPCs during mouse brain development resulted in viable offspring expressing high levels of ERVs in excitatory neurons in the adult brain. Neuronal ERV expression was linked to activated microglia and the presence of ERV-derived proteins in aggregate-like structures. This study demonstrates that brain development is a critical period for the silencing of ERVs and provides causal in vivo evidence demonstrating that transcriptional activation of ERV in neurons results in an inflammatory response.", "doi": "10.15252/embj.2020106423", "pmid": "33644903", "labels": {"Clinical Genomics Lund": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8090857"}], "notes": [], "created": "2021-11-23T14:25:25.979Z", "modified": "2024-01-16T13:48:39.814Z"}, {"entity": "publication", "iuid": "7a327b499a2f4fa39b9d39515a64fbfb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a327b499a2f4fa39b9d39515a64fbfb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a327b499a2f4fa39b9d39515a64fbfb"}}, "title": "ZBED6 binding motifs correlate with endogenous retroviruses and Syncytin genes.", "authors": [{"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Virus Evol", "issn": "2057-1577", "volume": "7", "issue": "1", "pages": "veaa083", "issn-l": null}, "abstract": "Retroviruses have infiltrated vertebrate germlines for millions of years as inherited endogenous retroviruses (ERVs). Mammalian genomes host large numbers of ERVs and transposable elements (TEs), including retrotransposons and DNA transposons, that contribute to genomic innovation and evolution as coopted genes and regulators of diverse functions. To explore features distinguishing coopted ERVs and TEs from other integrations, we focus on the potential role of ZBED6 and repeated ERV domestication as repurposed Syncytin genes. The placental mammal-specific ZBED6 is a DNA transposon-derived transcription regulator and we demonstrate that its binding motifs are associated with distinct Syncytins and that ZBED6 binding motifs are 2- to 3-fold more frequent in ERVs than in flanking DNA. Our observations suggest that ZBED6 could contribute an extended regulatory role of genomic expression, utilizing ERVs as platforms for genomic innovation and evolution.", "doi": "10.1093/ve/veaa083", "pmid": "33859827", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "veaa083"}, {"db": "pmc", "key": "PMC8035546"}], "notes": [], "created": "2022-11-09T15:45:21.805Z", "modified": "2024-01-16T13:48:40.979Z"}, {"entity": "publication", "iuid": "1e6e059a7b984acdbfb1404425966373", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e6e059a7b984acdbfb1404425966373.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e6e059a7b984acdbfb1404425966373"}}, "title": "Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups.", "authors": [{"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}], "type": "journal article", "published": "2019-02-20", "journal": {"volume": "10", "issn": "2073-4425", "issue": "2", "pages": "162", "title": "Genes", "issn-l": "2073-4425"}, "abstract": "Retroviruses have invaded vertebrate hosts for millions of years and left an extensive endogenous retrovirus (ERV) record in the host genomes, which provides a remarkable source for an evolutionary perspective on retrovirus-host associations. Here we identified ERV variation across whole-genomes from two chicken lines, derived from a common founder population subjected to 50 years of bi-directional selection on body weight, and a distantly related domestic chicken line as a comparison outgroup. Candidate ERV loci, where at least one of the chicken lines indicated distinct differences, were analyzed for adjacent host genomic landscapes, selective sweeps, and compared by sequence associations to reference assembly ERVs in phylogenetic analyses. Current data does not support selection acting on specific ERV loci in the domestic chicken lines, as determined by presence inside selective sweeps or composition of adjacent host genes. The varying ERV records among the domestic chicken lines associated broadly across the assembly ERV phylogeny, indicating that the observed insertion differences result from pre-existing and segregating ERV loci in the host populations. Thus, data suggest that the observed differences between the host lineages are best explained by substantial standing ERV variation within host populations, and indicates that even truncated, presumably old, ERVs have not yet become fixed in the host population.", "doi": "10.3390/genes10020162", "pmid": "30791656", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "genes10020162"}, {"db": "pmc", "key": "PMC6410134"}], "notes": [], "created": "2019-11-25T15:26:07.192Z", "modified": "2024-01-16T13:48:44.672Z"}]}