{"entity": "researcher", "timestamp": "2026-06-17T20:04:03.167Z", "family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8"}}, "publications": [{"entity": "publication", "iuid": "f74db641b67b4485b01bf07e453d5dd0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f74db641b67b4485b01bf07e453d5dd0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f74db641b67b4485b01bf07e453d5dd0"}}, "title": "Draft assemblies for 177 bird species enhance genus-level coverage.", "authors": [{"family": "Chen", "given": "Guangji", "initials": "G", "orcid": "0000-0002-9441-1155", "researcher": {"href": "https://publications.scilifelab.se/researcher/19514f67b1504dc6b4b7d393e97f8cc0.json"}}, 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"https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}, {"family": "Andersen", "given": "Michael J", "initials": "MJ", "orcid": "0000-0002-7220-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/15d3b310f2f34fc4969520d431a14f6d.json"}}, {"family": "Witt", "given": "Christopher C", "initials": "CC", "orcid": "0000-0003-2781-1543", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a6a535b32f94e59acf1398df72a8cd1.json"}}, {"family": "Phillips", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-0208-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/f35746710d7c4ae6a86d1b12e805ea14.json"}}, {"family": "Prum", "given": "Richard", "initials": "R", "orcid": "0000-0002-4741-7132", "researcher": {"href": "https://publications.scilifelab.se/researcher/28d15772cf924924b7e5630bfbdb5b89.json"}}, {"family": "Zyskowski", "given": "Kristof", "initials": "K", "orcid": "0000-0002-5680-6412", "researcher": {"href": "https://publications.scilifelab.se/researcher/49aadb5fab7b4fbebf1c65c9f3a04217.json"}}, {"family": "Goodman", "given": "Steven M", "initials": "SM"}, {"family": "Raherilalao", "given": "Marie Jeanne", "initials": "MJ", "orcid": "0000-0002-8618-7157", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5653450df494d96b15d77a12d77e932.json"}}, {"family": "Ottosson", "given": "Ulf", "initials": "U", "orcid": "0000-0001-7914-0484", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b035efe180248eaa188b0e1d23f2007.json"}}, {"family": "Barshep", "given": "Yahkat", "initials": "Y"}, {"family": "Ivande", "given": "Sam", "initials": "S", "orcid": "0000-0003-4949-1376", "researcher": {"href": "https://publications.scilifelab.se/researcher/181e4fbbf6ae40d1bebe504c5c24f797.json"}}, {"family": "Brl\u00edk", "given": "Vojt\u011bch", "initials": "V", "orcid": "0000-0002-7902-8123", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ed62d45f978413d9c983e53b07b7ad8.json"}}, {"family": "Okposio", "given": "Emmanuel", "initials": "E"}, {"family": "Koane", "given": "Bonny", "initials": "B", "orcid": "0000-0001-6770-5126", "researcher": {"href": "https://publications.scilifelab.se/researcher/966dc22dd4ca456294f7f2ed0a853c87.json"}}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Rahbek", "given": "Carsten", "initials": "C", "orcid": "0000-0003-4585-0300", "researcher": {"href": "https://publications.scilifelab.se/researcher/341ee33c55904249b6e70a9b55b5509a.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9cc44c016c4d099f674d182c08fbaa.json"}}, {"family": "Graves", "given": "Gary R", "initials": "GR", "orcid": "0000-0003-1406-5246", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3b9edee185456d971f5b596c3086fe.json"}}, {"family": "Feng", "given": "Shaohong", "initials": "S", "orcid": "0000-0002-2462-7348", "researcher": {"href": "https://publications.scilifelab.se/researcher/92ad360b09004877aee9cfde491c76a3.json"}}, {"family": "Hosner", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-7499-6224", "researcher": {"href": "https://publications.scilifelab.se/researcher/87a4c8cd6229436d9a39761aa77eeec2.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}], "type": "journal article", "published": "2026-05-09", "journal": {"title": "Gigascience", "issn": "2047-217X", "issn-l": "2047-217X"}, "abstract": "With over 10,000 recognized species, birds constitute one of the most diverse and widely distributed vertebrate groups. Although avian genomics has advanced rapidly over the past decade, substantial gaps remain across the global avifauna. Filling these gaps is essential for understanding macroevolutionary patterns, population structure, and the molecular basis of ecological and behavioral diversity. Worldwide museum collections represent invaluable resources for filling these gaps, yet the typically degraded DNA and limited quantities from historical specimens have posed significant challenges for generating high-quality genome assemblies.\n\nHere, the Bird Genome 10 K (B10K) Project adopted low-input sequencing strategies that reduce costs while improving assembly quality compared with earlier order- and family-level genomes. Using mainly stLFR, complemented by 10X Genomics and standard next-generation sequencing, we assembled 177 avian genomes from museum specimens and tissue collections representing 161 genera, including 102 newly sequenced at the genomic level. The assemblies average \u223c1.2 Gb in size, with scaffold N50 = 8.03 Mb, contig N50 = 120 kb, 93% BUSCO completeness, and Merqury QV score of 56.\n\nThese genomes greatly expand avian taxonomic coverage and demonstrate the efficiency of low-input sequencing for generating high-quality assemblies from limited and often degraded material sourced from museum specimens. This resource provides a foundation for comparative genomics, conservation genetics, and evolutionary studies across the avian tree of life.", "doi": "10.1093/gigascience/giag045", "pmid": "42104960", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "8675036"}], "notes": [], "created": "2026-06-08T17:18:43.899Z", "modified": "2026-06-08T17:18:48.101Z"}, {"entity": "publication", "iuid": "6ab751342fa740da8823811b82a1be91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ab751342fa740da8823811b82a1be91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ab751342fa740da8823811b82a1be91"}}, "title": "Standards recommendations for the Earth BioGenome Project.", "authors": [{"family": "Lawniczak", "given": "Mara K N", "initials": "MKN"}, {"family": "Durbin", "given": "Richard", "initials": "R"}, {"family": "Flicek", "given": "Paul", "initials": "P"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Wei", "given": "Xiaofeng", "initials": "X"}, {"family": "Archibald", "given": "John M", "initials": "JM", "orcid": "0000-0001-7255-780X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc225404ccd7449b95d00245b7d5df38.json"}}, {"family": "Baker", "given": "William J", "initials": "WJ", "orcid": "0000-0001-6727-1831", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9ec3e520cda41278664cd3620ba1b48.json"}}, {"family": "Belov", "given": "Katherine", "initials": "K"}, {"family": "Blaxter", "given": "Mark L", "initials": "ML"}, {"family": "Marques Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ea50a4fe3147f3b979ccaa8a2a0de4.json"}}, {"family": "Childers", "given": "Anna K", "initials": "AK", "orcid": "0000-0002-0747-8539", "researcher": {"href": "https://publications.scilifelab.se/researcher/23f9cda134ba47d8930eb56178a8978a.json"}}, {"family": "Coddington", "given": "Jonathan A", "initials": "JA", "orcid": "0000-0001-6004-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1b5d867f8df4d15912371407adea6e0.json"}}, {"family": "Crandall", "given": "Keith A", "initials": "KA", "orcid": "0000-0002-0836-3389", "researcher": {"href": "https://publications.scilifelab.se/researcher/1666c0dbe87b43948aa8ff8d50c52679.json"}}, {"family": "Crawford", "given": "Andrew J", "initials": "AJ"}, {"family": "Davey", "given": "Robert P", "initials": "RP"}, {"family": "Di Palma", "given": "Federica", "initials": "F"}, {"family": "Fang", "given": "Qi", "initials": "Q", "orcid": "0000-0002-9181-8689", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9ff76a9a8bb42c8973d968c7e39a216.json"}}, {"family": "Haerty", "given": "Wilfried", "initials": "W"}, {"family": "Hall", "given": "Neil", "initials": "N", "orcid": "0000-0003-2808-0009", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a7188f887fd44fbabfd13da8a00c358.json"}}, {"family": "Hoff", "given": "Katharina J", "initials": "KJ", "orcid": "0000-0002-7333-8390", "researcher": {"href": "https://publications.scilifelab.se/researcher/a58ca10406a3404180c23fc754a9f4b0.json"}}, {"family": "Howe", "given": "Kerstin", "initials": "K", "orcid": "0000-0003-2237-513X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee1dac1c74d3497aa987c5a615f2d6c4.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED"}, {"family": "Johnson", "given": "Warren E", "initials": "WE"}, {"family": "Johnson", "given": "Rebecca N", "initials": "RN", "orcid": "0000-0003-3035-2827", "researcher": {"href": 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"Adam M", "initials": "AM", "orcid": "0000-0003-2983-8934", "researcher": {"href": "https://publications.scilifelab.se/researcher/eadfad6b448a4438abee6a1b2f842b35.json"}}, {"family": "Poelchau", "given": "Monica F", "initials": "MF", "orcid": "0000-0002-4584-6056", "researcher": {"href": "https://publications.scilifelab.se/researcher/e93f7df3b5094901b083fa3927535da5.json"}}, {"family": "Pruitt", "given": "Kim D", "initials": "KD"}, {"family": "Rhie", "given": "Arang", "initials": "A", "orcid": "0000-0002-9809-8127", "researcher": {"href": "https://publications.scilifelab.se/researcher/17dfb02e5b09465ea5b24d4a45652799.json"}}, {"family": "Castilla-Rubio", "given": "Juan Carlos", "initials": "JC"}, {"family": "Sahu", "given": "Sunil Kumar", "initials": "SK", "orcid": "0000-0002-4742-9870", "researcher": {"href": "https://publications.scilifelab.se/researcher/78cf3dd01c304bf5a1405a8d3d25ffb0.json"}}, {"family": "Salmon", "given": "Nicholas A", "initials": "NA"}, {"family": "Soltis", "given": "Pamela S", "initials": "PS", "orcid": "0000-0001-9310-8659", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3b2364389a94073846c88bf56a939e3.json"}}, {"family": "Swarbreck", "given": "David", "initials": "D", "orcid": "0000-0002-5453-1013", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdc49aae6cf6484d8b80676433e2296c.json"}}, {"family": "Thibaud-Nissen", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "Wang", "given": "Sibo", "initials": "S"}, {"family": "Wegrzyn", "given": "Jill L", "initials": "JL", "orcid": "0000-0001-5923-0888", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d757abfda3a4cc28c4a5b642182f71b.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}, {"family": "Zhang", "given": "He", "initials": "H"}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2f6f17d3e4b4b7e8f47349bda4c1bb0.json"}}, {"family": "Richards", "given": "Stephen", "initials": "S", "orcid": "0000-0001-8959-5466", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f9973c2c5ee450097465fd75edaf316.json"}}], "type": "journal article", "published": "2022-01-25", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "119", "issue": "4", "pages": null}, "abstract": "A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.", "doi": "10.1073/pnas.2115639118", "pmid": "35042802", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Long read": "Collaborative"}, "xrefs": [{"db": "pii", "key": "2115639118"}], "notes": [], "created": "2022-01-31T20:23:10.964Z", "modified": "2022-03-29T04:45:09.368Z"}, {"entity": "publication", "iuid": "af1d860a40a54aff870af824f6fef807", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af1d860a40a54aff870af824f6fef807.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af1d860a40a54aff870af824f6fef807"}}, "title": "The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau.", "authors": [{"family": "Qu", "given": "Yanhua", "initials": "Y", "orcid": "0000-0002-4590-7787", "researcher": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a.json"}}, {"family": "Chen", "given": "Chunhai", "initials": "C", "orcid": "0000-0002-2882-4517", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dd523248fd54ae299c069b960312115.json"}}, {"family": "Chen", "given": "Xiumin", "initials": "X"}, {"family": "Hao", "given": "Yan", "initials": "Y", "orcid": "0000-0002-1415-7610", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c1a42ec6cf4f3f990220e6b4735bec.json"}}, {"family": "She", "given": "Huishang", "initials": "H", "orcid": "0000-0001-6259-7904", "researcher": {"href": "https://publications.scilifelab.se/researcher/a02a8db02a40437a87bd000b995d10c8.json"}}, {"family": "Wang", "given": "Mengxia", "initials": "M"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Lin", "given": "Haiyan", "initials": "H", "orcid": "0000-0002-1623-9361", "researcher": {"href": "https://publications.scilifelab.se/researcher/e54d1bf82275458794a989de37b58480.json"}}, {"family": "Cai", "given": "Tianlong", "initials": "T"}, {"family": "Song", "given": "Gang", "initials": "G", "orcid": "0000-0002-0190-8315", "researcher": {"href": "https://publications.scilifelab.se/researcher/f133bb6165494dfaba8173b0e8191765.json"}}, {"family": "Jia", "given": "Chenxi", "initials": "C"}, {"family": "Chen", "given": "Chunyan", "initials": "C", "orcid": "0000-0002-2882-4517", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dd523248fd54ae299c069b960312115.json"}}, {"family": "Zhang", "given": "Hailin", "initials": "H"}, {"family": "Li", "given": "Jiang", "initials": "J", "orcid": "0000-0003-2099-8165", "researcher": {"href": "https://publications.scilifelab.se/researcher/b64bd87a57e0468b879e6361e79e3000.json"}}, {"family": "Liang", "given": "Liping", "initials": "L"}, {"family": "Wu", "given": "Tianyu", "initials": "T"}, {"family": "Zhao", "given": "Jinyang", "initials": "J", "orcid": "0000-0002-8150-044X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d41f239fe612446194498f9e5ed06321.json"}}, {"family": "Gao", "given": "Qiang", "initials": "Q", "orcid": "0000-0001-9880-4944", "researcher": {"href": "https://publications.scilifelab.se/researcher/faf3d20ec8344174a8c001bac7464421.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}, {"family": "Zhai", "given": "Weiwei", "initials": "W", "orcid": "0000-0001-7938-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/e33e2ebb818449b9b95ba2484fccaa86.json"}}, {"family": "Zhang", "given": "Chi", "initials": "C"}, {"family": "Zhang", "given": "Yong E", "initials": "YE", "orcid": "0000-0003-3770-2383", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c91998c67674b75891a4473451916d6.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9cc44c016c4d099f674d182c08fbaa.json"}}], "type": "journal article", "published": "2021-03-30", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "13", "pages": "e2012398118", "issn-l": "0027-8424"}, "abstract": "Species in a shared environment tend to evolve similar adaptations under the influence of their phylogenetic context. Using snowfinches, a monophyletic group of passerine birds (Passeridae), we study the relative roles of ancestral and species-specific adaptations to an extreme high-elevation environment, the Qinghai-Tibet Plateau. Our ancestral trait reconstruction shows that the ancestral snowfinch occupied high elevations and had a larger body mass than most nonsnowfinches in Passeridae. Subsequently, this phenotypic adaptation diversified in the descendant species. By comparing high-quality genomes from representatives of the three phylogenetic lineages, we find that about 95% of genes under positive selection in the descendant species are different from those in the ancestor. Consistently, the biological functions enriched for these species differ from those of their ancestor to various degrees (semantic similarity values ranging from 0.27 to 0.5), suggesting that the three descendant species have evolved divergently from the initial adaptation in their common ancestor. Using a functional assay to a highly selective gene, DTL, we demonstrate that the nonsynonymous substitutions in the ancestor and descendant species have improved the repair capacity of ultraviolet-induced DNA damage. The repair kinetics of the DTL gene shows a twofold to fourfold variation across the ancestor and the descendants. Collectively, this study reveals an exceptional case of adaptive evolution to high-elevation environments, an evolutionary process with an initial adaptation in the common ancestor followed by adaptive diversification of the descendant species.", "doi": "10.1073/pnas.2012398118", "pmid": "33753478", "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": "2012398118"}, {"db": "pmc", "key": "PMC8020664"}], "notes": [], "created": "2021-06-09T12:15:45.569Z", "modified": "2024-01-16T13:48:40.345Z"}, {"entity": "publication", "iuid": "0cd1833de8764e41812f14260f5961b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cd1833de8764e41812f14260f5961b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cd1833de8764e41812f14260f5961b5"}}, "title": "Dense sampling of bird diversity increases power of comparative genomics.", "authors": [{"family": "Feng", "given": "Shaohong", "initials": "S", "orcid": "0000-0002-2462-7348", "researcher": {"href": "https://publications.scilifelab.se/researcher/92ad360b09004877aee9cfde491c76a3.json"}}, {"family": "Stiller", "given": "Josefin", "initials": "J", "orcid": "0000-0001-6009-9581", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e54e7b719bb422aa18ccd99d6c2edf6.json"}}, {"family": "Deng", "given": "Yuan", "initials": "Y"}, {"family": "Armstrong", "given": "Joel", "initials": "J", "orcid": "0000-0003-2077-4671", "researcher": {"href": "https://publications.scilifelab.se/researcher/63cfeea6ae9942b8a48e6e13ecf4bf0d.json"}}, {"family": "Fang", "given": "Qi", "initials": "Q", "orcid": "0000-0002-9181-8689", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9ff76a9a8bb42c8973d968c7e39a216.json"}}, {"family": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}}, {"family": "Xie", "given": "Duo", "initials": "D", "orcid": "0000-0001-7010-3601", "researcher": {"href": "https://publications.scilifelab.se/researcher/9258a952a3c54596add7d930e1432ebe.json"}}, {"family": "Chen", "given": "Guangji", "initials": "G", "orcid": "0000-0002-9441-1155", "researcher": {"href": "https://publications.scilifelab.se/researcher/19514f67b1504dc6b4b7d393e97f8cc0.json"}}, {"family": "Guo", "given": "Chunxue", "initials": "C"}, {"family": "Faircloth", "given": "Brant C", "initials": "BC", "orcid": "0000-0002-1943-0217", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df01b37d97a44ffb6f4d069085d7b64.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": 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"orcid": "0000-0003-1406-5246", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3b9edee185456d971f5b596c3086fe.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "587", "issue": "7833", "pages": "252-257", "issn-l": "0028-0836"}, "abstract": "Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.", "doi": "10.1038/s41586-020-2873-9", "pmid": "33177665", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-020-2873-9"}, {"db": "pmc", "key": "PMC7759463"}], "notes": [], "created": "2020-12-07T16:36:44.079Z", "modified": "2021-11-10T12:45:51.851Z"}, {"entity": "publication", "iuid": "1138e1f8b82c448587d58bae89ae15a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1138e1f8b82c448587d58bae89ae15a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1138e1f8b82c448587d58bae89ae15a5"}}, "title": "Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.", "authors": [{"family": "Xu", "given": "Luohao", "initials": "L"}, {"family": "Auer", "given": "Gabriel", "initials": "G"}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Deng", "given": "Yuan", "initials": "Y"}, {"family": "Feng", "given": "Shaohong", "initials": "S"}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Christidis", "given": "Les", "initials": "L"}, {"family": "Prost", "given": "Stefan", "initials": "S"}, {"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"}}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "3", "issn": "2397-334X", "issue": "5", "pages": "834-844", "title": "Nat Ecol Evol", "issn-l": "2397-334X"}, "abstract": "Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed 'evolutionary strata'. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.", "doi": "10.1038/s41559-019-0850-1", "pmid": "30936435", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-019-0850-1"}], "notes": [], "created": "2019-12-02T17:20:28.490Z", "modified": "2024-01-16T13:48:44.423Z"}]}