{"entity": "researcher", "timestamp": "2026-07-11T14:47:27.667Z", "family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120"}}, "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"}}, {"family": "Wang", "given": "Shuang", "initials": "S", "orcid": "0009-0008-9451-5684", "researcher": {"href": "https://publications.scilifelab.se/researcher/186a6001c26a403e8b0640a3cb516a1a.json"}}, {"family": "Bilyeli\u00a0\u00d8ksnebjerg", "given": "Daniel", "initials": "D"}, {"family": "Nielsen", "given": "Sascha Dreyer", "initials": "SD", "orcid": "0000-0003-2485-9314", "researcher": {"href": "https://publications.scilifelab.se/researcher/70ff8708bff74ea4b0c80c5f434329a8.json"}}, {"family": "Dai", "given": "Wei", "initials": "W", "orcid": "0000-0001-9286-759X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7c48f0de21d478ab23bc18b439472e0.json"}}, {"family": "Jiang", "given": "Wei", "initials": "W", "orcid": "0000-0003-1570-1208", "researcher": {"href": "https://publications.scilifelab.se/researcher/9908e45f950149e2963961d88783dabb.json"}}, {"family": "Liang", "given": "Jing", "initials": "J"}, {"family": "Han", "given": "Wei", "initials": "W"}, {"family": "Zhou", "given": "Chengran", "initials": "C", "orcid": "0000-0002-9468-5973", "researcher": {"href": "https://publications.scilifelab.se/researcher/49d36e1d73bb440184212119bf82858c.json"}}, {"family": "Li", "given": "Qiye", "initials": "Q", "orcid": "0000-0002-5993-0312", "researcher": {"href": "https://publications.scilifelab.se/researcher/d807a3a13669425c9b00e4a2b7db672a.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Monadjem", "given": "Ara", "initials": "A", "orcid": "0000-0003-1906-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/94671b1f708d49f5b9eebc0e6b78b82e.json"}}, {"family": "Bhembe", "given": "Zamekile D", "initials": "ZD", "orcid": "0009-0006-5354-5751", "researcher": {"href": "https://publications.scilifelab.se/researcher/d276b65085fa48bdb17d12ecb8b014ac.json"}}, {"family": "Maphalala", "given": "Machawe", "initials": "M", "orcid": "0000-0002-9304-1391", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eebd8acec5a4084b64c3be4a3627b67.json"}}, {"family": "Ocampo", "given": "Diego", "initials": "D"}, {"family": "Sandoval", "given": "Luis", "initials": "L", "orcid": "0000-0002-0793-6747", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8f560d617c2432aa26f9700d2311ac1.json"}}, {"family": "Fickel", "given": "J\u00f6rns", "initials": "J", "orcid": "0000-0002-0593-5820", "researcher": {"href": "https://publications.scilifelab.se/researcher/40018134351a481ab2d00b4113404c47.json"}}, {"family": "Greenwood", "given": "Alex D", "initials": "AD", "orcid": "0000-0002-8249-1565", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab62cca19d7641918b6dd9adbff919c5.json"}}, {"family": "Szentiks", "given": "Claudia A", "initials": "CA"}, {"family": "Roller", "given": "Marco", "initials": "M"}, {"family": "Birks", "given": "Sharon M", "initials": "SM"}, {"family": "Leach\u00e9", "given": "Adam D", "initials": "AD", "orcid": "0000-0001-8929-6300", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c9502316d344a1282bec0f444638222.json"}}, {"family": "Rico-Guevara", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-4067-5312", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe305adf4d234dce94a9c74ca873169d.json"}}, {"family": "Fuchs", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Vy", "given": "Nguyen Tran", "initials": "NT"}, {"family": "Hvilsom", "given": "Christina", "initials": "C", "orcid": "0000-0001-7870-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/19e68386a9414dad9162026abafad7ce.json"}}, {"family": "Berner", "given": "Juliana Andrea", "initials": "JA"}, {"family": "Lifjeld", "given": "Jan Terje", "initials": "JT"}, {"family": "Johnsen", "given": "Arild", "initials": "A", "orcid": "0000-0003-4864-6284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d610052c8e134f9a9ddff3eee7ed864d.json"}}, {"family": "Johannessen", "given": "Lars Erik", "initials": "LE", "orcid": "0000-0001-5981-9190", "researcher": {"href": "https://publications.scilifelab.se/researcher/838c1d1eb4bb4861a2408a5d83b616cb.json"}}, {"family": "Labuschagne", "given": "Kim", "initials": "K", "orcid": "0000-0003-2784-4767", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa0e1dbf2194c5bbcfb36769d1b2cf4.json"}}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "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": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}}, {"family": "Joseph", "given": "Leo", "initials": "L", "orcid": "0000-0001-7564-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a0b6c400914ba9aaca4a51587d1893.json"}}, {"family": "Hellgren", "given": "Olof", "initials": "O", "orcid": "0000-0002-4062-7276", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bca3b673a2447ecbc55eaf9edf56a02.json"}}, {"family": "Brumfield", "given": "Robb T", "initials": "RT", "orcid": "0000-0003-2307-0688", "researcher": {"href": "https://publications.scilifelab.se/researcher/71a3a36f83154d3dbe14e1a5290f425f.json"}}, {"family": "Burg", "given": "Theresa M", "initials": "TM", "orcid": "0000-0001-5096-3479", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab837fec0ea64df5bd66001038f505c5.json"}}, {"family": "Illera", "given": "Juan Carlos", "initials": "JC", "orcid": "0000-0002-4389-0264", "researcher": {"href": "https://publications.scilifelab.se/researcher/d137c193d3cd4f8c8b9fe09a6443033c.json"}}, {"family": "Aleixo", "given": "Alexandre", "initials": "A", "orcid": "0000-0002-7816-9725", "researcher": {"href": "https://publications.scilifelab.se/researcher/b397ed6da07246caa50a438c233820ab.json"}}, {"family": "Smit", "given": "Ben", "initials": "B"}, {"family": "Rheindt", "given": "Frank E", "initials": "FE", "orcid": "0000-0001-8946-7085", "researcher": {"href": "https://publications.scilifelab.se/researcher/744276ae56e24e7295f672854fbaf3d9.json"}}, {"family": "Lee", "given": "Jessica", "initials": "J", "orcid": "0000-0003-0757-4237", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec08a3cbe214f22b05c730bf94613aa.json"}}, {"family": "Nishiumi", "given": "Isao", "initials": "I"}, {"family": "Quesada", "given": "Javier", "initials": "J", "orcid": "0000-0002-6010-8473", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c4e889bf2fd424c915c6487038f7950.json"}}, {"family": "Dumbacher", "given": "John P", "initials": "JP", "orcid": "0000-0001-8942-1554", "researcher": {"href": "https://publications.scilifelab.se/researcher/6221be035944462989353d66f126a5c5.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "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 O", "initials": "RO", "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": "2026-01-21", "journal": {"title": "Gigascience", "issn": "2047-217X", "volume": "15", "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 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 Quality Value 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"}, {"db": "pmc", "key": "PMC13274736"}], "notes": [], "created": "2026-06-08T17:18:43.899Z", "modified": "2026-06-29T07:41:18.996Z"}, {"entity": "publication", "iuid": "397f0c6069f74329b30503eecca169d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/397f0c6069f74329b30503eecca169d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/397f0c6069f74329b30503eecca169d2"}}, "title": "Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks.", "authors": [{"family": "Sendell-Price", "given": "Ashley T", "initials": "AT", "orcid": "0000-0002-1227-8929", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2d5fb40391442c8a62c20b1ca9a3295.json"}}, {"family": "Tulenko", "given": "Frank J", "initials": "FJ"}, {"family": "Pettersson", "given": "Mats", "initials": "M", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Kang", "given": "Du", "initials": "D", "orcid": "0000-0002-1497-8945", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eda8755c14042289ac7196edeffca01.json"}}, {"family": "Montandon", "given": "Margo", "initials": "M", "orcid": "0000-0002-1707-0190", "researcher": {"href": "https://publications.scilifelab.se/researcher/db6f9463614b43c1aa3d41114a8f5086.json"}}, {"family": "Winkler", "given": "Sylke", "initials": "S", "orcid": "0000-0002-0915-3316", "researcher": {"href": "https://publications.scilifelab.se/researcher/f292bbf542f244278bef19506b21b031.json"}}, {"family": "Kulb", "given": "Kathleen", "initials": "K"}, {"family": "Naylor", "given": "Gavin P", "initials": "GP"}, {"family": "Phillippy", "given": "Adam", "initials": "A", "orcid": "0000-0003-2983-8934", "researcher": {"href": "https://publications.scilifelab.se/researcher/eadfad6b448a4438abee6a1b2f842b35.json"}}, {"family": "Fedrigo", "given": "Olivier", "initials": "O"}, {"family": "Mountcastle", "given": "Jacquelyn", "initials": "J"}, {"family": "Balacco", "given": "Jennifer R", "initials": "JR"}, {"family": "Dutra", "given": "Amalia", "initials": "A"}, {"family": "Dale", "given": "Rebecca E", "initials": "RE"}, {"family": "Haase", "given": "Bettina", "initials": "B"}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Myers", "given": "Gene", "initials": "G", "orcid": "0000-0002-6580-7839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9e5a63cadcf4ab995f3e989bc38c024.json"}}, {"family": "Burgess", "given": "Shawn M", "initials": "SM", "orcid": "0000-0003-1147-0596", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf85532f49bc4208b7e456d4ee2e8f76.json"}}, {"family": "Currie", "given": "Peter D", "initials": "PD", "orcid": "0000-0001-8874-8862", "researcher": {"href": "https://publications.scilifelab.se/researcher/13638faa71f94e13b088922cdfa01bb3.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Schartl", "given": "Manfred", "initials": "M", "orcid": "0000-0001-9882-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f97783b5013409ebc1a6bd2df5ca92c.json"}}], "type": "journal article", "published": "2023-10-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6628", "issn-l": "2041-1723"}, "abstract": "Sharks occupy diverse ecological niches and play critical roles in marine ecosystems, often acting as apex predators. They are considered a slow-evolving lineage and have been suggested to exhibit exceptionally low cancer rates. These two features could be explained by a low nuclear mutation rate. Here, we provide a direct estimate of the nuclear mutation rate in the epaulette shark (Hemiscyllium ocellatum). We generate a high-quality reference genome, and resequence the whole genomes of parents and nine offspring to detect de novo mutations. Using stringent criteria, we estimate a mutation rate of 7\u00d710-10 per base pair, per generation. This represents one of the lowest directly estimated mutation rates for any vertebrate clade, indicating that this basal vertebrate group is indeed a slowly evolving lineage whose ability to restore genetic diversity following a sustained population bottleneck may be hampered by a low mutation rate.", "doi": "10.1038/s41467-023-42238-x", "pmid": "37857613", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10587355"}, {"db": "pii", "key": "10.1038/s41467-023-42238-x"}], "notes": [], "created": "2023-12-18T15:04:16.059Z", "modified": "2024-01-16T13:48:31.927Z"}, {"entity": "publication", "iuid": "ac545b00aad54cdbb6eeaaed3124a362", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ac545b00aad54cdbb6eeaaed3124a362.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ac545b00aad54cdbb6eeaaed3124a362"}}, "title": "Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing.", "authors": [{"family": "Dahn", "given": "Hollis A", "initials": "HA", "orcid": "0000-0001-9777-2303", "researcher": {"href": "https://publications.scilifelab.se/researcher/b82ad0bd1207419ca7c3d8792a7822df.json"}}, {"family": "Mountcastle", "given": "Jacquelyn", "initials": "J", "orcid": "0000-0003-1078-4905", "researcher": {"href": "https://publications.scilifelab.se/researcher/a35e17870a5c4572bcef476c32184824.json"}}, {"family": "Balacco", "given": "Jennifer", "initials": "J", "orcid": "0000-0001-7102-1632", "researcher": {"href": "https://publications.scilifelab.se/researcher/db20cd17c783475aa2e575af1984fb75.json"}}, {"family": "Winkler", "given": "Sylke", "initials": "S", "orcid": "0000-0002-0915-3316", "researcher": {"href": "https://publications.scilifelab.se/researcher/f292bbf542f244278bef19506b21b031.json"}}, {"family": "Bista", "given": "Iliana", "initials": "I", "orcid": "0000-0002-6155-3093", "researcher": {"href": "https://publications.scilifelab.se/researcher/b180ce2a74b94142b5eb05511c537b2f.json"}}, {"family": "Schmitt", "given": "Anthony D", "initials": "AD"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Formenti", "given": "Giulio", "initials": "G", "orcid": "0000-0002-7554-5991", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdf78195993a481483d7cbbf1a6d64ed.json"}}, {"family": "Oliver", "given": "Karen", "initials": "K"}, {"family": "Smith", "given": "Michelle", "initials": "M", "orcid": "0000-0001-5288-0001", "researcher": {"href": "https://publications.scilifelab.se/researcher/a81888e8101a42e4a8aba00d6707b940.json"}}, {"family": "Tan", "given": "Wenhua", "initials": "W", "orcid": "0000-0002-5208-8126", "researcher": {"href": "https://publications.scilifelab.se/researcher/b57b8e811974434590b0e7159ff47a41.json"}}, {"family": "Kraus", "given": "Anne", "initials": "A"}, {"family": "Mac", "given": "Stephen", "initials": "S"}, {"family": "Komoroske", "given": "Lisa M", "initials": "LM", "orcid": "0000-0003-0676-7053", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc12b38235894a74aab116b986d83f88.json"}}, {"family": "Lama", "given": "Tanya", "initials": "T", "orcid": "0000-0002-7372-8081", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dfe6dd10e38419f8a2dc55c93780c34.json"}}, {"family": "Crawford", "given": "Andrew J", "initials": "AJ", "orcid": "0000-0003-3153-6898", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d8b6cfd6704ab8b4396ab35d68f49a.json"}}, {"family": "Murphy", "given": "Robert W", "initials": "RW", "orcid": "0000-0001-8555-2338", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7cdddea1d2e4c9aa19bca8bb4e48f54.json"}}, {"family": "Brown", "given": "Samara", "initials": "S", "orcid": "0000-0003-0391-2016", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc7d389ee6245dc99480159b31ed88f.json"}}, {"family": "Scott", "given": "Alan F", "initials": "AF", "orcid": "0000-0002-9706-7839", "researcher": {"href": "https://publications.scilifelab.se/researcher/0eabc1a858ca4011b1ef57e6ea0b537b.json"}}, {"family": "Morin", "given": "Phillip A", "initials": "PA", "orcid": "0000-0002-3279-1519", "researcher": {"href": "https://publications.scilifelab.se/researcher/cde9e06251774274a55f089acd3be6ab.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Fedrigo", "given": "Olivier", "initials": "O", "orcid": "0000-0002-6450-7551", "researcher": {"href": "https://publications.scilifelab.se/researcher/fae69dfab7d841d4850da7349714cd9c.json"}}], "type": "journal article", "published": "2022-08-10", "journal": {"title": "Gigascience", "issn": "2047-217X", "issn-l": "2047-217X", "volume": "11", "issue": null, "pages": null}, "abstract": "Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types.\r\n\r\nWe find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4\u00b0C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4\u00b0C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield.\r\n\r\nWe provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all \u223c70,000 extant vertebrate species.", "doi": "10.1093/gigascience/giac068", "pmid": "35946988", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Technology development", "NGI Long read": "Technology development", "National Genomics Infrastructure": "Technology development"}, "xrefs": [{"db": "pii", "key": "6659719"}, {"db": "pmc", "key": "PMC9364683"}], "notes": [], "created": "2022-11-21T10:23:04.540Z", "modified": "2022-11-21T10:23:30.973Z"}, {"entity": "publication", "iuid": "ee30e00b2af443009f454bd2fc3b373a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee30e00b2af443009f454bd2fc3b373a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee30e00b2af443009f454bd2fc3b373a"}}, "title": "Population genomics of the critically endangered k\u0101k\u0101p\u014d", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Morales", "given": "Hern\u00e1n E", "initials": "HE"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "D\u00edez-del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Foster", "given": "Yasmin", "initials": "Y"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}, {"family": "Rhie", "given": "Arang", "initials": "A", "orcid": "0000-0002-9809-8127", "researcher": {"href": "https://publications.scilifelab.se/researcher/17dfb02e5b09465ea5b24d4a45652799.json"}}, {"family": "Phillippy", "given": "Adam M", "initials": "AM", "orcid": "0000-0003-2983-8934", "researcher": {"href": "https://publications.scilifelab.se/researcher/eadfad6b448a4438abee6a1b2f842b35.json"}}, {"family": "Korlach", "given": "Jonas", "initials": "J"}, {"family": "Howe", "given": "Kerstin", "initials": "K", "orcid": "0000-0003-2237-513X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee1dac1c74d3497aa987c5a615f2d6c4.json"}}, {"family": "Chow", "given": "William", "initials": "W"}, {"family": "Pelan", "given": "Sarah", "initials": "S"}, {"family": "Mendes Damas", "given": "Joanna D", "initials": "JD"}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2f6f17d3e4b4b7e8f47349bda4c1bb0.json"}}, {"family": "Hastie", "given": "Alex R", "initials": "AR"}, {"family": "Formenti", "given": "Giulio", "initials": "G", "orcid": "0000-0002-7554-5991", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdf78195993a481483d7cbbf1a6d64ed.json"}}, {"family": "Fedrigo", "given": "Olivier", "initials": "O", "orcid": "0000-0002-6450-7551", "researcher": {"href": "https://publications.scilifelab.se/researcher/fae69dfab7d841d4850da7349714cd9c.json"}}, {"family": "Guhlin", "given": "Joseph", "initials": "J"}, {"family": "Harrop", "given": "Thomas W R", "initials": "TWR"}, {"family": "Le Lec", "given": "Marissa F", "initials": "MF"}, {"family": "Dearden", "given": "Peter K", "initials": "PK"}, {"family": "Haggerty", "given": "Leanne", "initials": "L"}, {"family": "Martin", "given": "Fergal J", "initials": "FJ"}, {"family": "Kodali", "given": "Vamsi", "initials": "V"}, {"family": "Thibaud-Nissen", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "Iorns", "given": "David", "initials": "D"}, {"family": "Knapp", "given": "Michael", "initials": "M"}, {"family": "Gemmell", "given": "Neil J", "initials": "NJ", "orcid": "0000-0003-0671-3637", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca2b0a676d84b878b3f9faa8748e148.json"}}, {"family": "Robertson", "given": "Fiona", "initials": "F"}, {"family": "Moorhouse", "given": "Ron", "initials": "R"}, {"family": "Digby", "given": "Andrew", "initials": "A"}, {"family": "Eason", "given": "Daryl", "initials": "D"}, {"family": "Vercoe", "given": "Deidre", "initials": "D"}, {"family": "Howard", "given": "Jason", "initials": "J"}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Robertson", "given": "Bruce C", "initials": "BC", "orcid": "0000-0002-5348-2731", "researcher": {"href": "https://publications.scilifelab.se/researcher/765ee347a5f04b29b28a17f14f707231.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": "2021-10-00", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "volume": "1", "issue": "1", "pages": "100002", "issn-l": null}, "abstract": null, "doi": "10.1016/j.xgen.2021.100002", "pmid": "36777713", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-04-28T06:50:35.104Z", "modified": "2023-06-19T12:48:03.795Z"}, {"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": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Wang", "given": "Zongji", "initials": "Z", "orcid": "0000-0002-5107-6246", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a18bde0ee684560ae3217db4b30a920.json"}}, {"family": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69266aa587d4126a23aa91c5bedfff8.json"}}, {"family": "Diekhans", "given": "Mark", "initials": "M", "orcid": "0000-0002-0430-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/da3441938f7b437b81cc92068bea158c.json"}}, {"family": "Chen", "given": "Wanjun", "initials": "W", "orcid": "0000-0002-4418-7650", "researcher": {"href": "https://publications.scilifelab.se/researcher/992e7029a2704d039ce578df2806f57f.json"}}, {"family": "Andreu-S\u00e1nchez", "given": "Sergio", "initials": "S"}, {"family": "Margaryan", "given": "Ashot", "initials": "A", "orcid": "0000-0002-2576-2429", "researcher": {"href": "https://publications.scilifelab.se/researcher/487f29e4a666414a8437f964e2052be7.json"}}, {"family": "Howard", "given": "Jason Travis", "initials": "JT"}, {"family": "Parent", "given": "Carole", "initials": "C"}, {"family": "Pacheco", "given": "George", "initials": "G", "orcid": "0000-0002-9367-6813", "researcher": {"href": "https://publications.scilifelab.se/researcher/449f532c61df4157b9bd1dc15deab965.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Puetz", "given": "Lara", "initials": "L", "orcid": "0000-0002-0323-799X", "researcher": {"href": "https://publications.scilifelab.se/researcher/986da811e11341379e73f5382b0f69ad.json"}}, {"family": "Cavill", "given": "Emily", "initials": "E", "orcid": "0000-0003-2198-8102", "researcher": {"href": "https://publications.scilifelab.se/researcher/eacd61b411f046d88c1e8942eb46cfff.json"}}, {"family": "Ribeiro", "given": "\u00c2ngela M", "initials": "\u00c2M"}, {"family": "Eckhart", "given": "Leopold", "initials": "L", "orcid": "0000-0002-5645-2036", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a24adae52741698457e9a733f36f6c.json"}}, {"family": "Fjelds\u00e5", "given": "Jon", "initials": "J", "orcid": "0000-0003-0790-3600", "researcher": {"href": "https://publications.scilifelab.se/researcher/f280ada51dfb41b2a3d035676a27ffb6.json"}}, {"family": "Hosner", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-7499-6224", "researcher": {"href": "https://publications.scilifelab.se/researcher/87a4c8cd6229436d9a39761aa77eeec2.json"}}, {"family": "Brumfield", "given": "Robb T", "initials": "RT", "orcid": "0000-0003-2307-0688", "researcher": {"href": "https://publications.scilifelab.se/researcher/71a3a36f83154d3dbe14e1a5290f425f.json"}}, {"family": "Christidis", 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"initials": "B"}, {"family": "Taylor", "given": "Scott A", "initials": "SA", "orcid": "0000-0001-9580-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/36c6baa1b23242e0bfd586d7e42c0cb9.json"}}, {"family": "Del-Rio", "given": "Glaucia", "initials": "G"}, {"family": "Aleixo", "given": "Alexandre", "initials": "A", "orcid": "0000-0002-7816-9725", "researcher": {"href": "https://publications.scilifelab.se/researcher/b397ed6da07246caa50a438c233820ab.json"}}, {"family": "Vasconcelos", "given": "Ana Tereza Ribeiro", "initials": "ATR", "orcid": "0000-0002-4632-2086", "researcher": {"href": "https://publications.scilifelab.se/researcher/69b1022e72a84534850b8d650ba2c1be.json"}}, {"family": "Mello", "given": "Claudio V", "initials": "CV", "orcid": "0000-0002-9826-8421", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9715cacaf7d45bda2337a32ea0ec526.json"}}, {"family": "Weir", "given": "Jason T", "initials": "JT", "orcid": "0000-0001-8372-9937", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c77b745d8b044d4aed9478d056be226.json"}}, {"family": "Haussler", "given": "David", "initials": "D", "orcid": "0000-0003-1533-4575", "researcher": {"href": "https://publications.scilifelab.se/researcher/de140026a4f24291be768e713e4881bb.json"}}, {"family": "Li", "given": "Qiye", "initials": "Q", "orcid": "0000-0002-5993-0312", "researcher": {"href": "https://publications.scilifelab.se/researcher/d807a3a13669425c9b00e4a2b7db672a.json"}}, {"family": "Yang", "given": "Huanming", "initials": "H"}, {"family": "Wang", "given": "Jian", "initials": "J"}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Rahbek", "given": "Carsten", "initials": "C"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Graves", "given": "Gary R", "initials": "GR", "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": "164404029f4a4a9a9c060ce21f1eb099", "links": {"self": {"href": "https://publications.scilifelab.se/publication/164404029f4a4a9a9c060ce21f1eb099.json"}, "display": {"href": "https://publications.scilifelab.se/publication/164404029f4a4a9a9c060ce21f1eb099"}}, "title": "Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.", "authors": [{"family": "K\u00fcnstner", "given": "Axel", "initials": "A"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JB", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}, {"family": "Whitney", "given": "Osceola", "initials": "O"}, {"family": "Balakrishnan", "given": "Christopher N", "initials": "CN", "orcid": "0000-0002-0788-0659", "researcher": {"href": "https://publications.scilifelab.se/researcher/363e6c4a51b647bba7e02e1c8e5464fd.json"}}, {"family": "Day", "given": "Lainy", "initials": "L", "orcid": "0000-0002-9122-3044", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a99dd326b9640629732a9fdbded2662.json"}}, {"family": "Edwards", "given": "Scott V", "initials": "SV"}, {"family": "Janes", "given": "Daniel E", "initials": "DE"}, {"family": "Schlinger", "given": "Barney A", "initials": "BA"}, {"family": "Wilson", "given": "Richard K", "initials": "RK"}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Warren", "given": "Wesley C", "initials": "WC"}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2010-03-00", "journal": {"volume": "19 Suppl 1", "issn": "1365-294X", "issue": "Suppl 1", "pages": "266-276", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with approximately 1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (d(S)) and chromosome size. Analyses of the mean d(N)/d(S) ratio (omega) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with omega as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.", "doi": "10.1111/j.1365-294X.2009.04487.x", "pmid": "20331785", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "mid", "key": "NIHMS216459"}, {"db": "pmc", "key": "PMC2904817"}, {"db": "pii", "key": "MEC4487"}], "notes": [], "created": "2017-05-04T14:57:12.592Z", "modified": "2023-06-19T11:19:36.049Z"}]}