Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

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dc.contributor.authorDalloul, Rami A.en
dc.contributor.authorLong, Julie A.en
dc.contributor.authorZimin, Aleksey V.en
dc.contributor.authorAslam, Luqmanen
dc.contributor.authorBeal, Kathrynen
dc.contributor.authorBlomberg, Le Annen
dc.contributor.authorBouffard, Pascalen
dc.contributor.authorBurt, David W.en
dc.contributor.authorCrasta, Oswalden
dc.contributor.authorCrooijmans, Richard P. M. A.en
dc.contributor.authorCooper, Kristalen
dc.contributor.authorCoulombe, Roger A.en
dc.contributor.authorDe, Supriyoen
dc.contributor.authorDelany, Mary E.en
dc.contributor.authorDodgson, Jerry B.en
dc.contributor.authorDong, Jennifer J.en
dc.contributor.authorEvans, Cliveen
dc.contributor.authorFrederickson, Karin M.en
dc.contributor.authorFlicek, Paulen
dc.contributor.authorFlorea, Lilianaen
dc.contributor.authorFolkerts, Ottoen
dc.contributor.authorGroenen, Martien A. M.en
dc.contributor.authorHarkins, Tim T.en
dc.contributor.authorHerrero, Javieren
dc.contributor.authorHoffmann, Steveen
dc.contributor.authorMegens, Hendrik-Janen
dc.contributor.authorJiang, Andrewen
dc.contributor.authorde Jong, Pieteren
dc.contributor.authorKaiser, Peteen
dc.contributor.authorKim, Heebalen
dc.contributor.authorKim, Kyu-Wonen
dc.contributor.authorKim, Sungwonen
dc.contributor.authorLangenberger, Daviden
dc.contributor.authorLee, Mi-Kyungen
dc.contributor.authorLee, Taeheonen
dc.contributor.authorMane, Shrinivasrao P.en
dc.contributor.authorMarcais, Guillaumeen
dc.contributor.authorMarz, Manjaen
dc.contributor.authorMcElroy, Audrey P.en
dc.contributor.authorModise, Theroen
dc.contributor.authorNefedov, Mikhailen
dc.contributor.authorNotredame, Cédricen
dc.contributor.authorPaton, Ian R.en
dc.contributor.authorPayne, William S.en
dc.contributor.authorPertea, Geoen
dc.contributor.authorPrickett, Dennisen
dc.contributor.authorPuiu, Danielaen
dc.contributor.authorQioa, Danen
dc.contributor.authorRaineri, Emanueleen
dc.contributor.authorRuffier, Magalien
dc.contributor.authorSalzberg, Steven L.en
dc.contributor.authorSchatz, Michael C.en
dc.contributor.authorScheuring, Chantelen
dc.contributor.authorSchmidt, Carl J.en
dc.contributor.authorSchroeder, Stevenen
dc.contributor.authorSearle, Stephen M. J.en
dc.contributor.authorSmith, Edward J.en
dc.contributor.authorSmith, Jacquelineen
dc.contributor.authorSonstegard, Tad S.en
dc.contributor.authorStadler, Peter F.en
dc.contributor.authorTafer, Hakimen
dc.contributor.authorTu, Zhijian Jakeen
dc.contributor.authorVan Tassell, Curtis P.en
dc.contributor.authorVilella, Albert J.en
dc.contributor.authorWilliams, Kelly P.en
dc.contributor.authorYorke, James A.en
dc.contributor.authorZhang, Liqingen
dc.contributor.authorZhang, Hong-Binen
dc.contributor.authorZhang, Xiaojunen
dc.contributor.authorZhang, Yangen
dc.contributor.authorReed, Kent M.en
dc.contributor.departmentAnimal and Poultry Sciencesen
dc.contributor.departmentBiochemistryen
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentFralin Life Sciences Instituteen
dc.date.accessioned2017-01-15T04:03:09Zen
dc.date.available2017-01-15T04:03:09Zen
dc.date.issued2010-09-01en
dc.description.abstractA synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (,1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.en
dc.description.sponsorshipFunding for sequencing was supported by Roche Applied Science, the University of Minnesota (College of Veterinary Medicine, and College of Food, Agricultural & Natural Resource Sciences), the Utah State University (Center for Integrated Biosystems), the Virginia Bioinformatics Institute Core Lab Facility, Virginia Tech University (College of Agriculture & Life Sciences, Virginia Bioinformatics Institute, Fralin Biotechnology Center, Office of Vice President for Research), the Intramural Research Programs of the USDA Agricultural Research Service and the NIH National Institute on Aging, and Multi-State Research Support Program (USDA-NIFA-NRSP8). Funding for assembly, annotation and genomic analyses was provided by The Center for Genomics regulation and the European Community (Barcelona, Spain), ‘‘Landesstipendium Sachsen’’, the Free State of Saxony under the auspices of the ‘‘Landesexzellenzinitiative LIFE’’ (Germany), the NIH National Human Genome Research Institute (#R01-HG002945), the NIH National Library of Medicine (#R01-LM006845), the National Science Foundation (#DMS0616585), The Quantomics Project from 7th Framework Programe of the European Union, the Spanish Ministry of Science, The Wellcome Trust, the USDA National Institute of Food and Agriculture Animal Genome Program (#’s 2005-35205-15451; 2007-0212704; 2007-35205-17880; 2008-04049; 2008-35205-18720; 2009-35205-05302; 2010-65205-20412) and Ministry of Science & Technology (Korea Science & Engineering Foundation) of Korea (R01-2007-000-20456-0). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.description.versionPublished versionen
dc.format.extent? - ? (21) page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.citationDalloul RA, Long JA, Zimin AV, Aslam L, Beal K, et al. (2010) Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis. PLoS Biol 8(9): e1000475.en
dc.identifier.doihttps://doi.org/10.1371/journal.pbio.1000475en
dc.identifier.issn1545-7885en
dc.identifier.issue9en
dc.identifier.urihttp://hdl.handle.net/10919/74315en
dc.identifier.volume8en
dc.language.isoenen
dc.publisherPLOSen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000282279200020&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons CC0 1.0 Universal Public Domain Dedicationen
dc.rights.urihttp://creativecommons.org/publicdomain/zero/1.0/en
dc.subjectBiochemistry & Molecular Biologyen
dc.subjectBiologyen
dc.subjectLife Sciences & Biomedicine - Other Topicsen
dc.subjectBIOLOGYen
dc.subjectHIGH-THROUGHPUTen
dc.subjectMONODELPHIS-DOMESTICAen
dc.subjectMOLECULAR PHYLOGENYen
dc.subjectCHICKEN GENOMEen
dc.subjectGENE FAMILYen
dc.subjectEVOLUTIONen
dc.subjectIDENTIFICATIONen
dc.subjectDIVERSITYen
dc.subjectBIRDSen
dc.subjectGALLIFORMESen
dc.titleMulti-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysisen
dc.title.serialPlos Biologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Animal and Poultry Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Engineeringen
pubs.organisational-group/Virginia Tech/Engineering/COE T&R Facultyen
pubs.organisational-group/Virginia Tech/Engineering/Computer Scienceen

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