Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

A 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 th...

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Autores principales:	Rami A Dalloul, Julie A Long, Aleksey V Zimin, Luqman Aslam, Kathryn Beal, Le Ann Blomberg, Pascal Bouffard, David W Burt, Oswald Crasta, Richard P M A Crooijmans, Kristal Cooper, Roger A Coulombe, Supriyo De, Mary E Delany, Jerry B Dodgson, Jennifer J Dong, Clive Evans, Karin M Frederickson, Paul Flicek, Liliana Florea, Otto Folkerts, Martien A M Groenen, Tim T Harkins, Javier Herrero, Steve Hoffmann, Hendrik-Jan Megens, Andrew Jiang, Pieter de Jong, Pete Kaiser, Heebal Kim, Kyu-Won Kim, Sungwon Kim, David Langenberger, Mi-Kyung Lee, Taeheon Lee, Shrinivasrao Mane, Guillaume Marcais, Manja Marz, Audrey P McElroy, Thero Modise, Mikhail Nefedov, Cédric Notredame, Ian R Paton, William S Payne, Geo Pertea, Dennis Prickett, Daniela Puiu, Dan Qioa, Emanuele Raineri, Magali Ruffier, Steven L Salzberg, Michael C Schatz, Chantel Scheuring, Carl J Schmidt, Steven Schroeder, Stephen M J Searle, Edward J Smith, Jacqueline Smith, Tad S Sonstegard, Peter F Stadler, Hakim Tafer, Zhijian Jake Tu, Curtis P Van Tassell, Albert J Vilella, Kelly P Williams, James A Yorke, Liqing Zhang, Hong-Bin Zhang, Xiaojun Zhang, Yang Zhang, Kent M Reed
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/202b20ab287a4e41a67ff5edaf644d18
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spelling	oai:doaj.org-article:202b20ab287a4e41a67ff5edaf644d182021-11-18T05:34:52ZMulti-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.1544-91731545-788510.1371/journal.pbio.1000475https://doaj.org/article/202b20ab287a4e41a67ff5edaf644d182010-09-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20838655/?tool=EBIhttps://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885A 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.Rami A DalloulJulie A LongAleksey V ZiminLuqman AslamKathryn BealLe Ann BlombergPascal BouffardDavid W BurtOswald CrastaRichard P M A CrooijmansKristal CooperRoger A CoulombeSupriyo DeMary E DelanyJerry B DodgsonJennifer J DongClive EvansKarin M FredericksonPaul FlicekLiliana FloreaOtto FolkertsMartien A M GroenenTim T HarkinsJavier HerreroSteve HoffmannHendrik-Jan MegensAndrew JiangPieter de JongPete KaiserHeebal KimKyu-Won KimSungwon KimDavid LangenbergerMi-Kyung LeeTaeheon LeeShrinivasrao ManeGuillaume MarcaisManja MarzAudrey P McElroyThero ModiseMikhail NefedovCédric NotredameIan R PatonWilliam S PayneGeo PerteaDennis PrickettDaniela PuiuDan QioaEmanuele RaineriMagali RuffierSteven L SalzbergMichael C SchatzChantel ScheuringCarl J SchmidtSteven SchroederStephen M J SearleEdward J SmithJacqueline SmithTad S SonstegardPeter F StadlerHakim TaferZhijian Jake TuCurtis P Van TassellAlbert J VilellaKelly P WilliamsJames A YorkeLiqing ZhangHong-Bin ZhangXiaojun ZhangYang ZhangKent M ReedPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 8, Iss 9 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Rami A Dalloul Julie A Long Aleksey V Zimin Luqman Aslam Kathryn Beal Le Ann Blomberg Pascal Bouffard David W Burt Oswald Crasta Richard P M A Crooijmans Kristal Cooper Roger A Coulombe Supriyo De Mary E Delany Jerry B Dodgson Jennifer J Dong Clive Evans Karin M Frederickson Paul Flicek Liliana Florea Otto Folkerts Martien A M Groenen Tim T Harkins Javier Herrero Steve Hoffmann Hendrik-Jan Megens Andrew Jiang Pieter de Jong Pete Kaiser Heebal Kim Kyu-Won Kim Sungwon Kim David Langenberger Mi-Kyung Lee Taeheon Lee Shrinivasrao Mane Guillaume Marcais Manja Marz Audrey P McElroy Thero Modise Mikhail Nefedov Cédric Notredame Ian R Paton William S Payne Geo Pertea Dennis Prickett Daniela Puiu Dan Qioa Emanuele Raineri Magali Ruffier Steven L Salzberg Michael C Schatz Chantel Scheuring Carl J Schmidt Steven Schroeder Stephen M J Searle Edward J Smith Jacqueline Smith Tad S Sonstegard Peter F Stadler Hakim Tafer Zhijian Jake Tu Curtis P Van Tassell Albert J Vilella Kelly P Williams James A Yorke Liqing Zhang Hong-Bin Zhang Xiaojun Zhang Yang Zhang Kent M Reed Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
description	A 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.
format	article
author	Rami A Dalloul Julie A Long Aleksey V Zimin Luqman Aslam Kathryn Beal Le Ann Blomberg Pascal Bouffard David W Burt Oswald Crasta Richard P M A Crooijmans Kristal Cooper Roger A Coulombe Supriyo De Mary E Delany Jerry B Dodgson Jennifer J Dong Clive Evans Karin M Frederickson Paul Flicek Liliana Florea Otto Folkerts Martien A M Groenen Tim T Harkins Javier Herrero Steve Hoffmann Hendrik-Jan Megens Andrew Jiang Pieter de Jong Pete Kaiser Heebal Kim Kyu-Won Kim Sungwon Kim David Langenberger Mi-Kyung Lee Taeheon Lee Shrinivasrao Mane Guillaume Marcais Manja Marz Audrey P McElroy Thero Modise Mikhail Nefedov Cédric Notredame Ian R Paton William S Payne Geo Pertea Dennis Prickett Daniela Puiu Dan Qioa Emanuele Raineri Magali Ruffier Steven L Salzberg Michael C Schatz Chantel Scheuring Carl J Schmidt Steven Schroeder Stephen M J Searle Edward J Smith Jacqueline Smith Tad S Sonstegard Peter F Stadler Hakim Tafer Zhijian Jake Tu Curtis P Van Tassell Albert J Vilella Kelly P Williams James A Yorke Liqing Zhang Hong-Bin Zhang Xiaojun Zhang Yang Zhang Kent M Reed
author_facet	Rami A Dalloul Julie A Long Aleksey V Zimin Luqman Aslam Kathryn Beal Le Ann Blomberg Pascal Bouffard David W Burt Oswald Crasta Richard P M A Crooijmans Kristal Cooper Roger A Coulombe Supriyo De Mary E Delany Jerry B Dodgson Jennifer J Dong Clive Evans Karin M Frederickson Paul Flicek Liliana Florea Otto Folkerts Martien A M Groenen Tim T Harkins Javier Herrero Steve Hoffmann Hendrik-Jan Megens Andrew Jiang Pieter de Jong Pete Kaiser Heebal Kim Kyu-Won Kim Sungwon Kim David Langenberger Mi-Kyung Lee Taeheon Lee Shrinivasrao Mane Guillaume Marcais Manja Marz Audrey P McElroy Thero Modise Mikhail Nefedov Cédric Notredame Ian R Paton William S Payne Geo Pertea Dennis Prickett Daniela Puiu Dan Qioa Emanuele Raineri Magali Ruffier Steven L Salzberg Michael C Schatz Chantel Scheuring Carl J Schmidt Steven Schroeder Stephen M J Searle Edward J Smith Jacqueline Smith Tad S Sonstegard Peter F Stadler Hakim Tafer Zhijian Jake Tu Curtis P Van Tassell Albert J Vilella Kelly P Williams James A Yorke Liqing Zhang Hong-Bin Zhang Xiaojun Zhang Yang Zhang Kent M Reed
author_sort	Rami A Dalloul
title	Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
title_short	Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
title_full	Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
title_fullStr	Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
title_full_unstemmed	Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
title_sort	multi-platform next-generation sequencing of the domestic turkey (meleagris gallopavo): genome assembly and analysis.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/202b20ab287a4e41a67ff5edaf644d18
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Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

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