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

被引：300

作者：

Dalloul, Rami A. ^{[1
]}

Long, Julie A. ^{[2
]}

Zimin, Aleksey V. ^{[3
]}

Aslam, Luqman ^{[4
]}

Beal, Kathryn ^{[5
]}

Blomberg, Le Ann ^{[2
]}

Bouffard, Pascal ^{[6
]}

Burt, David W. ^{[7
,8
]}

Crasta, Oswald ^{[9
,10
]}

Crooijmans, Richard P. M. A. ^{[4
]}

Cooper, Kristal ^{[9
]}

Coulombe, Roger A. ^{[11
]}

De, Supriyo ^{[12
]}

Delany, Mary E. ^{[13
]}

Dodgson, Jerry B. ^{[14
]}

Dong, Jennifer J. ^{[15
]}

Evans, Clive ^{[9
]}

Frederickson, Karin M. ^{[6
]}

Flicek, Paul ^{[5
]}

Florea, Liliana

Folkerts, Otto ^{[9
,10
]}

Groenen, Martien A. M. ^{[4
]}

Harkins, Tim T. ^{[6
]}

Herrero, Javier ^{[5
]}

Hoffmann, Steve ^{[16
,17
,18
]}

Megens, Hendrik-Jan ^{[4
]}

Jiang, Andrew ^{[13
]}

de Jong, Pieter ^{[19
]}

Kaiser, Pete ^{[20
]}

Kim, Heebal ^{[21
]}

Kim, Kyu-Won ^{[21
]}

Kim, Sungwon ^{[1
]}

Langenberger, David ^{[16
,17
]}

Lee, Mi-Kyung ^{[15
]}

Lee, Taeheon ^{[21
]}

Mane, Shrinivasrao ^{[9
]}

Marcais, Guillaume ^{[3
]}

Marz, Manja ^{[16
,17
,22
]}

McElroy, Audrey P. ^{[1
]}

Modise, Thero ^{[9
]}

Nefedov, Mikhail ^{[19
]}

Notredame, Cedric ^{[23
]}

Paton, Ian R. ^{[7
,8
]}

Payne, William S. ^{[14
]}

Pertea, Geo

Prickett, Dennis ^{[20
]}

Puiu, Daniela

Qioa, Dan ^{[24
]}

Raineri, Emanuele ^{[23
]}

Ruffier, Magali ^{[25
]}

机构：

[1] Virginia Tech, Dept Anim & Poultry Sci, Avian Immunobiol Lab, Blacksburg, VA 24061 USA

[2] ARS, Anim Biosci & Biotechnol Lab, USDA, Beltsville, MD USA

[3] Univ Maryland, Inst Phys Sci & Technol, College Pk, MD 20742 USA

[4] Wageningen Univ, Anim Breeding & Genom Ctr, Wageningen, Netherlands

[5] European Bioinformat Inst, Cambridge, England

[6] Roche Appl Sci, Indianapolis, IN USA

[7] Univ Edinburgh, Roslin Inst, Roslin, Midlothian, Scotland

[8] Univ Edinburgh, Royal Dick Sch Vet Studies, Roslin, Midlothian, Scotland

[9] Virginia Tech, Virginia Bioinformat Inst, Blacksburg, VA USA

[10] Chromatin Inc, Champaign, IL USA

[11] Utah State Univ, Dept Vet Sci, Logan, UT 84322 USA

[12] NIA, Gene Express & Genom Unit, NIH, Baltimore, MD 21224 USA

[13] Univ Calif Davis, Dept Anim Sci, Davis, CA 95616 USA

[14] Michigan State Univ, Dept Microbiol & Mol Genet, E Lansing, MI 48824 USA

[15] Texas A&M Univ, Dept Soil & Crop Sci, College Stn, TX 77843 USA

[16] Univ Leipzig, Interdisciplinary Ctr Bioinformat, Leipzig, Germany

[17] Univ Leipzig, Dept Comp Sci, Leipzig, Germany

[18] Univ Leipzig, LIFE Project, Leipzig, Germany

[19] Childrens Hosp & Res Ctr Oakland, Oakland, CA USA

[20] Inst Anim Hlth, Compton, Berks, England

[21] Seoul Natl Univ, Dept Agr Biotechnol, Lab Bioinformat & Populat Genet, Seoul, South Korea

[22] Univ Marburg, Marburg, Germany

[23] Univ Pompeus Fabre, Ctr Genom Regulat CRG, Barcelona, Spain

[24] Virginia Tech, Dept Comp Sci, Blacksburg, VA USA

[25] Wellcome Trust Sanger Inst, Cambridge, England

[26] Univ Maryland, Dept Comp Sci, Ctr Bioinformat & Computat Biol, College Pk, MD 20742 USA

[27] Univ Delaware, Dept Anim & Food Sci, Newark, DE USA

[28] Univ Minnesota, Coll Vet Med, Dept Vet & Biomed Sci, St Paul, MN 55108 USA

[29] ARS, Anim Improvement Programs Lab, USDA, Beltsville Agr Res Ctr, Beltsville, MD USA

[30] Virginia Tech, Dept Biochem, Blacksburg, VA USA

[31] Santa Fe Inst, Santa Fe, NM 87501 USA

[32] Univ Vienna, Dept Theoret Chem, Vienna, Austria

[33] Fraunhofer Inst Zelltherapie & Immunol, Leipzig, Germany

[34] Max Planck Inst Math Sci, Leipzig, Germany

[35] ARS, Bovine Funct Genom Lab, USDA, Beltsville Agr Res Ctr, Beltsville, MD USA

来源：

PLOS BIOLOGY | 2010年 / 8卷 / 09期

基金：

美国国家科学基金会; 英国生物技术与生命科学研究理事会; 美国食品与农业研究所; 英国惠康基金;

关键词：

CHICKEN; EVOLUTION; GENE; IDENTIFICATION; GALLIFORMES; DIVERSITY; DISCOVERY; PHYLOGENY; DATABASE; MOUSE;

D O I：

10.1371/journal.pbio.1000475

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 (similar to 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.

引用

页数：21

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