Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis

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 FloreaOtto 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 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

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Article numbere1000475
JournalPLoS biology
Volume8
Issue number9
DOIs
StatePublished - Sep 2010
Externally publishedYes

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)

Fingerprint Dive into the research topics of 'Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis'. Together they form a unique fingerprint.

Cite this