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

PLoS Biology2010Vol. 8(9), pp. e1000475–e1000475

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Rami A. Dalloul, Julie A. Long, Aleksey V. Zimin, Muhammad Luqman Aslam, Kathryn Beal, Le Ann Blomberg, Pascal Bouffard, David W. Burt, Oswald Crasta, R.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 Harkins, Javier Herrero, Steve Hoffmann, Hendrik‐Jan Megens, Andrew Jiang, Pieter de Jong, Pete Kaiser, Heebal Kim, Kyu‐Won Kim, Sung‐Won Kim, David Langenberger, Mi-Kyung Lee, Taeheon Lee, Shrinivasrao P. Mane, Guillaume Marçais, Manja Marz, A.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 F. Scheuring, Carl J. Schmidt, Steven Schroeder, Stephen M. J. Searle, E. 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

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.

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Abstract

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