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

Turkey genome authors 

Published September 7, 2010

PLOSbiology: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000475

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.

Received: December 21, 2009; Accepted: July 27, 2010; Published: September 7, 2010

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Abbreviations: BAC, bacterial artificial chromosome; BES, BAC end sequence; CNV, copy number variation; ESTs, expressed sequence tags; FISH, fluorescence in situ hybridization; GO, gene ontology; LINE, long interspersed nuclear element; MHC, major histocompatibility complex; miRNA, micro-RNA; ncRNA, non-coding RNA; NGS, next-generation sequencing; RPG, rate pattern group; SINE, short interspersed nuclear element; snoRNA, small nucleolar RNA; SNP, single nucleotide polymorphism; SNV, single nucleotide variant (SNP/indel); TE, transposable element; TLR, Toll-like receptor; WGS, whole genome shotgun

Citation: Dalloul 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. doi:10.1371/journal.pbio.1000475

* E-mail: reedx054@umn.edu