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[[Turkey genome authors]] <br />
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PLOSbiology: <a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000475">http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000475</a><br />
<h2 xpathlocation="noSelect">Abstract</h2>
<p xpathlocation="/article[1]/front[1]/article-meta[1]/abstract[2]/p[1]">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 (<em>Meleagris gallopavo</em>). 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.<br />
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<div class="abstract" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:aml="http://topazproject.org/aml/" xpathlocation="/article[1]/front[1]/article-meta[1]/abstract[3]"><a id="abstract2" title="Author Summary" name="abstract2" toc="abstract2"></a><h2 xpathlocation="noSelect">Author Summary</h2><p xpathlocationfont size="/article[1]/front[1]/article-meta[1]/abstract[3]/p[1]">In contrast to the compact sequence of viruses and bacteria, determining the complete genome sequence of complex vertebrate genomes can be a daunting task. With the advent of “next-generation” sequencing platforms, it is now possible to rapidly sequence and assemble a vertebrate genome, especially for species for which genomic resources—genetic maps and markers—are currently available. We used a combination of two next-generation sequencing platforms, Roche 454 and Illumina GAII, and unique assembly tools to sequence the genome of the agriculturally important turkey, <emstrong>Meleagris gallopavoReceived:</emstrong>. Our draft assembly comprises approximately 1.1 gigabases of which 917 megabytes are assigned to specific chromosomes. Comparisons of the turkey genome sequence with those of the chickenDecember 21, 2009; <emstrong>Gallus gallusAccepted:</emstrong>July 27, and the zebra finch, 2010; <emstrong>Taeniopygia guttataPublished:</emstrong>September 7, provide insights into the evolution of the avian lineage. This genome sequence will facilitate discovery of agriculturally important genetic variants.2010</pfont></h2>
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<p><strong>Citation: </strong>Dalloul RAThis is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, Long JAonce placed in the public domain, Zimin AVthis work may be freely reproduced, Aslam Ldistributed, Beal Ktransmitted, et al. (2010) Multi-Platform Next-Generation Sequencing of the Domestic Turkey (<em>Meleagris gallopavo</em>): Genome Assembly and Analysis. PLoS Biol 8(9): e1000475. doi:10.1371/journal.pbio.1000475</p><p><strong>Academic Editor: </strong>Richard J. Robertsmodified, New England Biolabsbuilt upon, United States of Americaor otherwise used by anyone for any lawful purpose.</p>
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<p><strong>Abbreviations: </strong>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</p>
<p><a name="cor1"></a>* E-mail: <a href="mailto:reedx054@umn.edu"><font color="#0066cc">reedx054@umn.edu</font></a><br />
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