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Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics

The white-tailed deer (Odocoileus virginianus) represents one of the most successful and widely distributed large mammal species within North America, yet very little nucleotide sequence information is available. We utilized massively parallel pyrosequencing of a reduced representation library (RRL)...

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Autores principales: Seabury, Christopher M., Bhattarai, Eric K., Taylor, Jeremy F., Viswanathan, Ganesh G., Cooper, Susan M., Davis, Donald S., Dowd, Scot E., Lockwood, Mitch L., Seabury, Paul M.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023705/
https://www.ncbi.nlm.nih.gov/pubmed/21283515
http://dx.doi.org/10.1371/journal.pone.0015811
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author Seabury, Christopher M.
Bhattarai, Eric K.
Taylor, Jeremy F.
Viswanathan, Ganesh G.
Cooper, Susan M.
Davis, Donald S.
Dowd, Scot E.
Lockwood, Mitch L.
Seabury, Paul M.
author_facet Seabury, Christopher M.
Bhattarai, Eric K.
Taylor, Jeremy F.
Viswanathan, Ganesh G.
Cooper, Susan M.
Davis, Donald S.
Dowd, Scot E.
Lockwood, Mitch L.
Seabury, Paul M.
author_sort Seabury, Christopher M.
collection PubMed
description The white-tailed deer (Odocoileus virginianus) represents one of the most successful and widely distributed large mammal species within North America, yet very little nucleotide sequence information is available. We utilized massively parallel pyrosequencing of a reduced representation library (RRL) and a random shotgun library (RSL) to generate a complete mitochondrial genome sequence and identify a large number of putative single nucleotide polymorphisms (SNPs) distributed throughout the white-tailed deer nuclear and mitochondrial genomes. A SNP validation study designed to test specific classes of putative SNPs provides evidence for as many as 10,476 genome-wide SNPs in the current dataset. Based on cytogenetic evidence for homology between cow (Bos taurus) and white-tailed deer chromosomes, we demonstrate that a divergent genome may be used for estimating the relative distribution and density of de novo sequence contigs as well as putative SNPs for species without draft genome assemblies. Our approach demonstrates that bioinformatic tools developed for model or agriculturally important species may be leveraged to support next-generation research programs for species of biological, ecological and evolutionary importance. We also provide a functional annotation analysis for the de novo sequence contigs assembled from white-tailed deer pyrosequencing reads, a mitochondrial phylogeny involving 13,722 nucleotide positions for 10 unique species of Cervidae, and a median joining haplotype network as a putative representation of mitochondrial evolution in O. virginianus. The results of this study are expected to provide a detailed template enabling genome-wide sequence-based studies of threatened, endangered or conservationally important non-model organisms.
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spelling pubmed-30237052011-01-31 Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics Seabury, Christopher M. Bhattarai, Eric K. Taylor, Jeremy F. Viswanathan, Ganesh G. Cooper, Susan M. Davis, Donald S. Dowd, Scot E. Lockwood, Mitch L. Seabury, Paul M. PLoS One Research Article The white-tailed deer (Odocoileus virginianus) represents one of the most successful and widely distributed large mammal species within North America, yet very little nucleotide sequence information is available. We utilized massively parallel pyrosequencing of a reduced representation library (RRL) and a random shotgun library (RSL) to generate a complete mitochondrial genome sequence and identify a large number of putative single nucleotide polymorphisms (SNPs) distributed throughout the white-tailed deer nuclear and mitochondrial genomes. A SNP validation study designed to test specific classes of putative SNPs provides evidence for as many as 10,476 genome-wide SNPs in the current dataset. Based on cytogenetic evidence for homology between cow (Bos taurus) and white-tailed deer chromosomes, we demonstrate that a divergent genome may be used for estimating the relative distribution and density of de novo sequence contigs as well as putative SNPs for species without draft genome assemblies. Our approach demonstrates that bioinformatic tools developed for model or agriculturally important species may be leveraged to support next-generation research programs for species of biological, ecological and evolutionary importance. We also provide a functional annotation analysis for the de novo sequence contigs assembled from white-tailed deer pyrosequencing reads, a mitochondrial phylogeny involving 13,722 nucleotide positions for 10 unique species of Cervidae, and a median joining haplotype network as a putative representation of mitochondrial evolution in O. virginianus. The results of this study are expected to provide a detailed template enabling genome-wide sequence-based studies of threatened, endangered or conservationally important non-model organisms. Public Library of Science 2011-01-19 /pmc/articles/PMC3023705/ /pubmed/21283515 http://dx.doi.org/10.1371/journal.pone.0015811 Text en Seabury et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Seabury, Christopher M.
Bhattarai, Eric K.
Taylor, Jeremy F.
Viswanathan, Ganesh G.
Cooper, Susan M.
Davis, Donald S.
Dowd, Scot E.
Lockwood, Mitch L.
Seabury, Paul M.
Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics
title Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics
title_full Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics
title_fullStr Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics
title_full_unstemmed Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics
title_short Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics
title_sort genome-wide polymorphism and comparative analyses in the white-tailed deer (odocoileus virginianus): a model for conservation genomics
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023705/
https://www.ncbi.nlm.nih.gov/pubmed/21283515
http://dx.doi.org/10.1371/journal.pone.0015811
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