Abstract
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.
Highlights
Organisms traditionally considered of ‘‘minor’’ importance by national and international funding agencies generally suffer from a paucity of genome-wide sequence and polymorphism data which severely limits the implementation of genomic approaches for addressing biological questions in these species
Genomic sequence information derived from our representation library (RRL) contigs will contribute to establishing an annotated white-tailed deer repeat library, and may help elucidate potential copy number variants
We have generated a substantial number of high quality white-tailed deer nuclear sequence contigs which were unambiguously aligned to the bovine genome assembly despite 32.5 million years of species divergence, as predicted from a mitochondrial CYTB and 16S rRNA analysis [53]
Summary
Organisms traditionally considered of ‘‘minor’’ importance by national and international funding agencies generally suffer from a paucity of genome-wide sequence and polymorphism data which severely limits the implementation of genomic approaches for addressing biological questions in these species. One such underserved species is the white-tailed deer (Odocoileus virginianus), a highly successful and widely distributed ruminant mammal species of the order Artiodactyla and family Cervidae [1,2,3]. Within the genus Odocoileus, the primary species are the white-tailed deer (O. virginianus) and mule deer (O. hemionus; for review see [2,3]), with these species possessing equivalent karyotypes (2n = 70) [4]. White-tailed deer have adapted to a variety of landscapes and environmental conditions while exhibiting exceptional potential for recruitment [6,7,8], and despite historic overexploitation, appear to possess relatively high levels of genetic diversity [7,9,10]
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