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

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.

Polymorphic Integrations of an Endogenous Gammaretrovirus in the Mule Deer Genome

“…The number of LTRs, including the solitary LTRs, is 2-to 3-fold higher. We were able to detect seven copies of CrERV␥ LTR in a 52-Mb portion of the white-tailed deer genome that was recently reported (43). Considering an average mammalian haploid genome size of 3,000 Mb and uniform distribution of LTR across the genome, this would yield approximately 400 LTR copies per white-tailed deer genome, a number that is consistent with our quantitative PCR estimates.…”

The phylogenetic status of typical Chinese native pigs: analyzed by Asian and European pig mitochondrial genome sequences

“…For evolution research, a number of studies of the D-loop region sequence mutation in mtDNA have also been investigated [12-15]. And thus also has been frequently used for phylogenetic analysis of closely related groups, especially for determining intra-specific phylogenies [16]. …”

A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla)

“…It is important to calculate the proportion of TEs in a genome from the single, cleaned reads and not from low coverage assemblies to avoid the pitfall of an underrepresentation or of skewing the TE data. We encountered such problems when analyzing the white-tailed deer genome assembly (Seabury et al, 2011) which to date is the only sequenced cervid (deers and allies). Cervidae is another species-rich group in Ruminantia (Fig.…”

“…Transposable element values were extracted from the respective genome publications for human (Homo sapiens), cow (Bos taurus), minke whale (Balaenoptera acutorostrata, Mysticeti), Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and a second alpaca genome assembly (Lander et al, 2001;Chinwalla et al, 2002;Elsik et al, 2009;Yim et al, 2014;Wu et al, 2014). In addition, the low-coverage assembly of the whitetailed deer (Odocoileus virginianus) genome was analyzed (Seabury et al, 2011) for comparison with values obtained from high-coverage genomes and the survey-sequenced genomes.…”