DOI: 10.5061/dryad.79kh0
title: Data from: "White-tailed deer (Odocoileus virginianus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 June 2013-31 July 2013

description: White-tailed deer (Odocoileus virginianus) are among the most abundant and
 widespread large mammals in the Americas, comprising up to 38 subspecies
 ranging from Northern Canada to Peru. Although believed to have high
 genetic diversity, surprisingly few genomic resources are currently
 available, despite the species’ ecological and economic importance.
 White-tailed deer and other cervids throughout central North America are
 currently being afflicted by chronic wasting disease (CWD), one of the
 degenerative prion diseases collectively known as transmissible spongiform
 encephalopathies. Although CWD is of major importance to white-tailed deer
 management, little is currently known about innate resistance or
 susceptibility to CWD outside of polymorphisms in the prion protein gene,
 Prnp, though a recent study using microsatellites suggests that the
 disease may have additional underlying genetic components. Further
 association analysis is hindered by low marker density. In this study, we
 used high-throughput SOLiD sequencing to create novel sequence data for
 white-tailed deer and identify single-nucleotide polymorphisms, using the
 pooled blood transcriptomes of six individuals. In total, we generated
 14,010 contigs of length ≥ 200 nt, representing 4,104,760 nt of unique
 sequence data, and we identified 66,596 SNPs. This data represents one of
 the largest genetic resources currently available for any cervid. We hope
 it will facilitate future research for population genomics and assist with
 the identification of genetic factors that underlie disease resistance and
 other traits relevant for conservation and management.
description: Trimmed Un-mapped Data
 assemblyResultant BAM file from
 a pool of rRNA-depleted, non-normalized cDNA of six white-tailed deer from
 the University of Saskatchewan's Specialized Livestock Research
 Facility that was assembled de novo in CLC Genomics Workbench
 6.0.1.BLAST
 resultsTop BLAST results of
 consensus contigs extracted from the .bam file. blastx+ 2.2.27 was used
 with an e-value threshold of 0.000001 against a custom database of RefSeq
 eutherian protein sequences.blast.txtdbSNP ss Accession NumbersList of SNP ss accession numbers detected in the assembly using CLC Genomics Workbench 6.0.1. These SNPs will be available online in the next dbSNP update, currently scheduled for Oct. 2013.Malenfant_04_05_2013.vcf.reformatted.loaded.rep.txtWhite-tailed deer SNPs (VCF file)We detected SNPs using CLC’s quality-based variant detection algorithm (min. average quality of five flanking bases on either side of SNP = 15; min. quality of central base = 20; min. coverage = 20; max. coverage = 1000; min. variant frequency = 15%; min. variant count = 4), discarding all reads with non-specific alignments. Multiallelic SNPs were discarded as they may result from incorrect alignment of reads from paralogous genes in the transcriptome data. All SNPs have been submitted to dbSNP and will be available online in the October 2013 update. This VCF file is available in the interim.wtd_SNPs.vcf.txt