DoGSD: the dog and wolf genome SNP database

Abstract

The rapid advancement of next-generation sequencing technology has generated a deluge of genomic data from domesticated dogs and their wild ancestor, grey wolves, which have simultaneously broadened our understanding of domestication and diseases that are shared by humans and dogs. To address the scarcity of single nucleotide polymorphism (SNP) data provided by authorized databases and to make SNP data more easily/friendly usable and available, we propose DoGSD (http://dogsd.big.ac.cn), the first canidae-specific database which focuses on whole genome SNP data from domesticated dogs and grey wolves. The DoGSD is a web-based, open-access resource comprising ∼19 million high-quality whole-genome SNPs. In addition to the dbSNP data set (build 139), DoGSD incorporates a comprehensive collection of SNPs from two newly sequenced samples (1 wolf and 1 dog) and collected SNPs from three latest dog/wolf genetic studies (7 wolves and 68 dogs), which were taken together for analysis with the population genetic statistics, Fst. In addition, DoGSD integrates some closely related information including SNP annotation, summary lists of SNPs located in genes, synonymous and non-synonymous SNPs, sampling location and breed information. All these features make DoGSD a useful resource for in-depth analysis in dog-/wolf-related studies.

Lessons from the canine Oxtr gene: populations, variants and functional aspects

“…The novel −74C/G SNP and seven additional canine Oxtr polymorphisms deposited in public databases [dbSNP, Ensembl, DoGSD (Bai et al )] or described in (Kis et al ): −50C/G, −94T/C, −213A/G (formerly: −212A/G), rs22927829, rs8679682 rs8679684 and 19208A/G (formerly: 19131A/G) were genotyped in a larger population involving nearly 700 dogs from 10 breeds and 40 wolves. Our results showed that these SNPs are polymorphic in canines, however, allele frequencies showed marked differences between both species/subspecies (Fig.…”

Adaptive evolution to a high purine and fat diet of carnivorans revealed by gut microbiomes and host genomes

“…To extend the scope of Felidae and Candidae species utilized in this analysis, lion, snow leopard, wolf and grey wolf whole genome sequencing data were incorporated. Wolf (sample: CHW, CRW and ISW) and grey wolf (sample: SolidGW1, LUPWCHN00001 and LUPWRUS00001) SNP variations were downloaded directly from the Dog Genome SNP Database (Bai et al, 2015). For lions and snow leopards, genomic Illumina reads were downloaded (http://biodisk.org) (DOI: 10.1038/ncomms3433), and the Siberian tiger reference sequence was used to call SNPs using the SAMTOOLS-VCFTOOLS pipeline.…”

YARS2 Missense Variant in Belgian Shepherd Dogs with Cardiomyopathy and Juvenile Mortality

“…To predict the functional effects of the called variants, SnpEff [11] software together with NCBI annotation release 105 for the CanFam 3.1 genome reference assembly was used. We used a vcf-file containing 648 dog and 8 wolf genomes, which were either publicly available [12,13] or produced during other projects of our group [10]. We excluded 10 genome sequences from other Belgian Shepherd dogs from filtering to minimize the risk of having any unrecognized carriers in the control cohort.…”