Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque

Abstract

BackgroundRhesus macaque (Macaca mulatta) is the most widely used nonhuman primate animal in biomedical research. A global map of genetic variations in rhesus macaque is valuable for both evolutionary and functional studies.ResultsUsing next-generation sequencing technology, we sequenced a Chinese rhesus macaque genome with 11.56-fold coverage. In total, 96% of the reference Indian macaque genome was covered by at least one read, and we identified 2.56 million homozygous and 2.94 million heterozygous SNPs. We also detected a total of 125,150 structural variations, of which 123,610 were deletions with a median length of 184 bp (ranging from 25 bp to 10 kb); 63% of these deletions were located in intergenic regions and 35% in intronic regions. We further annotated 5,187 and 962 nonsynonymous SNPs to the macaque orthologs of human disease and drug-target genes, respectively. Finally, we set up a genome-wide genetic variation database with the use of Gbrowse.ConclusionsGenome sequencing and construction of a global sequence variation map in Chinese rhesus macaque with the concomitant database provide applicable resources for evolutionary and biomedical research.