Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque
- Equal contributors
1 Beijing Genomics Institute-Shenzhen, Chinese Academy of Sciences, Shenzhen 518083, China
2 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology and Kunming Primate Research Center, Chinese Academy of Sciences, Kunming 650223, China
3 Graduate School of Chinese Academy of Sciences, Beijing 100039, China
4 Current address: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
Genome Biology 2011, 12:R63 doi:10.1186/gb-2011-12-7-r63Published: 6 July 2011
Rhesus 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.
Using 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.
Genome 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.