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

Xiaodong Fang1, Yanfeng Zhang23, Rui Zhang24, Lixin Yang23, Ming Li23, Kaixiong Ye2, Xiaosen Guo1, Jun Wang1* and Bing Su2*

Author affiliations

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

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Citation and License

Genome Biology 2011, 12:R63  doi:10.1186/gb-2011-12-7-r63

Published: 6 July 2011

Abstract

Background

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.

Results

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.

Conclusions

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.