July 21, 2011 BGI (previously known as the Beijing Genomics Institute) and Kunming Institute of Zoology, Chinese Academy of Sciences, together published the whole sequence variation map of rhesus macaque (Macaca mulatta) in Genome Biology on July 6th, 2011. The study provides available resources for evolutionary and biomedical research.
Rhesus macaque, also called the Rhesus monkey, is one of the best known species of old world monkeys. Human and Rhesus macaque share a most recent common ancestor about 25 million years ago with 93.5% identify of their genome sequences. Due to its close relationship to human genetically and physiologically, rhesus macaque is the most extensively used non-human primate animals in biomedical research and animal models for human diseases research.
"Rhesus macaque is the second non-human primate to be sequenced in the world, which is a critical non-human primate animal model. The studies on genetic variations in rhesus macaque will pose an important significance to biomedical research," stated Xiaodong Fang, project principal of BGI and the co-lead author of the study.
With the advanced genome sequencing capability of BGI, researchers sequenced a Chinese rhesus macaque genome with 11.56-fold coverage. All sequenced reads were aligned to the reference Indian rhesus macaque genome (rheMac2) by using SOAP2, BGI's improved Short Oligonucleotide Alignment Program. There is 96% of the reference Indian macaque genome covered by at least one read. Compared with the sequenced reference Indian macaque genome, 5.5 million SNPs, including 2.56 million homozygous and 2.94 million heterozygous SNPs, were identified and 125,150 structural variations (SV) were detected. They also annotated 5,187 and 962 nonsynonymous SNPs to the macaque orthologs of human disease and drug-target genes, respectively.
"The variation map of rhesus macaque provides a useful framework for further genome-wide association studies and also has important applications to evolutionary and functional studies.
This study is only a part in our research on the genetics of rhesus macaque, and more detailed results will be published in the future," said professor Fang.
Researchers also established a genome-wide genetic variation database named the Chinese macaque single nucleotide polymorphism (CMSNP) database for data visualization. It can be accessed at http://monkey.genomics.org.cn.
Scientists from BGI-Shenzhen (Shenzhen, China), Kunming Institute of Zoology and Kunming Primate Research Center, Chinese Academy of Sciences (Kunming, China), Graduate School of Chinese Academy of Sciences (Beijing, China) contributed to this study.
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- Xiaodong Fang, Yanfeng Zhang, Rui Zhang, Lixin Yang, Ming Li, Kaixiong Ye, Xiaosen Guo, Jun Wang, Bing Su. Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque. Genome Biology, 2011; 12 (7): R63 DOI: 10.1186/gb-2011-12-7-r63
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