title: Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque.
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.
authors: Beijing Genomics Institute-Shenzhen, Chinese Academy of Sciences, Shenzhen 518083, China.
authors: Xiaodong
authors: X
authors: Fang
authors: Yanfeng
authors: Y
authors: Zhang
authors: Rui
authors: R
authors: Zhang
authors: Lixin
authors: L
authors: Yang
authors: Ming
authors: M
authors: Li
authors: Kaixiong
authors: K
authors: Ye
authors: Xiaosen
authors: X
authors: Guo
authors: Jun
authors: J
authors: Wang
authors: Bing
authors: B
authors: Su
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D016678:Genome; D020407:Internet; D008253:Macaca mulatta / Q000235:genetics*; D008297:Male; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D014584:User-Computer Interface