Rhesus Monkey Genome Project
Rhesus Monkey Genome Project
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About the Project
The BCM-HGSC has sequenced the genome of the rhesus monkey (rhesus macaque, Macaca mulatta). The rhesus macaque is an Old World monkey. This primate model organism, while more distant from humans than chimpanzees or orangutans, is important for study of human disease due to its genetic, physiologic and metabolic similarity to humans. Rhesus monkeys are used for essential research in neuroscience, behavioral biology, reproductive physiology, endocrinology, cardiovascular studies, pharmacology and other areas.
The Macaque Genome Sequencing Consortium is led by the Baylor College of Medicine Human Genome Sequencing Center, and in collaboration with the J. Craig Venter Institute Joint Technology Center, and the Genome Sequencing Center at Washington University, St. Louis. The goals of the project were to produce a seven-fold WGS shotgun assembly, using small insert plasmids as well as large insert clone ends from BACs, Fosmids, and 50kb linking clones. There are finishing and BAC sequencing components of the project to investigate interesting regions for human diseases and to highlight primate evolution.
The rhesus macaque genome sequencing project began in 2002 with consultations between the BCM-HGSC and primate researchers. The project was compelling both because of the intense interest in this organism as a biomedical research model—including SIV and AIDS research—and because of its unique placement in the evolutionary tree relative to the human. A white paper was given high priority in early 2003 by NHGRI. The project was a 5x WGS draft assembly with additional finished regions (up to 500 Mb) and an undefined BAC component, as needed to ensure overall quality. A BAC library from a male was available and the Genome Centre in Vancouver expressed interest in building a fingerprint map. New methods of mapping BACs by pool genomic indexing (PGI) were developed.
The Southwest National Primate Research Center provided DNA from a single female rhesus, sacrificed for health reasons. BCM-HGSC and Wash U each sequenced 2.5x WGS and JCVI 1x. After sufficient data for 4x coverage, an "interim assembly" was generated by the HGSC to test overall fidelity of the work. This was displayed on the UCSC browser in April 2005. After the WGS data was complete, independent assemblies were performed at each sequencing center using different approaches. A working group was convened to coordinate evaluation and comparison of each assembly and guide melding into a single assembly. The "melded assembly" used the fingerprint map and, at the very highest level (i.e., super-contig placement on the chromosomes), it referred to the human sequence. Statistically this is a high quality 5x WGS assembly, rivaling the rat, which contained a complete BAC scaffold. This assembly was released in Feb 2006, was used for gene predictions, and ongoing analysis.
The sequencing and comparative analysis is funded by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).
Access to the Data
A draft assembly is available for download using the FTP Data link in the sidebar. In addition, the data can be searched by using the BLAST link.
Resources
Southwest National Primate Research Center
J. Craig Venter Institute Joint Technology Center
Washington University rhesus site
International Genome Consortium Database
Macaca mulatta White Paper (PDF)
Fingerprint Database - BC Genome Sciences Center
BAC Resources - Children's Hospital Oakland Research Institute
Comparative Map - BCM Bioinformatics Research Laboratory rhesus site
Rhesus Macaque Genome Resource web site at NCBI
Rhesus macaque companion publications are found in Science, April 13, 2007.
Selected PubMed Citations
Harris, RA, Rogers, J, Milosavljevic, A. Human-specific changes of genome structure detected by genomic triangulation. Science 2007 Apr 13; 316(5822):235-7. [PubMed]
Hernandez, RD, Hubisz, MJ, Wheeler, DA, Smith, DG, Ferguson, B, Rogers, J, Nazareth, L, Indap, A, Bourquin, T et al. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science 2007 Apr 13; 316(5822):240-3. [PubMed]
Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs, RA, Rogers, J, Katze, MG, Bumgarner, R, Weinstock, GM, Mardis, ER, Remington, KA, Strausberg, RL et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science 2007 Apr 13; 316(5822):222-34. [PubMed]