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. 2007 May 9;2(5):e438.
doi: 10.1371/journal.pone.0000438.

MamuSNP: a resource for Rhesus Macaque (Macaca mulatta) genomics

Ripan S Malhi  1 , Brad Sickler, Dawei Lin, Jessica Satkoski, Raul Y Tito, Debbie George, Sreetharan Kanthaswamy, David Glenn Smith
Affiliations

MamuSNP: a resource for Rhesus Macaque (Macaca mulatta) genomics

Ripan S Malhi et al. PLoS One. .

Abstract

We developed a novel method for identifying SNPs widely distributed throughout the coding and non-coding regions of a genome. The method uses large-scale parallel pyrosequencing technology in combination with bioinformatics tools. We used this method to generate approximately 23,000 candidate SNPs throughout the Macaca mulatta genome. We estimate that over 60% of the SNPs will be of high frequency and useful for mapping QTLs, genetic management, and studies of individual relatedness, whereas other less frequent SNPs may be useful as population specific markers for ancestry identification. We have created a web resource called MamuSNP to view the SNPs and associated information online. This resource will also be useful for researchers using a wide variety of Macaca species in their research.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Proportion of 454 pyrosequencing DNA fragments that exhibited SNPs.
No match indicates a DNA fragment not from M. mulatta. A near match indicates a DNA fragment with at least a 98% match to M. mulatta but unsuitable for SNP detection. A perfect match indicates a DNA fragment with a 100% match with M. mulatta. A SNP indicates a DNA fragment with a near perfect match with M. mulatta and suitable sequence for SNP detection.
Figure 2
Figure 2. Distribution of Candidate SNPs across genome.
Figure 3
Figure 3. Distribution of overlap SNPs across the genome.
See this image and copyright information in PMC

References

    1. Rhesus Macaque Genome Sequencing and Analysis Consortium. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007;316:222–234. - PubMed
    1. Ferguson B, Street SL, Wright H, Pearson C, Jia Y, et al. Single nucleotide polymorphisms (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta). BMC Genomics. 2007;8:43. - PMC - PubMed
    1. Hernandez RD, Hubisz MJ, Wheeler D, Smith DG, Ferguson B, et al. Demographic Histories and Patterns of Linkage Disequilibrium for Chinese and Indian Rhesus Macaques. Science. 2007;316:240–243. - PubMed
    1. Nobrega MA, Ovcharenko I, Afzal V, Rubin EM. Scanning human gene deserts for long-range enhancers. Science. 2003;302:413. - PubMed
    1. Doxiadis GG, Rouweler AJ, deGroot NH, Louwerse A, Otting N, et al. Extensive sharing of MHC class II alleles between rhesus and cynomolgus macaques. Immunogenetics. 2006;58:259–68. - PubMed

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