Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

Finding the Factors of Reduced Genetic Diversity on X Chromosomes of Macaca fascicularis: Male-Driven Evolution, Demography, and Natural Selection

“…While observed ratios in the IGS regions fell in the expected distributions, CDS regions showed significant reduction from the expected distribution in the both populations (P = 0.00028 and P = 0.00076 in Indonesian-Malaysian and Philippine population, respectively; two-tailed test), indicating that natural selection is further reducing the X/A diversity ratio in the CDS regions. Simulation results with a low recombination rate on the X chromosomes were qualitatively the same as the result of the first case, and the results are presented in Figure S3.To further support the evidence of stronger reduction of polymorphisms near CDS on the X chromosomes than on autosomes, we utilized a recently determined female Vietnamese M. fascicularis genome sequence using massively parallel sequencing (Yan et al 2011). We mapped the short-read sequences to the rhesus macaque genome sequence and estimated the rate of heterozygous SNPs on autosomes (0.29%) and the X chromosome (0.15%), which are fairly close to the values in the previous report using a different read mapping and SNP calling pipeline (Yan et al 2011).…”

“…We mapped the short-read sequences to the rhesus macaque genome sequence and estimated the rate of heterozygous SNPs on autosomes (0.29%) and the X chromosome (0.15%), which are fairly close to the values in the previous report using a different read mapping and SNP calling pipeline (Yan et al 2011). The number of SNPs between two sequenced chromosomes was summed into bins according to the distance from the nearest exons.…”

A Review of Plasmodium coatneyi–Macaque Models of Severe Malaria

“…The ability to elicit severe disease appears to be more consistent in the rhesus than in the cynomolgus macaques. While both species are used extensively in medical research and their genomes have been fully sequenced, 123 it is the experimental reproducibility in the rhesus of the pathologic parameters of falciparum disease in humans that makes the P. coatneyi-rhesus macaque model of infection useful for the modeling of severe malaria in humans. …”

Primate genome architecture influences structural variation mechanisms and functional consequences

“…Comparative analyses of reference genome assemblies of the chimpanzee (9), orang-utan (10), and rhesus macaque (11) have provided some initial insights into large-scale structural changes in primate genome evolution (12). Microarray technology-based surveys have provided additional glimpses of the abundance of polymorphic unbalanced SVs (i.e., copy number variants) in different primate species, enabling the construction of SV maps at a resolution of tens to hundreds of kilobases (13-16).Thus far, despite ongoing progress in assessing SNP variation in primates (10,(17)(18)(19), no study has leveraged MPS technology for ascertaining inter-and intraspecies SVs in different primates. We, therefore, performed MPS-based genome analyses in five individuals from each of these primate species, Pan troglodytes (chimpanzee), Pongo abelii (orang-utan), and Macaca mulatta (rhesus macaque), to construct comprehensive SV maps in these species.…”

“…Thus far, despite ongoing progress in assessing SNP variation in primates (10,(17)(18)(19), no study has leveraged MPS technology for ascertaining inter-and intraspecies SVs in different primates. We, therefore, performed MPS-based genome analyses in five individuals from each of these primate species, Pan troglodytes (chimpanzee), Pongo abelii (orang-utan), and Macaca mulatta (rhesus macaque), to construct comprehensive SV maps in these species.…”