Characterization of perfect microsatellite based on genome-wide and chromosome level in Rhesus monkey (Macaca mulatta)

• The perfect microsatellites distribution characteristics and composition mode of Rhesus monkey on genome and chromosome level were analyzed.
• The correlation analysis of microsatellite parameters involving the SSR number, relative abundance, density and GC content were described.
• The SSRs GC content on chromosome X (accounting for 16.71%) was found to be the highest in female Rhesus monkey.

Microsatellite studies based on chromosomes level would contribute to the biometric correlation analysis of chromosome and microsatellite applications on the specific chromosome. In this study, the total microsatellite length of 1,141,024 loci was 21.8 Mb, which covered about 0.74% of the male Rhesus monkey genome. Perfect mononucleotide SSRs were the most abundant, followed by the pattern: perfect di- > tetra- > tri- > penta- > hexanucleotide SSRs. The main range of repeat times focused on 12 – 32 times (mono-), 7 – 23 times (di-), 5 – 10 times (tri-), 4 – 14 times (tetra-), 4 – 9 times (penta-), 4 – 8 times (hexa-), respectively. The largest SSRs number was found in chromosome 1 with 94,347 loci, followed by chromosome 3, 2, 7 and 5, and the smallest number was in chromosome 18. The predominant repeat types in male Rhesus monkey genome and chromosome Y were basically A, AC, AG, AAT, AAC, AAAT, AAAC, AAAG, AAACA and AAACAA. SSRs number of all chromosomes was closely positively correlated with chromosome sequence size (r = 0.969, p < 0.01), and significantly negatively correlated with abundance (r = − 0.24, 0.01 < p < 0.05). The lengths of all chromosomes were significantly negatively correlated with microsatellite density (r = − 0.456, 0.01 < p < 0.05), and relative abundance and density of SSRs in all chromosomes were significantly negatively correlated with SSR GC content (r = − 0.939/− 0.928, p < 0.01). The SSRs GC content on chromosome X (accounting for 16.71%) was found to be the highest in female Rhesus monkey, which might contributed to the DNA methylation of CpG islands for sex chromosome X inactivation and expression regulation. These results and exported tetranucleotide repeat sequences in each chromosome for primer design would facilitate the exploration of microsatellites structural function, composition mode and molecular markers development in Rhesus monkey genome.