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Genome-wide mining and comparative analysis of microsatellites in three macaque species

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Abstract

Microsatellites are found in taxonomically different organisms, and such repeats are related with genomic structure, function and certain diseases. To characterize microsatellites for macaques, we searched and compared SSRs with 1–6 bp nucleotide motifs in rhesus, cynomolgus and pigtailed macaque. A total of 1395671, 1284929 and 1266348 perfect SSRs were mined, respectively. The most frequent perfect SSRs were mononucleotide SSRs. The most GC-content was in dinucleotide SSRs and the least was in the mononucleotide SSRs. Chromosome size was positively correlated with SSR number and negatively correlated with the relative frequency and density of SSRs. The GC content of chromosome SSRs were negatively correlated with relative frequency of SSRs and GC content of chromosome sequences. The features of microsatellite distribution in assembled genomes of the three species were greatly similar, which revealed that the distributional pattern of microsatellites is probably conservative in genus Macaca. The degenerated number of repeat motifs was found to be different in pentanucleotide and hexanucleotide repeats. Species-specific motifs for each macaque were significantly underrepresented. Overall, SSR frequencies of each chromosome in rhesus macaque were higher than in cynomolgus macaque. The maximum repeat times of mono- to pentanucleotide repeats in cynomolgus macaque was more than other two macaques. These results emphasize the genetic diversity and phylogenetic relationship of genus Macaca species. Our data will be beneficial for comparative genome mapping, understanding the distribution of SSRs and genome structure between these animal models, and provide a foundation for further development and identification of more macaque-specific SSRs.

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Acknowledgements

We thank Chen Wang and Changjun Peng for assistance with statistical work. This research was supported by the National Natural Science Foundation of China (Grants No. 31270431 and No. 31501871), the State Key Program of National Natural Science Foundation of China (Grants No. 31530068) and the Sichuan Application Foundation Project (2015JY0268).

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Authors and Affiliations

  1. Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People’s Republic of China

    Sanxu Liu, Wei Hou, Tianlin Sun, Yongtao Xu, Peng Li, Bisong Yue, Zhenxin Fan & Jing Li

  2. Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People’s Republic of China

    Bisong Yue & Jing Li

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  1. Sanxu Liu
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  2. Wei Hou
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  3. Tianlin Sun
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  5. Peng Li
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Correspondence to Jing Li.

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Communicated by S. Hohmann.

S. Liu and W. Hou have contributed equally to the work.

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Liu, S., Hou, W., Sun, T. et al. Genome-wide mining and comparative analysis of microsatellites in three macaque species. Mol Genet Genomics 292, 537–550 (2017). https://doi.org/10.1007/s00438-017-1289-1

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