1
|
Liu S, Hou W, Sun T, Xu Y, Li P, Yue B, Fan Z, Li J. Genome-wide mining and comparative analysis of microsatellites in three macaque species. Mol Genet Genomics 2017; 292:537-550. [PMID: 28160080 DOI: 10.1007/s00438-017-1289-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/09/2017] [Indexed: 12/13/2022]
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.
Collapse
Affiliation(s)
- Sanxu Liu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Wei Hou
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Tianlin Sun
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Yongtao Xu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Peng Li
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Zhenxin Fan
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China. .,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
| |
Collapse
|
2
|
Bunlungsup S, Imai H, Hamada Y, Gumert MD, San AM, Malaivijitnond S. Morphological characteristics and genetic diversity of Burmese long-tailed Macaques (Macaca fascicularis aurea). Am J Primatol 2015; 78:441-455. [DOI: 10.1002/ajp.22512] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/23/2015] [Accepted: 11/21/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Srichan Bunlungsup
- Department of Biology, Faculty of Science; Chulalongkorn University; Bangkok Thailand
| | - Hiroo Imai
- Molecular Biology Section, Primate Research Institute; Kyoto University; Aichi Japan
| | - Yuzuru Hamada
- Evolutionary Morphology Section, Primate Research Institute; Kyoto University; Aichi Japan
| | - Michael D. Gumert
- Division of Psychology, School of Humanities and Social Sciences; Nanyang Technological University; Singapore
| | - Aye Mi San
- Department of Zoology; Mawlamyine University; Mawlamyine Myanmar
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science; Chulalongkorn University; Bangkok Thailand
- National Primate Research Center of Thailand; Saraburi Thailand
| |
Collapse
|
3
|
Nikzad S, Tan SG, Yong Seok Yien C, Ng J, Alitheen NB, Khan R, Rovie-Ryan JJ, Valdiani A, Khajeaian P, Kanthaswamy S. Genetic diversity and population structure of long-tailed macaque (Macaca fascicularis) populations in Peninsular Malaysia. J Med Primatol 2014; 43:433-44. [PMID: 24930735 DOI: 10.1111/jmp.12130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2014] [Indexed: 11/28/2022]
Abstract
BACKGROUND The genetic diversity and structure of long-tailed macaques (Macaca fascicularis) in Peninsular Malaysia, a widely used non-human primate species in biomedical research, have not been thoroughly characterized. METHODS Thirteen sites of wild populations of long-tailed macaques representing six states were sampled and analyzed with 18 STR markers. RESULTS The Sunggala and Penang Island populations showed the highest genetic diversity estimates, while the Jerejak Island population was the most genetically discrete due to isolation from the mainland shelf. Concordant with pairwise F(st) estimates, STRUCTURE analyses of the seven PCA-correlated clusters revealed low to moderate differentiation among the sampling sites. No association between geographic and genetic distances exists, suggesting that the study sites, including island study sites, are genetically if not geographically contiguous. CONCLUSIONS The status of the genetic structure and composition of long-tailed macaque populations require further scrutiny to develop this species as an important animal model in biomedical research.
Collapse
Affiliation(s)
- Sonia Nikzad
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | | | | | | | | | | | | | | | | | | |
Collapse
|