Genome-wide mining and comparative analysis of microsatellites in three macaque species
Genome-wide mining and comparative analysis of microsatellites in three macaque species
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三种猕猴微卫星的全基因组挖掘和比较分析
DOI：
10.1007/s00438-017-1289-1
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发表时间：
2017-06-01
影响因子：
3.1
通讯作者：
Li, Jing
中科院分区：
文献类型：
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作者：
Liu, Sanxu;Hou, Wei;Li, Jing
微卫星存在于不同分类的生物体中，这类重复序列与基因组结构、功能以及某些疾病相关。为了对猕猴的微卫星进行特征分析，我们在恒河猴、食蟹猴和豚尾猴中搜索并比较了具有1 - 6个碱基核苷酸基序的简单序列重复（SSR）。分别挖掘出了1395671个、1284929个和1266348个完美SSR。最常见的完美SSR是单核苷酸SSR。二核苷酸SSR的GC含量最高，单核苷酸SSR的GC含量最低。染色体大小与SSR数量呈正相关，与SSR的相对频率和密度呈负相关。染色体SSR的GC含量与SSR的相对频率以及染色体序列的GC含量呈负相关。这三个物种组装基因组中微卫星的分布特征极为相似，这表明微卫星的分布模式在猕猴属中可能具有保守性。发现五核苷酸和六核苷酸重复中重复基序的退化数量存在差异。每种猕猴的物种特异性基序明显代表性不足。总体而言，恒河猴各染色体的SSR频率高于食蟹猴。食蟹猴中单核苷酸至五核苷酸重复的最大重复次数多于其他两种猕猴。这些结果突出了猕猴属物种的遗传多样性和系统发育关系。我们的数据将有助于比较基因组图谱绘制，理解这些动物模型之间SSR的分布和基因组结构，并为进一步开发和鉴定更多猕猴特异性SSR奠定基础。
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.