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刘三许, 侯伟, 张雪艳, 彭长军, 岳碧松, 范振鑫, 李静. 2018: 基于全基因组重测序鉴定和分析藏酋猴微卫星. 动物学研究, 39(4): 291-300. DOI: 10.24272/j.issn.2095-8137.2018.047
引用本文: 刘三许, 侯伟, 张雪艳, 彭长军, 岳碧松, 范振鑫, 李静. 2018: 基于全基因组重测序鉴定和分析藏酋猴微卫星. 动物学研究, 39(4): 291-300. DOI: 10.24272/j.issn.2095-8137.2018.047
San-Xu Liu, Wei Hou, Xue-Yan Zhang, Chang-Jun Peng, Bi-Song Yue, Zhen-Xin Fan, Jing Li. 2018: Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data. Zoological Research, 39(4): 291-300. DOI: 10.24272/j.issn.2095-8137.2018.047
Citation: San-Xu Liu, Wei Hou, Xue-Yan Zhang, Chang-Jun Peng, Bi-Song Yue, Zhen-Xin Fan, Jing Li. 2018: Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data. Zoological Research, 39(4): 291-300. DOI: 10.24272/j.issn.2095-8137.2018.047

基于全基因组重测序鉴定和分析藏酋猴微卫星

Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data

  • 摘要: 藏酋猴是中国特有的濒危灵长类动物,被世界自然保护联盟(IUCN)列为近危(Near Endangered)物种。微卫星是基因组中长度为1-6 bp的重复序列,分布在各种生物的基因组中,是种群遗传学研究中的重要分子标记。为了阐明藏酋猴全基因组水平微卫星的分布特征和理解藏酋猴个体之间微卫星的差异,本研究基于峨眉山、简阳和黄山种群的5个藏酋猴重测序数据对藏酋猴进行了全基因组微卫星分析。我们从组装的藏酋猴基因组(N50为4 966 bp)中共计鉴定了1 077 790个完美型微卫星,约占基因组的0.78%。单核苷酸重复是最丰富的类型,其次是四核苷酸和二核苷酸重复序列。六核苷酸重复是最少的。微卫星GC含量和重复次数的分布与其他猕猴属物种大致相同。我们使用软件lobSTR观察到藏酋猴微卫星的碱基缺失比例高于插入(P < 0.05, t-test),峨眉山和简阳种群个体比黄山种群有更多的杂合微卫星位点(P < 0.05, t-test)。峨眉山和简阳个体STR等位基因碱基的插入比例和平均变异略高于黄山个体,揭示了不同藏酋猴种群微卫星等位基因大小的差异。此外,我们以恒河猴基因组为参考,鉴定出3 325个在藏酋猴个体中多态性高的四核苷酸微卫星位点,并随机选择了其中10个位点进行实验验证。初步筛选后将其中6个位点进行了荧光标记及基因分型分析,结果表明这些微卫星位点具有良好的扩增效果和较高的多态性,可用于藏酋猴种群遗传学研究。邻接树按照地理分布将5个个体划分为两个分支,显示黄山和四川种群具有较大的遗传分化。本研究阐明了藏酋猴基因组中微卫星的分布特征和藏酋猴不同个体之间的微卫星的差异,为鉴定和筛选基因组中多态性的微卫星标记提供了快速有效的方法。同时也为未来进一步研究猕猴属物种的遗传变异奠定了基础。

     

    Abstract: The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN). Short tandem repeats (STRs) refer to repetitive elements of genome sequence that range in length from 1–6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software (lobSTR), we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals (P<0.05, t-test). We also found a greater number of homozygous STRs than heterozygous STRs (P<0.05, t-test), with the Emei and Jianyang Tibetan macaques showing more heterozygous loci than Huangshan Tibetan macaques. The proportion of insertions and mean variation of alleles in the Emei and Jianyang individuals were slightly higher than those in the Huangshan individuals, thus revealing differences in STR allele size between the two populations. The polymorphic STR loci identified based on the reference genome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.

     

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