基于 2b-RAD 简化基因组测序的中国实验用猕猴遗传多样性分析。

Genetic diversity of Chinese laboratory macaques based on 2b-RAD simplified genome sequencing.

机构信息

Guangdong Laboratory, Animals Monitoring Institute, Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China.

Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.

出版信息

J Med Primatol. 2022 Apr;51(2):101-107. doi: 10.1111/jmp.12571. Epub 2022 Feb 15.

DOI:10.1111/jmp.12571

PMID:35165897

Abstract

BACKGROUND

Currently, Chinese laboratory macaques are widely used in biomedical research. Correspondingly, clarity regarding the genetic diversity of Chinese laboratory macaques is important for both vendors and users.

METHODS

Genome sequences of 55 laboratory macaques (40 cynomolgus macaques and 15 rhesus macaques) bred in South China were analyzed using 2b-RAD simplified genome sequencing.

RESULTS

A total of 115,681 single-nucleotide polymorphisms (SNPs) were found that were distributed in 21 chromosomes and an unplaced scaffold. Genetic diversity indices varied across populations and exhibited low values. The results of principal coordinate analysis (PCA) were consistent with those of the arithmetic mean (UPGMA) clustered tree and supported the structure analysis, demonstrating that the genetic differentiation in rhesus macaques was higher than that in cynomolgus macaques. Introgressive hybridization with the Chinese rhesus macaque was supported in more than 80% (32/40) of cynomolgus macaques.

CONCLUSIONS

Chinese laboratory macaques had relatively low genetic diversity at the genomic level, and genetic differentiation in Chinese rhesus macaques was higher than in cynomolgus macaques. The genome of cynomolgus macaques has been shaped by introgression after hybridization with the Chinese rhesus macaques.

摘要

背景

目前，中国实验用猕猴被广泛应用于生物医学研究。相应地，明确中国实验用猕猴的遗传多样性对于供应商和使用者都很重要。

方法

采用 2b-RAD 简化基因组测序技术，对华南地区 55 只（40 只食蟹猴和 15 只恒河猴）实验用猕猴的基因组序列进行分析。

结果

共发现 115681 个单核苷酸多态性（SNP），分布在 21 条染色体和一条未定位的支架上。遗传多样性指数在不同种群之间存在差异，且数值较低。主坐标分析（PCA）的结果与算术平均值（UPGMA）聚类树一致，支持结构分析，表明恒河猴的遗传分化高于食蟹猴。80%以上（32/40）的食蟹猴存在与中国恒河猴的渐渗杂交。