Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome.
Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome.
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DOI：
10.1186/gb-2012-13-7-r58
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发表时间：
2012-07-02
期刊：
影响因子：
12.3
通讯作者：
Osada N
中科院分区：
文献类型：
--
作者：
Higashino A;Sakate R;Kameoka Y;Takahashi I;Hirata M;Tanuma R;Masui T;Yasutomi Y;Osada N
食蟹猴（Macaca fascicularis）的遗传背景由于其高度的遗传多样性、种群结构和来自近亲恒河猴（Macaca mulatta）的基因渗入而变得复杂。在此，我们报告了马来西亚食蟹猴雄性的全基因组序列，其覆盖范围超过40倍，使用基于印度恒河猴基因组的重测序方法确定。我们在马来西亚食蟹和印度恒河猴的基因组中发现了大约970万个单核苷酸变异（snv）。与人类相比，食蟹猕猴的非同义/同义SNV比更小，表明更有效地去除轻微有害的突变。两种食蟹猴（马来西亚和越南）和两种恒河猴（印度和中国）猕猴基因组的比较，包括先前发表的猕猴基因组，表明印度支那食蟹猴更容易受到来自恒河猴的基因渗入的影响。我们进一步鉴定了60个完全区分食蟹猴和恒河猴基因组的非同义snv，这些snv可能是确定物种对药物和病原体特异性反应的重要候选变异。利用基因组序列数据进行的人口统计学推断显示，马来西亚食蟹猕猴至少经历了三个种群瓶颈。该全基因组snv列表将对许多未来的应用有用，例如基于阵列的猕猴个体基因分型系统。食蟹猴基因组的高质量全基因组测序可能有助于研究发现猕猴表型多样性的遗传差异，并可能有助于控制个体之间的遗传背景。
The genetic background of the cynomolgus macaque (Macaca fascicularis) is made complex by the high genetic diversity, population structure, and gene introgression from the closely related rhesus macaque (Macaca mulatta). Herein we report the whole-genome sequence of a Malaysian cynomolgus macaque male with more than 40-fold coverage, which was determined using a resequencing method based on the Indian rhesus macaque genome. We identified approximately 9.7 million single nucleotide variants (SNVs) between the Malaysian cynomolgus and the Indian rhesus macaque genomes. Compared with humans, a smaller nonsynonymous/synonymous SNV ratio in the cynomolgus macaque suggests more effective removal of slightly deleterious mutations. Comparison of two cynomolgus (Malaysian and Vietnamese) and two rhesus (Indian and Chinese) macaque genomes, including previously published macaque genomes, suggests that Indochinese cynomolgus macaques have been more affected by gene introgression from rhesus macaques. We further identified 60 nonsynonymous SNVs that completely differentiated the cynomolgus and rhesus macaque genomes, and that could be important candidate variants for determining species-specific responses to drugs and pathogens. The demographic inference using the genome sequence data revealed that Malaysian cynomolgus macaques have experienced at least three population bottlenecks. This list of whole-genome SNVs will be useful for many future applications, such as an array-based genotyping system for macaque individuals. High-quality whole-genome sequencing of the cynomolgus macaque genome may aid studies on finding genetic differences that are responsible for phenotypic diversity in macaques and may help control genetic backgrounds among individuals.
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通讯作者：
FOODEN, J
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