Integrated analysis of the complete sequence of a macaque genome

doi:10.1038/s41586-025-08596-w

	Integrated analysis of the complete sequence of a macaque genome
	Zhang, Shilong 1,2; Xu, Ning 3,4,5,6; Fu, Lianting 1,2; Yang, Xiangyu 1; Ma, Kaiyue 1; Li, Yamei 3,4,5; Yang, Zikun 1; Li, Zhengtong 1; Feng, Yu 7; Jiang, Xinrui 1; Han, Junmin 1; Hu, Ruixing 1; Zhang, Lu3,5,8,9 ; Lian, Da 1; de Gennaro, Luciana 10; Paparella, Annalisa 10; Ryabov, Fedor 11; Meng, Dan 1; He, Yaoxi 5,12,13; Wu, Dongya 2,14,15,16; Yang, Chentao 14,15; Mao, Yuxiang 3,4,5,6; Bian, Xinyan 3,5; Lu, Yong 3,5; Antonacci, Francesca 10; Ventura, Mario 10; Shepelev, Valery A.17; Miga, Karen H.18; Alexandrov, Ivan A.19,20; Logsdon, Glennis A.21; Phillippy, Adam M.22; Su, Bing 5,12,13; Zhang, Guojie 2,14,15,16; Eichler, Evan E.; Lu, Qing 1; Shi, Yongyong 1,3; Sun, Qiang 3,4,5,6; Mao, Yafei 1,2
	2025-02-01
发表期刊	NATURE (IF:50.5[JCR-2023],54.4[5-Year])
ISSN	0028-0836
EISSN	1476-4687
发表状态	已发表
DOI	10.1038/s41586-025-08596-w
摘要	The crab-eating macaques (Macaca fascicularis) and rhesus macaques (Macacamulatta) are pivotal in biomedical and evolutionary research1, 2-3. However, their genomic complexity and interspecies genetic differences remain unclear4. Here, we present a complete genome assembly of a crab-eating macaque, revealing 46% fewer segmental duplications and 3.83 times longer centromeres than those of humans5,6. We also characterize 93 large-scale genomic differences between macaques and humans at a single-base-pair resolution, highlighting their impact on gene regulation in primate evolution. Using ten long-read macaque genomes, hundreds of short-read macaque genomes and full-length transcriptome data, we identified roughly 2 Mbp of fixed-genetic variants, roughly 240 Mbp of complex loci, 16.76 Mbp genetic differentiation regions and 110 alternative splice events, potentially associated with various phenotypic differences between the two macaque species. In summary, the integrated genetic analysis enhances understanding of lineage-specific phenotypes, adaptation and primate evolution, thereby improving their biomedical applications in human disease research.
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收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:001437421500001
出版者	NATURE PORTFOLIO
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/500264
专题	生命科学与技术学院生命科学与技术学院_博士生
通讯作者	Sun, Qiang; Mao, Yafei
作者单位	1.Shanghai Jiao Tong Univ, Biox Inst, Key Lab Genet Dev & Neuropsychiat Disorders, Minist Educ, Shanghai, Peoples R China 2.Zhejiang Univ, Affiliated Hosp 4, Int Inst Med, Dept Radiol,Sch Med, Yiwu 322000, Peoples R China 3.Chinese Acad Sci, Ctr Excellence Brain Sci & Intelligence Technol, State Key Lab Neurosci, Inst Neurosci, Shanghai, Peoples R China 4.Shanghai Ctr Brain Sci & Brain Inspired Technol, Shanghai, Peoples R China 5.Chinese Acad Sci, Kunming Inst Zool, Natl Key Lab Genet Evolut & Anim Model, Kunming, Peoples R China 6.Univ Chinese Acad Sci, Beijing, Peoples R China 7.Chinese Acad Sci, Chengdu Inst Biol, Chengdu, Peoples R China 8.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai, Peoples R China 9.Shanghai Ctr Brain Sci & Brain inspired Technol, Lingang Lab, Shanghai, Peoples R China 10.Univ Bari Aldo Moro, Dept Biosci Biotechnol & Environm, Bari, Italy 11.Univ Higher Sch Econ, Masters Program Natl Res, Moscow, Russia 12.Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming, Peoples R China 13.Yunnan Key Lab Stomatol, Kunming, Peoples R China 14.Zhejiang Univ, Ctr Evolutionary & Organismal Biol, Hangzhou, Peoples R China 15.Zhejiang Univ, Womens Hosp, Sch Med, Hangzhou, Peoples R China 16.Zhejiang Univ, Sch Med, Hangzhou, Peoples R China 17.Russian Acad Sci, Inst Mol Genet, Moscow, Russia 18.Univ Calif Santa Cruz, Santa Cruz, CA USA 19.Tel Aviv Univ, Fac Med & Hlth Sci, Dept Anat & Anthropol, Tel Aviv, Israel 20.Tel Aviv Univ, Fac Med & Hlth Sci, Dept Human Mol Genet & Biochem, Tel Aviv, Israel 21.Univ Penn, Perelman Sch Med, Dept Genet, Epigenet Inst, Philadelphia, PA USA 22.Natl Human Genome Res Inst, Ctr Genom & Data Sci Res, NIH, Genome Informat Sect, Bethesda, MD USA
推荐引用方式 GB/T 7714	Zhang, Shilong,Xu, Ning,Fu, Lianting,et al. Integrated analysis of the complete sequence of a macaque genome[J]. NATURE,2025.
APA	Zhang, Shilong.,Xu, Ning.,Fu, Lianting.,Yang, Xiangyu.,Ma, Kaiyue.,...&Mao, Yafei.(2025).Integrated analysis of the complete sequence of a macaque genome.NATURE.
MLA	Zhang, Shilong,et al."Integrated analysis of the complete sequence of a macaque genome".NATURE (2025).