Integrated analysis of the complete sequence of a macaque genome

Shilong Zhang, Ning Xu, Lianting Fu, Xiangyu Yang, Kaiyue Ma, Yamei Li, Zikun Yang, Zhengtong Li, Yu Feng, Xinrui Jiang, Junmin Han, Ruixing Hu, Lu Zhang, Da Lian, Luciana Gennaro, Annalisa Paparella, Fedor Ryabov, Dan Meng, Yaoxi He, Dongya Wu, Chentao Yang, Yuxiang Mao, Xinyan Bian, Yong Lu, Francesca Antonacci, Mario Ventura, Valery A. Shepelev, Karen H. Miga, Ivan A. Alexandrov, Glennis A. Logsdon, Adam M. Phillippy, Bing Su, Guojie Zhang, Evan E. Eichler, Qing Lu, Yongyong Shi, Qiang Sun () and Yafei Mao ()
Additional contact information
Shilong Zhang: Shanghai Jiao Tong University
Ning Xu: Chinese Academy of Sciences
Lianting Fu: Shanghai Jiao Tong University
Xiangyu Yang: Shanghai Jiao Tong University
Kaiyue Ma: Shanghai Jiao Tong University
Yamei Li: Chinese Academy of Sciences
Zikun Yang: Shanghai Jiao Tong University
Zhengtong Li: Shanghai Jiao Tong University
Yu Feng: Chinese Academy of Sciences
Xinrui Jiang: Shanghai Jiao Tong University
Junmin Han: Shanghai Jiao Tong University
Ruixing Hu: Shanghai Jiao Tong University
Lu Zhang: Chinese Academy of Sciences
Da Lian: Shanghai Jiao Tong University
Luciana Gennaro: University of Bari Aldo Moro
Annalisa Paparella: University of Bari Aldo Moro
Fedor Ryabov: Masters Program in National Research University Higher School of Economics
Dan Meng: Shanghai Jiao Tong University
Yaoxi He: Chinese Academy of Sciences
Dongya Wu: Zhejiang University
Chentao Yang: Zhejiang University
Yuxiang Mao: Chinese Academy of Sciences
Xinyan Bian: Chinese Academy of Sciences
Yong Lu: Chinese Academy of Sciences
Francesca Antonacci: University of Bari Aldo Moro
Mario Ventura: University of Bari Aldo Moro
Valery A. Shepelev: Russian Academy of Sciences
Karen H. Miga: University of California Santa Cruz
Ivan A. Alexandrov: Tel Aviv University
Glennis A. Logsdon: University of Pennsylvania
Adam M. Phillippy: National Institutes of Health
Bing Su: Chinese Academy of Sciences
Guojie Zhang: Zhejiang University
Evan E. Eichler: University of Washington School of Medicine
Qing Lu: Shanghai Jiao Tong University
Yongyong Shi: Shanghai Jiao Tong University
Qiang Sun: Chinese Academy of Sciences
Yafei Mao: Shanghai Jiao Tong University

Nature, 2025, vol. 640, issue 8059, 714-721

Abstract: Abstract The crab-eating macaques (Macaca fascicularis) and rhesus macaques (Macaca mulatta) are pivotal in biomedical and evolutionary research1–3. 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.

Date: 2025
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DOI: 10.1038/s41586-025-08596-w

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