Integrated analysis of the complete sequence of a macaque genome

• 成果类型: Article
• 署名作者: Zhang, Shilong; Xu, Ning; Fu, Lianting; Yang, Xiangyu; Ma, Kaiyue; Li, Yamei; Yang, Zikun; Li, Zhengtong; Feng, Yu; Jiang, Xinrui; Han, Junmin; Hu, Ruixing; Zhang, Lu; Lian, Da; de Gennaro, Luciana; Paparella, Annalisa; Ryabov, Fedor; Meng, Dan; He, Yaoxi; Wu, Dongya; Yang, Chentao; Mao, Yuxiang; Bian, Xinyan; Lu, Yong; Antonacci, Francesca; Ventura, Mario; Shepelev, Valery A.; Miga, Karen H.; Alexandrov, Ivan A.; Logsdon, Glennis A.; Phillippy, Adam M.; Su, Bing; Zhang, Guojie; Eichler, Evan E.; Lu, Qing; Shi, Yongyong; Sun, Qiang; Mao, Yafei
• 署名单位: Shanghai Jiao Tong University; Zhejiang University; Chinese Academy of Sciences; Center for Excellence in Brain Science and Intelligence Technology, CAS; Shanghai Center for Brain Science & Brain-Inspired Technology; Chinese Academy of Sciences; Kunming Institute of Zoology, CAS; Chinese Academy of Sciences; University of Chinese Academy of Sciences, CAS; Chinese Academy of Sciences; Chengdu Institute of Biology, CAS; ShanghaiTech University; Lingang Laboratory; Shanghai Center for Brain Science & Brain-Inspired Technology; Universita degli Studi di Bari Aldo Moro; HSE University (National Research University Higher School of Economics); Chinese Academy of Sciences; Kunming Institute of Zoology, CAS; Zhejiang University; Zhejiang University; Zhejiang University; Russian Academy of Sciences; University of California System; University of California Santa Cruz; Tel Aviv University; Tel Aviv University; University of Pennsylvania; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI)
• 刊物名称: Nature
• ISSN/ISSBN: 0028-2939
• DOI: 10.1038/s41586-025-08596-w
• 发表日期: 2025-04-17
• 关键词: alpha-satellite dna; genetic-variation; evolutionary; generation; glutamate; monkey

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.