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PreprintCited by 48Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsGenomic variations and chromosomal abnormalities

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Comparative genomics of macaques and integrated insights into genetic variation and population history

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Zhang, Shilong, Xu, Ning, Fu, Lianting, Yang, Xiangyu, Li, Yamei, Yang, Zikun, Feng, Yu, Ma, Kaiyue, Jiang, Xinrui, Han, Junmin, Hu, Ruixing, Zhang, Lu, de Gennaro, Luciana, Ryabov, Fedor, Meng, Dan, He, Yaoxi, Wu, Dongya, Yang, Chentao, Paparella, Annalisa, 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·2024·Nature
DOI 10.1101/2024.04.07.588379PMC PMC12003069

Preprint — published as 10.1038/s41586-025-08596-w · Paper page

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Abstract

The crab-eating macaques ( Macaca fascicularis ) and rhesus macaques ( M. mulatta ) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is ∼42% lower, while centromeres are ∼3.7 times longer than those in humans. The characterization of ∼2 Mbp fixed genetic variants and ∼240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g., CYP2C76 and EHBP1L1 ). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g., PNPO ). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g., FOLH1 and PIEZO2 ). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g., STAB1 , SEMA3F , and HOXD13 ). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.

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Metadata

Authors
Zhang, S., Xu, N., Fu, L., Yang, X., Li, Y., Yang, Z., Feng, Y., Ma, K., Jiang, X., Han, J., Hu, R., Zhang, L., de Gennaro, L., Ryabov, F., Meng, D., He, Y., Wu, D., Yang, C., Paparella, A., Mao, Y., Bian, X., Lu, Y., Antonacci, F., Ventura, M., Shepelev, V. A., Miga, K. H., Alexandrov, I. A., Logsdon, G. A., Phillippy, A. M., Su, B., Zhang, G., Eichler, E. E., Lu, Q., Shi, Y., Sun, Q., & Mao, Y.
Affiliations
  • Shanghai Jiao Tong University (CN)
  • Kunming Institute of Zoology (CN)
  • Chinese Academy of Sciences (CN)
  • University of Bari Aldo Moro (IT)
  • National Research University Higher School of Economics (RU)
  • Women's Hospital, School of Medicine, Zhejiang University (CN)
  • Russian Academy of Sciences (RU)
  • University of California, Santa Cruz (US)
  • Tel Aviv University (IL)
  • University of Pennsylvania (US)
  • National Institutes of Health (US)
  • Howard Hughes Medical Institute (US)
Corresponding author
  • Mao, Yuxiang
  • Sun, Qiang
  • Mao, Yafei
ORCID
Venue
Nature
Publisher
openRxiv
Published
2024-04-08
Volume
640
Issue
8059
Pages
714-721
ISSN
0028-0836 (ISSN-L)
DOI
10.1101/2024.04.07.588379
PMC
PMC12003069
OpenAlex
W4407956951
Cited by
48
References
1
Citations by year
2026: 26 · 2025: 19 · 2024: 3
FWCI
13.53
Type
journal article
Language
en
Open access
Locations
  • Nature (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
Funders
  • National Natural Science Foundation of China (2021ZD0200900, 82021001, WH510363001, 31825018)
  • Chinese Academy of Sciences (2021ZD0200900, KFJ-BRP-005, 82021001)
  • China Postdoctoral Science Foundation
  • Shanghai Jiao Tong University
  • National Science and Technology Major Project (2021ZD0200900)
  • National Institutes of Health
  • High Performance Research Computing, Texas A and M University
  • National Key Research and Development Program of China (2022YFF0710901)
  • National Human Genome Research Institute (R01HG011274, R01HG002385, R01HG010169)
  • National Institute of General Medical Sciences (R00GM147352)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Keywords
Macaca fascicularis, rhesus monkeys, complete genome assembly, segmental duplication, alternative splicing, primate evolution, gene expression regulation

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