Integrated analysis of the complete sequence of a macaque genome
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Abstract
The crab-eating macaques (Macaca fascicularis) and rhesus macaques (Macaca mulatta) are pivotal in biomedical and evolutionary research 1-3. However, their genomic complexity and interspecies genetic differences remain unclear 4. 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 humans 5,6. 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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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Genome-wide detection and characterization of positive selection in human populations
The International HapMap Consortium, Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E. H., McCarroll, S. A., et al. (2007) · Nature · doi:10.1038/nature06250 · Cited by 2,131 · see citing works
Wenger, A. M., Peluso, P., Rowell, W. J., Chang, P.-C., Hall, R. J., Concepcion, G. T., Ebler, J., Fungtammasan, A., Kolesnikov, A., Olson, N. D., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0217-9 · Cited by 1,841 · see citing works
Self-citationA universal SNP and small-indel variant caller using deep neural networks
Poplin, R., Chang, P.-C., Alexander, D., Schwartz, S., Colthurst, T., Ku, A., Newburger, D., Dijamco, J., Nguyen, N., Afshar, P. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4235 · Cited by 1,840 · see citing works
A genomic mutational constraint map using variation in 76,156 human genomes
Chen, S., Francioli, L. C., Goodrich, J. K., Collins, R. L., Kanai, M., Wang, Q., Alföldi, J., Watts, N. A., Vittal, C., Gauthier, L. D., et al. (2024) · Nature · doi:10.1038/s41586-023-06045-0 · Cited by 1,727 · see citing works
Genome-wide association analysis identifies 13 new risk loci for schizophrenia
Multicenter Genetic Studies of Schizophrenia Consortium, Ripke, S., Psychosis Endophenotypes International Consortium, Wellcome Trust Case Control Consortium 2, O'Dushlaine, C., Chambert, K., Moran, J. L., Kähler, A. K., Akterin, S., Bergen, S. E., et al. (2013) · Nature Genetics · doi:10.1038/ng.2742 · Cited by 1,496 · see citing works
Evolutionary and biomedical insights from the rhesus macaque genome.
Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., et al. (2007) · Science · doi:10.1126/science.1139247 · Cited by 1,403 · see citing works
Self-citationA draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129 · see citing works
Self-citationInsights into human genetic variation and population history from 929 diverse genomes
Bergström, A., McCarthy, S. A., Hui, R., Almarri, M. A., Ayub, Q., Danecek, P., Chen, Y., Felkel, S., Hallast, P., Kamm, J., et al. (2020) · Science · doi:10.1126/science.aay5012 · Cited by 1,020 · see citing works
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702 · see citing works
Self-citationHuman-specific gene <i>ARHGAP11B</i> promotes basal progenitor amplification and neocortex expansion
Florio, M., Albert, M., Taverna, E., Namba, T., Brandl, H., Lewitus, E., Haffner, C., Sykes, A., Wong, F. K., Peters, J., et al. (2015) · Science · doi:10.1126/science.aaa1975 · Cited by 632 · see citing works
Segmental duplications and their variation in a complete human genome
Vollger, M. R., Guitart, X., Dishuck, P. C., Mercuri, L., Harvey, W. T., Gershman, A., Diekhans, M., Sulovari, A., Munson, K. M., Lewis, A. P., et al. (2022) · Science · doi:10.1126/science.abj6965 · Cited by 350 · see citing works
Self-citationEbler, J., Ebert, P., Clarke, W. E., Rausch, T., Audano, P. A., Houwaart, T., Mao, Y., Korbel, J. O., Eichler, E. E., Zody, M. C., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01043-w · Cited by 277 · see citing works
Self-citationEvolution of genetic and genomic features unique to the human lineage
O'Bleness, M., Searles, V. B., Varki, A., Gagneux, P., & Sikela, J. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3336 · Cited by 168 · see citing works
A catalog of single nucleotide changes distinguishing modern humans from archaic hominins
Kuhlwilm, M., & Boeckx, C. (2019) · Scientific Reports · doi:10.1038/s41598-019-44877-x · Cited by 108 · see citing works
Increased mutation and gene conversion within human segmental duplications
Vollger, M. R., Dishuck, P. C., Harvey, W. T., DeWitt, W. S., Guitart, X., Goldberg, M. E., Rozanski, A. N., Lucas, J., Asri, M., Human Pangenome Reference Consortium, et al. (2023) · Nature · doi:10.1038/s41586-023-05895-y · Cited by 104 · see citing works
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- Authors
- Zhang, S., Xu, N., Fu, L., Yang, X., Ma, K., Li, Y., Yang, Z., Li, Z., Feng, Y., Jiang, X., Han, J., Hu, R., Zhang, L., Lian, D., de Gennaro, L., Paparella, A., Ryabov, F., Meng, D., He, Y., Wu, D., Yang, C., 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
- Zhang, Shilong
- Fu, Lianting
- Yang, Xiangyu
- Ma, Kaiyue
- Li, Yamei
- Yang, Zikun
- Li, Zhengtong
- Jiang, Xinrui
- Hu, Ruixing
- Ryabov, Fedor
- Meng, Dan
- He, Yaoxi
- Wu, Dongya
- Yang, Chentao
- Mao, Yuxiang
- Antonacci, Francesca
- Ventura, Mario
- 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
- Venue
- Nature
- Published
- 2025-02-26
- Volume
- 640
- Issue
- 8059
- Pages
- 714-721
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC12003069
- OpenAlex
- W4407956951
- Cited by
- 48
- References
- 16
- Citations by year
- 2026: 26 · 2025: 19 · 2024: 3
- FWCI
- 13.53
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- 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 › Agricultural and Biological Sciences › Plant Science › 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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