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Evolutionary and biomedical insights from a marmoset diploid genome assembly

Author

Listed:
  • Chentao Yang

    (BGI-Shenzhen
    University of Copenhagen)

  • Yang Zhou

    (BGI-Shenzhen)

  • Stephanie Marcus

    (The Rockefeller University)

  • Giulio Formenti

    (The Rockefeller University
    The Rockefeller University)

  • Lucie A. Bergeron

    (University of Copenhagen)

  • Zhenzhen Song

    (University of the Chinese Academy of Sciences)

  • Xupeng Bi

    (BGI-Shenzhen)

  • Juraj Bergman

    (Aarhus University)

  • Marjolaine Marie C. Rousselle

    (Aarhus University)

  • Chengran Zhou

    (BGI-Shenzhen)

  • Long Zhou

    (BGI-Shenzhen)

  • Yuan Deng

    (BGI-Shenzhen
    University of Copenhagen)

  • Miaoquan Fang

    (BGI-Shenzhen)

  • Duo Xie

    (BGI-Shenzhen)

  • Yuanzhen Zhu

    (BGI-Shenzhen)

  • Shangjin Tan

    (BGI-Shenzhen)

  • Jacquelyn Mountcastle

    (The Rockefeller University)

  • Bettina Haase

    (The Rockefeller University)

  • Jennifer Balacco

    (The Rockefeller University)

  • Jonathan Wood

    (Wellcome Sanger Institute)

  • William Chow

    (Wellcome Sanger Institute)

  • Arang Rhie

    (National Human Genome Research Institute, National Institutes of Health)

  • Martin Pippel

    (Max Planck Institute of Molecular Cell Biology and Genetics
    Center for Systems Biology)

  • Margaret M. Fabiszak

    (The Rockefeller University)

  • Sergey Koren

    (National Human Genome Research Institute, National Institutes of Health)

  • Olivier Fedrigo

    (The Rockefeller University)

  • Winrich A. Freiwald

    (The Rockefeller University
    The Rockefeller University)

  • Kerstin Howe

    (Wellcome Sanger Institute)

  • Huanming Yang

    (BGI-Shenzhen
    University of the Chinese Academy of Sciences
    James D. Watson Institute of Genome Sciences
    Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen)

  • Adam M. Phillippy

    (National Human Genome Research Institute, National Institutes of Health)

  • Mikkel Heide Schierup

    (Aarhus University)

  • Erich D. Jarvis

    (The Rockefeller University
    The Rockefeller University
    Howard Hughes Medical Institute)

  • Guojie Zhang

    (University of Copenhagen
    Chinese Academy of Sciences
    China National GeneBank, BGI-Shenzhen
    Chinese Academy of Sciences)

Abstract

The accurate and complete assembly of both haplotype sequences of a diploid organism is essential to understanding the role of variation in genome functions, phenotypes and diseases1. Here, using a trio-binning approach, we present a high-quality, diploid reference genome, with both haplotypes assembled independently at the chromosome level, for the common marmoset (Callithrix jacchus), an primate model system that is widely used in biomedical research2,3. The full spectrum of heterozygosity between the two haplotypes involves 1.36% of the genome—much higher than the 0.13% indicated by the standard estimation based on single-nucleotide heterozygosity alone. The de novo mutation rate is 0.43 × 10−8 per site per generation, and the paternal inherited genome acquired twice as many mutations as the maternal. Our diploid assembly enabled us to discover a recent expansion of the sex-differentiation region and unique evolutionary changes in the marmoset Y chromosome. In addition, we identified many genes with signatures of positive selection that might have contributed to the evolution of Callithrix biological features. Brain-related genes were highly conserved between marmosets and humans, although several genes experienced lineage-specific copy number variations or diversifying selection, with implications for the use of marmosets as a model system.

Suggested Citation

  • Chentao Yang & Yang Zhou & Stephanie Marcus & Giulio Formenti & Lucie A. Bergeron & Zhenzhen Song & Xupeng Bi & Juraj Bergman & Marjolaine Marie C. Rousselle & Chengran Zhou & Long Zhou & Yuan Deng & , 2021. "Evolutionary and biomedical insights from a marmoset diploid genome assembly," Nature, Nature, vol. 594(7862), pages 227-233, June.
  • Handle: RePEc:nat:nature:v:594:y:2021:i:7862:d:10.1038_s41586-021-03535-x
    DOI: 10.1038/s41586-021-03535-x
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    Cited by:

    1. Taotao Li & Duo Du & Dandan Zhang & Yicheng Lin & Jiakang Ma & Mengyu Zhou & Weida Meng & Zelin Jin & Ziqiang Chen & Haozhe Yuan & Jue Wang & Shulong Dong & Shaoyang Sun & Wenjing Ye & Bosen Li & Houb, 2023. "CRISPR-based targeted haplotype-resolved assembly of a megabase region," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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