Aarhus University Seal

Evolutionary and biomedical insights from a marmoset diploid genome assembly

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Documents

DOI

  • Chentao Yang, BGI-Shenzhen, University of Copenhagen
  • ,
  • Yang Zhou, BGI-Shenzhen
  • ,
  • Stephanie Marcus, Rockefeller University
  • ,
  • Giulio Formenti, Rockefeller University
  • ,
  • Lucie A. Bergeron, University of Copenhagen
  • ,
  • Zhenzhen Song, University of Chinese Academy of Sciences
  • ,
  • Xupeng Bi, BGI-Shenzhen
  • ,
  • Juraj Bergman
  • Marjolaine Marie C. Rousselle
  • 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, Rockefeller University
  • ,
  • Bettina Haase, Rockefeller University
  • ,
  • Jennifer Balacco, Rockefeller University
  • ,
  • Jonathan Wood, Wellcome Sanger Institute
  • ,
  • William Chow, Wellcome Sanger Institute
  • ,
  • Arang Rhie, National Institutes of Health
  • ,
  • Martin Pippel, Max Planck Institute of Molecular Cell Biology and Genetics, Center for Systems Biology Dresden
  • ,
  • Margaret M. Fabiszak, Rockefeller University
  • ,
  • Sergey Koren, National Institutes of Health
  • ,
  • Olivier Fedrigo, Rockefeller University
  • ,
  • Winrich A. Freiwald, Rockefeller University
  • ,
  • Kerstin Howe, Wellcome Sanger Institute
  • ,
  • Huanming Yang, BGI-Shenzhen, University of Chinese Academy of Sciences, Zhejiang University
  • ,
  • Adam M. Phillippy, National Institutes of Health
  • ,
  • Mikkel Heide Schierup
  • Erich D. Jarvis, Rockefeller University, Howard Hughes Medical Institute
  • ,
  • Guojie Zhang, University of Copenhagen, CAS - Kunming Institute of Zoology, China National GeneBank

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.

Original languageEnglish
JournalNature
Volume594
Issue7862
Pages (from-to)227-233
Number of pages7
ISSN0028-0836
DOIs
Publication statusPublished - Jun 2021

Bibliographical note

Publisher Copyright:
© 2021, The Author(s).

See relations at Aarhus University Citationformats

ID: 224426784