Evolutionary and biomedical insights from a marmoset diploid genome assembly

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, Miaoquan Fang, Duo Xie, Yuanzhen Zhu, Shangjin Tan, Jacquelyn Mountcastle, Bettina Haase, Jennifer Balacco, Jonathan Wood, William Chow, Arang Rhie, Martin Pippel, Margaret M. Fabiszak, Sergey Koren, Olivier Fedrigo, Winrich A. Freiwald, Kerstin Howe, Huanming Yang, Adam M. Phillippy, Mikkel Heide Schierup, Erich D. Jarvis and Guojie Zhang ()
Additional contact information
Chentao Yang: BGI-Shenzhen
Yang Zhou: BGI-Shenzhen
Stephanie Marcus: The Rockefeller University
Giulio Formenti: 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
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
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
Kerstin Howe: Wellcome Sanger Institute
Huanming Yang: 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
Guojie Zhang: University of Copenhagen

Nature, 2021, vol. 594, issue 7862, 227-233

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41586-021-03535-x

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