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 WoodWilliam 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, Guojie Zhang*

*Corresponding author for this work

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

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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
Pages (from-to)227-233
Number of pages7
Publication statusPublished - Jun 2021


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