Evolutionary and biomedical insights from a marmoset diploid genome assembly.

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Yang, C; Zhou, Y; Marcus, S; Formenti, G; Bergeron, LA; Song, Z; Bi, X; Bergman, J; Rousselle, MMC; Zhou, C; Zhou, L; Deng, Y; Fang, M; Xie, D; Zhu, Y; Tan, S; Mountcastle, J; Haase, B; Balacco, J; Wood, J; Chow, W; Rhie, A; Pippel, M; Fabiszak, MM; Koren, S; Fedrigo, O; Freiwald, WA; Howe, K; Yang, H; Phillippy, AM; Schierup, MH; Jarvis, ED; Zhang, G

Published Date

  • June 2021

Published In

Volume / Issue

  • 594 / 7862

Start / End Page

  • 227 - 233

PubMed ID

  • 33910227

Pubmed Central ID

  • PMC8189906

Electronic International Standard Serial Number (EISSN)

  • 1476-4687

Digital Object Identifier (DOI)

  • 10.1038/s41586-021-03535-x

Language

  • eng

Conference Location

  • England