Evolutionary and biomedical insights from a marmoset diploid genome assembly

Journal article

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 diseases 1 . 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 research 2,3 . 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.

Authors: Yang, C; Zhou, Y; Marcus, S; Formenti, G; Bergeron, LA

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Nature Research
• Journal: Nature
• Volume: 594
• Issue: 7862
• Pages: 227-233
• Publication date: 2021-04-28
• DOI: 10.1038/s41586-021-03535-x
• EISSN: 1476-4687
• ISSN: 0028-0836
• Language: English
• Keywords: Marmoset; Biology; Genome; Evolutionary biology; Ploidy; Ecology; Genetics; Gene; Computational biology