Evolutionary and biomedical insights from a marmoset diploid genome assembly

• DOI: 10.1038/s41586-021-03535-x
• Publication Date: 2021-04-28T16:57:48Z
• Authors: Chentao Yang; Yang Zhou; Stephanie Marcus; Giulio Formenti; Lucie A. Bergeron; Zhenzhen Song; Xupeng Bi; Juraj Bergman; Marjolaine Marie ...; Chengran Zhou; Long Zhou; Yuan Deng; Miaoquan Fang; Duo Xie; Yuanzhen Zhu; Shangjin Tan; Jacquelyn Mountca...; 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 Schi...; Erich D. Jarvis; Guojie Zhang
• Keywords: Male; Heterozygote; 0303 health sciences; Biomedical Research; Genome; Sex Differentiation; DNA Copy Number Variations; Callithrix; Genomics; Reference Standards; Diploidy; Article; Evolution, Molecular; 03 medical and health sciences; Haplotypes; INDEL Mutation; Y Chromosome; Animals; Humans; Female; Selection, Genetic; Germ-Line Mutation

Abstract The accurate and complete assembly of both haplotype sequences a diploid organism is essential to understanding the role variation in genome functions, phenotypes diseases 1 . Here, using trio-binning approach, we present high-quality, reference genome, with haplotypes assembled independently at chromosome level, for common marmoset ( Callithrix jacchus ), an primate model system that widely used biomedical research 2,3 full spectrum heterozygosity between two involves 1.36% genome—much higher than 0.13% indicated by standard estimation based on single-nucleotide alone. de novo mutation rate 0.43 × 10 −8 per site generation, paternal inherited acquired twice as many mutations maternal. Our enabled us discover recent expansion sex-differentiation region unique evolutionary changes Y chromosome. In addition, identified genes signatures positive selection might have contributed evolution biological features. Brain-related were highly conserved marmosets humans, although several experienced lineage-specific copy number variations or diversifying selection, implications use system.