TY - JOUR
T1 - Evolutionary and biomedical insights from a marmoset diploid genome assembly
AU - Yang, Chentao
AU - Zhou, Yang
AU - Marcus, Stephanie
AU - Formenti, Giulio
AU - Bergeron, Lucie A.
AU - Song, Zhenzhen
AU - Bi, Xupeng
AU - Bergman, Juraj
AU - Rousselle, Marjolaine Marie C.
AU - Zhou, Chengran
AU - Zhou, Long
AU - Deng, Yuan
AU - Fang, Miaoquan
AU - Xie, Duo
AU - Zhu, Yuanzhen
AU - Tan, Shangjin
AU - Mountcastle, Jacquelyn
AU - Haase, Bettina
AU - Balacco, Jennifer
AU - Wood, Jonathan
AU - Chow, William
AU - Rhie, Arang
AU - Pippel, Martin
AU - Fabiszak, Margaret M.
AU - Koren, Sergey
AU - Fedrigo, Olivier
AU - Freiwald, Winrich A.
AU - Howe, Kerstin
AU - Yang, Huanming
AU - Phillippy, Adam M.
AU - Schierup, Mikkel Heide
AU - Jarvis, Erich D.
AU - Zhang, Guojie
N1 - Publisher Copyright:
© 2021, The Author(s).
PY - 2021/6
Y1 - 2021/6
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85105160881&partnerID=8YFLogxK
U2 - 10.1038/s41586-021-03535-x
DO - 10.1038/s41586-021-03535-x
M3 - Journal article
C2 - 33910227
AN - SCOPUS:85105160881
SN - 0028-0836
VL - 594
SP - 227
EP - 233
JO - Nature
JF - Nature
IS - 7862
ER -