%0 Journal Article %1 Yang2021-ox %A Yang, Chentao %A Zhou, Yang %A Marcus, Stephanie %A Formenti, Giulio %A Bergeron, Lucie A %A Song, Zhenzhen %A Bi, Xupeng %A Bergman, Juraj %A Rousselle, Marjolaine Marie C %A Zhou, Chengran %A Zhou, Long %A Deng, Yuan %A Fang, Miaoquan %A Xie, Duo %A Zhu, Yuanzhen %A Tan, Shangjin %A Mountcastle, Jacquelyn %A Haase, Bettina %A Balacco, Jennifer %A Wood, Jonathan %A Chow, William %A Rhie, Arang %A Pippel, Martin %A Fabiszak, Margaret M %A Koren, Sergey %A Fedrigo, Olivier %A Freiwald, Winrich A %A Howe, Kerstin %A Yang, Huanming %A Phillippy, Adam M %A Schierup, Mikkel Heide %A Jarvis, Erich D %A Zhang, Guojie %D 2021 %I Springer Science and Business Media LLC %J Nature %K %N 7862 %P 227--233 %T Evolutionary and biomedical insights from a marmoset diploid genome assembly %V 594 %X 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 $\times$ 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.

@article{Yang2021-ox, 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 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 $\times$ 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.}, added-at = {2024-09-10T11:56:37.000+0200}, author = {Yang, Chentao and Zhou, Yang and Marcus, Stephanie and Formenti, Giulio and Bergeron, Lucie A and Song, Zhenzhen and Bi, Xupeng and Bergman, Juraj and Rousselle, Marjolaine Marie C and Zhou, Chengran and Zhou, Long and Deng, Yuan and Fang, Miaoquan and Xie, Duo and Zhu, Yuanzhen and Tan, Shangjin and Mountcastle, Jacquelyn and Haase, Bettina and Balacco, Jennifer and Wood, Jonathan and Chow, William and Rhie, Arang and Pippel, Martin and Fabiszak, Margaret M and Koren, Sergey and Fedrigo, Olivier and Freiwald, Winrich A and Howe, Kerstin and Yang, Huanming and Phillippy, Adam M and Schierup, Mikkel Heide and Jarvis, Erich D and Zhang, Guojie}, biburl = {https://puma.scadsai.uni-leipzig.de/bibtex/2c645add969a76fd7d588b0aa4048584a/scadsfct}, copyright = {https://creativecommons.org/licenses/by/4.0}, interhash = {408437f3394c47f31f414b0cdb6b1391}, intrahash = {c645add969a76fd7d588b0aa4048584a}, journal = {Nature}, keywords = {}, language = {en}, month = jun, number = 7862, pages = {227--233}, publisher = {Springer Science and Business Media LLC}, timestamp = {2024-09-10T15:15:57.000+0200}, title = {Evolutionary and biomedical insights from a marmoset diploid genome assembly}, volume = 594, year = 2021 }