Evolutionary and biomedical insights from a marmoset diploid genome assembly

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Evolutionary and biomedical insights from a marmoset diploid genome assembly. / Yang, Chentao; Zhou, Yang; Marcus, Stephanie; Formenti, Giulio; Bergeron, Lucie A.; Song, Zhenzhen; Bi, Xupeng; Bergman, Juraj; Rousselle, Marjolaine Marie C.; Zhou, Chengran; Zhou, Long; Deng, Yuan; Fang, Miaoquan; Xie, Duo; Zhu, Yuanzhen; Tan, Shangjin; Mountcastle, Jacquelyn; Haase, Bettina; Balacco, Jennifer; Wood, Jonathan; Chow, William; Rhie, Arang; Pippel, Martin; Fabiszak, Margaret M.; Koren, Sergey; Fedrigo, Olivier; Freiwald, Winrich A.; Howe, Kerstin; Yang, Huanming; Phillippy, Adam M.; Schierup, Mikkel Heide; Jarvis, Erich D.; Zhang, Guojie.

In: Nature, Vol. 594, 2021, p. 227-233.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

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 2021, 'Evolutionary and biomedical insights from a marmoset diploid genome assembly', Nature, vol. 594, pp. 227-233. https://doi.org/10.1038/s41586-021-03535-x

APA

Yang, C., Zhou, Y., Marcus, S., Formenti, G., Bergeron, L. A., Song, Z., Bi, X., Bergman, J., Rousselle, M. M. C., Zhou, C., Zhou, L., Deng, Y., Fang, M., Xie, D., Zhu, Y., Tan, S., Mountcastle, J., Haase, B., Balacco, J., ... Zhang, G. (2021). Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature, 594, 227-233. https://doi.org/10.1038/s41586-021-03535-x

Vancouver

Yang C, Zhou Y, Marcus S, Formenti G, Bergeron LA, Song Z et al. Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature. 2021;594:227-233. https://doi.org/10.1038/s41586-021-03535-x

Author

Yang, Chentao ; Zhou, Yang ; Marcus, Stephanie ; Formenti, Giulio ; Bergeron, Lucie A. ; Song, Zhenzhen ; Bi, Xupeng ; Bergman, Juraj ; Rousselle, Marjolaine Marie C. ; Zhou, Chengran ; Zhou, Long ; Deng, Yuan ; Fang, Miaoquan ; Xie, Duo ; Zhu, Yuanzhen ; Tan, Shangjin ; Mountcastle, Jacquelyn ; Haase, Bettina ; Balacco, Jennifer ; Wood, Jonathan ; Chow, William ; Rhie, Arang ; Pippel, Martin ; Fabiszak, Margaret M. ; Koren, Sergey ; Fedrigo, Olivier ; Freiwald, Winrich A. ; Howe, Kerstin ; Yang, Huanming ; Phillippy, Adam M. ; Schierup, Mikkel Heide ; Jarvis, Erich D. ; Zhang, Guojie. / Evolutionary and biomedical insights from a marmoset diploid genome assembly. In: Nature. 2021 ; Vol. 594. pp. 227-233.

Bibtex

@article{428b837e3d4a41b5809a6d910f609e3d,

title = "Evolutionary and biomedical insights from a marmoset diploid genome assembly",

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 important primate model system widely used in biomedical research2,3. The full heterozygosity spectrum between the two haplotypes involves 1.36% of the genome, much higher than the 0.13% indicated by the standard single nucleotide heterozygosity estimation alone. The de novo mutation rate is 0.43 × 10-8 per site per generation, where 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 differentiated region and unique evolutionary changes in the marmoset Y chromosome. Additionally, 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, though several genes experienced lineage-specific copy number variations or diversifying selection, providing important implications for the application of marmosets as a model system.",

author = "Chentao Yang and Yang Zhou and Stephanie Marcus and Giulio Formenti and Bergeron, {Lucie A.} and Zhenzhen Song and Xupeng Bi and Juraj Bergman and Rousselle, {Marjolaine Marie C.} and Chengran Zhou and Long Zhou and Yuan Deng and Miaoquan Fang and Duo Xie and Yuanzhen Zhu and Shangjin Tan and Jacquelyn Mountcastle and Bettina Haase and Jennifer Balacco and Jonathan Wood and William Chow and Arang Rhie and Martin Pippel and Fabiszak, {Margaret M.} and Sergey Koren and Olivier Fedrigo and Freiwald, {Winrich A.} and Kerstin Howe and Huanming Yang and Phillippy, {Adam M.} and Schierup, {Mikkel Heide} and Jarvis, {Erich D.} and Guojie Zhang",

note = "Publisher Copyright: {\textcopyright} 2021, The Author(s).",

year = "2021",

doi = "10.1038/s41586-021-03535-x",

language = "English",

volume = "594",

pages = "227--233",

journal = "Nature",

issn = "0028-0836",

publisher = "nature publishing group",

}

RIS

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

PY - 2021

Y1 - 2021

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 important primate model system widely used in biomedical research2,3. The full heterozygosity spectrum between the two haplotypes involves 1.36% of the genome, much higher than the 0.13% indicated by the standard single nucleotide heterozygosity estimation alone. The de novo mutation rate is 0.43 × 10-8 per site per generation, where 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 differentiated region and unique evolutionary changes in the marmoset Y chromosome. Additionally, 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, though several genes experienced lineage-specific copy number variations or diversifying selection, providing important implications for the application 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 important primate model system widely used in biomedical research2,3. The full heterozygosity spectrum between the two haplotypes involves 1.36% of the genome, much higher than the 0.13% indicated by the standard single nucleotide heterozygosity estimation alone. The de novo mutation rate is 0.43 × 10-8 per site per generation, where 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 differentiated region and unique evolutionary changes in the marmoset Y chromosome. Additionally, 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, though several genes experienced lineage-specific copy number variations or diversifying selection, providing important implications for the application of marmosets as a model system.

U2 - 10.1038/s41586-021-03535-x

DO - 10.1038/s41586-021-03535-x

M3 - Journal article

C2 - 33910227

AN - SCOPUS:85105160881

VL - 594

SP - 227

EP - 233

JO - Nature

JF - Nature

SN - 0028-0836

ER -

ID: 272022266

Department of Biology