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Juraj Bergman

Evolutionary and biomedical insights from a marmoset diploid genome assembly

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

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Evolutionary and biomedical insights from a marmoset diploid genome assembly. / Yang, Chentao; Zhou, Yang; Marcus, Stephanie et al.

I: Nature, Bind 594, Nr. 7862, 06.2021, s. 227-233.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer 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, bind 594, nr. 7862, s. 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(7862), 227-233. https://doi.org/10.1038/s41586-021-03535-x

CBE

Yang C, Zhou Y, Marcus S, Formenti G, Bergeron LA, Song Z, Bi X, Bergman J, Rousselle MMC, Zhou C, et al. 2021. Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature. 594(7862):227-233. https://doi.org/10.1038/s41586-021-03535-x

MLA

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 jun.;594(7862):227-233. doi: 10.1038/s41586-021-03535-x

Author

Yang, Chentao ; Zhou, Yang ; Marcus, Stephanie et al. / Evolutionary and biomedical insights from a marmoset diploid genome assembly. I: Nature. 2021 ; Bind 594, Nr. 7862. s. 227-233.

Bibtex

@article{c180c86b633f46098515ee61216629cf,
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 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.",
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",
month = jun,
doi = "10.1038/s41586-021-03535-x",
language = "English",
volume = "594",
pages = "227--233",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7862",

}

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

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

VL - 594

SP - 227

EP - 233

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7862

ER -