A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals

Research output: Contribution to journalJournal articlepeer-review

Standard

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. / Li, Jing; Zhang, Jilin; Liu, Jing; Zhou, Yang; Cai, Cheng; Xu, Luohao; Dai, Xuelei; Feng, Shaohong; Guo, Chunxue; Rao, Jinpeng; Wei, Kai; Jarvis, Erich D.; Jiang, Yu; Zhou, Zhengkui; Zhang, Guojie; Zhou, Qi.

In: GigaScience, Vol. 10, No. 1, giaa142, 2021.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Li, J, Zhang, J, Liu, J, Zhou, Y, Cai, C, Xu, L, Dai, X, Feng, S, Guo, C, Rao, J, Wei, K, Jarvis, ED, Jiang, Y, Zhou, Z, Zhang, G & Zhou, Q 2021, 'A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals', GigaScience, vol. 10, no. 1, giaa142. https://doi.org/10.1093/gigascience/giaa142

APA

Li, J., Zhang, J., Liu, J., Zhou, Y., Cai, C., Xu, L., Dai, X., Feng, S., Guo, C., Rao, J., Wei, K., Jarvis, E. D., Jiang, Y., Zhou, Z., Zhang, G., & Zhou, Q. (2021). A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. GigaScience, 10(1), [giaa142]. https://doi.org/10.1093/gigascience/giaa142

Vancouver

Li J, Zhang J, Liu J, Zhou Y, Cai C, Xu L et al. A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. GigaScience. 2021;10(1). giaa142. https://doi.org/10.1093/gigascience/giaa142

Author

Li, Jing ; Zhang, Jilin ; Liu, Jing ; Zhou, Yang ; Cai, Cheng ; Xu, Luohao ; Dai, Xuelei ; Feng, Shaohong ; Guo, Chunxue ; Rao, Jinpeng ; Wei, Kai ; Jarvis, Erich D. ; Jiang, Yu ; Zhou, Zhengkui ; Zhang, Guojie ; Zhou, Qi. / A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. In: GigaScience. 2021 ; Vol. 10, No. 1.

Bibtex

@article{26e20b5e3f004c478e9c83a6334a12ec,
title = "A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals",
abstract = "Background: Ducks have a typical avian karyotype that consists of macro-and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multiplatform scaffolding techniques. Results: A major improvement of genome assembly and annotation quality resulted from the successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly. We found that the duck topologically associated domains (TAD) are demarcated by putative binding sites of the insulator protein CTCF, housekeeping genes, or transitions of active/inactive chromatin compartments, indicating conserved mechanisms of spatial chromosome folding with mammals. There are extensive overlaps of TAD boundaries between duck and chicken, and also between the TAD boundaries and chromosome inversion breakpoints. This suggests strong natural selection pressure on maintaining regulatory domain integrity, or vulnerability of TAD boundaries to DNA double-strand breaks. The duck W chromosome retains 2.5-fold more genes relative to chicken. Similar to the independently evolved human Y chromosome, the duck W evolved massive dispersed palindromic structures, and a pattern of sequence divergence with the Z chromosome that reflects stepwise suppression of homologous recombination. Conclusions: Our results provide novel insights into the conserved and convergently evolved chromosome features of birds and mammals, and also importantly add to the genomic resources for poultry studies.",
keywords = "chromosome inversion, duck genome, sex chromosomes, topologically associated domain",
author = "Jing Li and Jilin Zhang and Jing Liu and Yang Zhou and Cheng Cai and Luohao Xu and Xuelei Dai and Shaohong Feng and Chunxue Guo and Jinpeng Rao and Kai Wei and Jarvis, {Erich D.} and Yu Jiang and Zhengkui Zhou and Guojie Zhang and Qi Zhou",
year = "2021",
doi = "10.1093/gigascience/giaa142",
language = "English",
volume = "10",
journal = "GigaScience",
issn = "2047-217X",
publisher = "Oxford Academic",
number = "1",

}

RIS

TY - JOUR

T1 - A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals

AU - Li, Jing

AU - Zhang, Jilin

AU - Liu, Jing

AU - Zhou, Yang

AU - Cai, Cheng

AU - Xu, Luohao

AU - Dai, Xuelei

AU - Feng, Shaohong

AU - Guo, Chunxue

AU - Rao, Jinpeng

AU - Wei, Kai

AU - Jarvis, Erich D.

AU - Jiang, Yu

AU - Zhou, Zhengkui

AU - Zhang, Guojie

AU - Zhou, Qi

PY - 2021

Y1 - 2021

N2 - Background: Ducks have a typical avian karyotype that consists of macro-and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multiplatform scaffolding techniques. Results: A major improvement of genome assembly and annotation quality resulted from the successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly. We found that the duck topologically associated domains (TAD) are demarcated by putative binding sites of the insulator protein CTCF, housekeeping genes, or transitions of active/inactive chromatin compartments, indicating conserved mechanisms of spatial chromosome folding with mammals. There are extensive overlaps of TAD boundaries between duck and chicken, and also between the TAD boundaries and chromosome inversion breakpoints. This suggests strong natural selection pressure on maintaining regulatory domain integrity, or vulnerability of TAD boundaries to DNA double-strand breaks. The duck W chromosome retains 2.5-fold more genes relative to chicken. Similar to the independently evolved human Y chromosome, the duck W evolved massive dispersed palindromic structures, and a pattern of sequence divergence with the Z chromosome that reflects stepwise suppression of homologous recombination. Conclusions: Our results provide novel insights into the conserved and convergently evolved chromosome features of birds and mammals, and also importantly add to the genomic resources for poultry studies.

AB - Background: Ducks have a typical avian karyotype that consists of macro-and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multiplatform scaffolding techniques. Results: A major improvement of genome assembly and annotation quality resulted from the successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly. We found that the duck topologically associated domains (TAD) are demarcated by putative binding sites of the insulator protein CTCF, housekeeping genes, or transitions of active/inactive chromatin compartments, indicating conserved mechanisms of spatial chromosome folding with mammals. There are extensive overlaps of TAD boundaries between duck and chicken, and also between the TAD boundaries and chromosome inversion breakpoints. This suggests strong natural selection pressure on maintaining regulatory domain integrity, or vulnerability of TAD boundaries to DNA double-strand breaks. The duck W chromosome retains 2.5-fold more genes relative to chicken. Similar to the independently evolved human Y chromosome, the duck W evolved massive dispersed palindromic structures, and a pattern of sequence divergence with the Z chromosome that reflects stepwise suppression of homologous recombination. Conclusions: Our results provide novel insights into the conserved and convergently evolved chromosome features of birds and mammals, and also importantly add to the genomic resources for poultry studies.

KW - chromosome inversion

KW - duck genome

KW - sex chromosomes

KW - topologically associated domain

U2 - 10.1093/gigascience/giaa142

DO - 10.1093/gigascience/giaa142

M3 - Journal article

C2 - 33406261

AN - SCOPUS:85100230777

VL - 10

JO - GigaScience

JF - GigaScience

SN - 2047-217X

IS - 1

M1 - giaa142

ER -

ID: 257324617