Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda

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Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda. / Guang, Xuanmin; Lan, Tianming; Wan, Qiu Hong; Huang, Yan; Li, Hong; Zhang, Mingchun; Li, Rengui; Zhang, Zhizhong; Lei, Yinghu; Zhang, Ling; Zhang, Heming; Li, Desheng; Li, Xiaoping; Li, Haimeng; Xu, Yan; Qiao, Maiju; Wu, Daifu; Tang, Keyi; Zhao, Pengpeng; Lin, Jian-Qing; Sahu, Sunil Kumar; Liang, Qiqi; Jiang, Wenkai; Zhang, Danhui; Xu, Xun; Liu, Xin; Lisby, Michael; Yang, Huanming; Kristiansen, Karsten; Liu, Huan; Fang, Sheng-Guo.

In: Science Bulletin, Vol. 66, No. 19, 2021, p. 2002-2013.

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

Harvard

Guang, X, Lan, T, Wan, QH, Huang, Y, Li, H, Zhang, M, Li, R, Zhang, Z, Lei, Y, Zhang, L, Zhang, H, Li, D, Li, X, Li, H, Xu, Y, Qiao, M, Wu, D, Tang, K, Zhao, P, Lin, J-Q, Sahu, SK, Liang, Q, Jiang, W, Zhang, D, Xu, X, Liu, X, Lisby, M, Yang, H, Kristiansen, K, Liu, H & Fang, S-G 2021, 'Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda', Science Bulletin, vol. 66, no. 19, pp. 2002-2013. https://doi.org/10.1016/j.scib.2021.02.002

APA

Guang, X., Lan, T., Wan, Q. H., Huang, Y., Li, H., Zhang, M., Li, R., Zhang, Z., Lei, Y., Zhang, L., Zhang, H., Li, D., Li, X., Li, H., Xu, Y., Qiao, M., Wu, D., Tang, K., Zhao, P., ... Fang, S-G. (2021). Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda. Science Bulletin, 66(19), 2002-2013. https://doi.org/10.1016/j.scib.2021.02.002

Vancouver

Guang X, Lan T, Wan QH, Huang Y, Li H, Zhang M et al. Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda. Science Bulletin. 2021;66(19):2002-2013. https://doi.org/10.1016/j.scib.2021.02.002

Author

Guang, Xuanmin ; Lan, Tianming ; Wan, Qiu Hong ; Huang, Yan ; Li, Hong ; Zhang, Mingchun ; Li, Rengui ; Zhang, Zhizhong ; Lei, Yinghu ; Zhang, Ling ; Zhang, Heming ; Li, Desheng ; Li, Xiaoping ; Li, Haimeng ; Xu, Yan ; Qiao, Maiju ; Wu, Daifu ; Tang, Keyi ; Zhao, Pengpeng ; Lin, Jian-Qing ; Sahu, Sunil Kumar ; Liang, Qiqi ; Jiang, Wenkai ; Zhang, Danhui ; Xu, Xun ; Liu, Xin ; Lisby, Michael ; Yang, Huanming ; Kristiansen, Karsten ; Liu, Huan ; Fang, Sheng-Guo. / Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda. In: Science Bulletin. 2021 ; Vol. 66, No. 19. pp. 2002-2013.

Bibtex

@article{b57eadb86bfb4133ae9e004b15f2e6fd,
title = "Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda",
abstract = "Extant giant pandas are divided into Sichuan and Qinling subspecies. The giant panda has many species-specific characteristics, including comparatively small organs for body size, small genitalia of male individuals, and low reproduction. Here, we report the most contiguous, high-quality chromosome-level genomes of two extant giant panda subspecies to date, with the first genome assembly of the Qinling subspecies. Compared with the previously assembled giant panda genomes based on short reads, our two assembled genomes increased contiguity over 200-fold at the contig level. Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago. Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2 (DACH2) gene and specific changes in the synaptotagmin 6 (SYT6) gene, which may be responsible for the reduced fertility of the giant panda. Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D (IQCD) gene may at least partly explain the different reproduction rates of the two subspecies. Furthermore, several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements, which may contribute to the reduced inner organ sizes of the giant panda.",
keywords = "Chromosome-level genome, Divergence time, Giant panda, Inner organ size, Reduced fertility",
author = "Xuanmin Guang and Tianming Lan and Wan, {Qiu Hong} and Yan Huang and Hong Li and Mingchun Zhang and Rengui Li and Zhizhong Zhang and Yinghu Lei and Ling Zhang and Heming Zhang and Desheng Li and Xiaoping Li and Haimeng Li and Yan Xu and Maiju Qiao and Daifu Wu and Keyi Tang and Pengpeng Zhao and Jian-Qing Lin and Sahu, {Sunil Kumar} and Qiqi Liang and Wenkai Jiang and Danhui Zhang and Xun Xu and Xin Liu and Michael Lisby and Huanming Yang and Karsten Kristiansen and Huan Liu and Sheng-Guo Fang",
year = "2021",
doi = "10.1016/j.scib.2021.02.002",
language = "English",
volume = "66",
pages = "2002--2013",
journal = "Science Bulletin",
issn = "2095-9273",
publisher = "Springer Science+Business Media",
number = "19",

}

RIS

TY - JOUR

T1 - Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda

AU - Guang, Xuanmin

AU - Lan, Tianming

AU - Wan, Qiu Hong

AU - Huang, Yan

AU - Li, Hong

AU - Zhang, Mingchun

AU - Li, Rengui

AU - Zhang, Zhizhong

AU - Lei, Yinghu

AU - Zhang, Ling

AU - Zhang, Heming

AU - Li, Desheng

AU - Li, Xiaoping

AU - Li, Haimeng

AU - Xu, Yan

AU - Qiao, Maiju

AU - Wu, Daifu

AU - Tang, Keyi

AU - Zhao, Pengpeng

AU - Lin, Jian-Qing

AU - Sahu, Sunil Kumar

AU - Liang, Qiqi

AU - Jiang, Wenkai

AU - Zhang, Danhui

AU - Xu, Xun

AU - Liu, Xin

AU - Lisby, Michael

AU - Yang, Huanming

AU - Kristiansen, Karsten

AU - Liu, Huan

AU - Fang, Sheng-Guo

PY - 2021

Y1 - 2021

N2 - Extant giant pandas are divided into Sichuan and Qinling subspecies. The giant panda has many species-specific characteristics, including comparatively small organs for body size, small genitalia of male individuals, and low reproduction. Here, we report the most contiguous, high-quality chromosome-level genomes of two extant giant panda subspecies to date, with the first genome assembly of the Qinling subspecies. Compared with the previously assembled giant panda genomes based on short reads, our two assembled genomes increased contiguity over 200-fold at the contig level. Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago. Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2 (DACH2) gene and specific changes in the synaptotagmin 6 (SYT6) gene, which may be responsible for the reduced fertility of the giant panda. Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D (IQCD) gene may at least partly explain the different reproduction rates of the two subspecies. Furthermore, several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements, which may contribute to the reduced inner organ sizes of the giant panda.

AB - Extant giant pandas are divided into Sichuan and Qinling subspecies. The giant panda has many species-specific characteristics, including comparatively small organs for body size, small genitalia of male individuals, and low reproduction. Here, we report the most contiguous, high-quality chromosome-level genomes of two extant giant panda subspecies to date, with the first genome assembly of the Qinling subspecies. Compared with the previously assembled giant panda genomes based on short reads, our two assembled genomes increased contiguity over 200-fold at the contig level. Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago. Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2 (DACH2) gene and specific changes in the synaptotagmin 6 (SYT6) gene, which may be responsible for the reduced fertility of the giant panda. Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D (IQCD) gene may at least partly explain the different reproduction rates of the two subspecies. Furthermore, several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements, which may contribute to the reduced inner organ sizes of the giant panda.

KW - Chromosome-level genome

KW - Divergence time

KW - Giant panda

KW - Inner organ size

KW - Reduced fertility

U2 - 10.1016/j.scib.2021.02.002

DO - 10.1016/j.scib.2021.02.002

M3 - Journal article

AN - SCOPUS:85103703056

VL - 66

SP - 2002

EP - 2013

JO - Science Bulletin

JF - Science Bulletin

SN - 2095-9273

IS - 19

ER -

ID: 261374111