Genome sequence and genetic diversity of the common carp, Cyprinus carpio

Peng Xu, Xiaofeng Zhang, Xumin Wang, Jiongtang Li, Guiming Liu, Youyi Kuang, Jian Xu, Xianhu Zheng, Lufeng Ren, Guoliang Wang, Yan Zhang, Linhe Huo, Zixia Zhao, Dingchen Cao, Cuiyun Lu, Chao Li, Yi Zhou, Zhanjiang Liu, Zhonghua Fan, Guangle ShanXingang Li, Shuangxiu Wu, Lipu Song, Guangyuan Hou, Yanliang Jiang, Z. Jeney, Dan Yu, Li Wang, Changjun Shao, Lai Song, Jing Sun, Peifeng Ji, Jian Wang, Qiang Li, Liming Xu, Fanyue Sun, Jianxin Feng, Chenghui Wang, Shaolin Wang, Baosen Wang, Yan Li, Yaping Zhu, Wei Xue, Lan Zhao, Jintu Wang, Ying Gu, Weihua Lv, Kejing Wu, Jingfa Xiao, Jiayan Wu, Zhang Zhang, Jun Yu, Xiaowen Sun

Research output: Article

229 Citations (Scopus)

Abstract

The common carp, Cyprinus carpio, is one of the most important cyprinid species and globally accounts for 10% of freshwater aquaculture production. Here we present a draft genome of domesticated C. carpio (strain Songpu), whose current assembly contains 52,610 protein-coding genes and approximately 92.3% coverage of its paleotetraploidized genome (2n = 100). The latest round of whole-genome duplication has been estimated to have occurred approximately 8.2 million years ago. Genome resequencing of 33 representative individuals from worldwide populations demonstrates a single origin for C. carpio in 2 subspecies (C. carpio Haematopterus and C. carpio carpio). Integrative genomic and transcriptomic analyses were used to identify loci potentially associated with traits including scaling patterns and skin color. In combination with the high-resolution genetic map, the draft genome paves the way for better molecular studies and improved genome-assisted breeding of C. carpio and other closely related species.

Original languageEnglish
Pages (from-to)1212-1219
Number of pages8
JournalNature Genetics
Volume46
Issue number11
DOIs
Publication statusPublished - nov. 5 2014

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Carps
Genome
Skin Pigmentation
Aquaculture
Fresh Water
Breeding
Population

ASJC Scopus subject areas

  • Genetics
  • Medicine(all)

Cite this

Xu, P., Zhang, X., Wang, X., Li, J., Liu, G., Kuang, Y., ... Sun, X. (2014). Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nature Genetics, 46(11), 1212-1219. https://doi.org/10.1038/ng.3098

Genome sequence and genetic diversity of the common carp, Cyprinus carpio. / Xu, Peng; Zhang, Xiaofeng; Wang, Xumin; Li, Jiongtang; Liu, Guiming; Kuang, Youyi; Xu, Jian; Zheng, Xianhu; Ren, Lufeng; Wang, Guoliang; Zhang, Yan; Huo, Linhe; Zhao, Zixia; Cao, Dingchen; Lu, Cuiyun; Li, Chao; Zhou, Yi; Liu, Zhanjiang; Fan, Zhonghua; Shan, Guangle; Li, Xingang; Wu, Shuangxiu; Song, Lipu; Hou, Guangyuan; Jiang, Yanliang; Jeney, Z.; Yu, Dan; Wang, Li; Shao, Changjun; Song, Lai; Sun, Jing; Ji, Peifeng; Wang, Jian; Li, Qiang; Xu, Liming; Sun, Fanyue; Feng, Jianxin; Wang, Chenghui; Wang, Shaolin; Wang, Baosen; Li, Yan; Zhu, Yaping; Xue, Wei; Zhao, Lan; Wang, Jintu; Gu, Ying; Lv, Weihua; Wu, Kejing; Xiao, Jingfa; Wu, Jiayan; Zhang, Zhang; Yu, Jun; Sun, Xiaowen.

In: Nature Genetics, Vol. 46, No. 11, 05.11.2014, p. 1212-1219.

Research output: Article

Xu, P, Zhang, X, Wang, X, Li, J, Liu, G, Kuang, Y, Xu, J, Zheng, X, Ren, L, Wang, G, Zhang, Y, Huo, L, Zhao, Z, Cao, D, Lu, C, Li, C, Zhou, Y, Liu, Z, Fan, Z, Shan, G, Li, X, Wu, S, Song, L, Hou, G, Jiang, Y, Jeney, Z, Yu, D, Wang, L, Shao, C, Song, L, Sun, J, Ji, P, Wang, J, Li, Q, Xu, L, Sun, F, Feng, J, Wang, C, Wang, S, Wang, B, Li, Y, Zhu, Y, Xue, W, Zhao, L, Wang, J, Gu, Y, Lv, W, Wu, K, Xiao, J, Wu, J, Zhang, Z, Yu, J & Sun, X 2014, 'Genome sequence and genetic diversity of the common carp, Cyprinus carpio', Nature Genetics, vol. 46, no. 11, pp. 1212-1219. https://doi.org/10.1038/ng.3098
Xu P, Zhang X, Wang X, Li J, Liu G, Kuang Y et al. Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nature Genetics. 2014 nov. 5;46(11):1212-1219. https://doi.org/10.1038/ng.3098
Xu, Peng ; Zhang, Xiaofeng ; Wang, Xumin ; Li, Jiongtang ; Liu, Guiming ; Kuang, Youyi ; Xu, Jian ; Zheng, Xianhu ; Ren, Lufeng ; Wang, Guoliang ; Zhang, Yan ; Huo, Linhe ; Zhao, Zixia ; Cao, Dingchen ; Lu, Cuiyun ; Li, Chao ; Zhou, Yi ; Liu, Zhanjiang ; Fan, Zhonghua ; Shan, Guangle ; Li, Xingang ; Wu, Shuangxiu ; Song, Lipu ; Hou, Guangyuan ; Jiang, Yanliang ; Jeney, Z. ; Yu, Dan ; Wang, Li ; Shao, Changjun ; Song, Lai ; Sun, Jing ; Ji, Peifeng ; Wang, Jian ; Li, Qiang ; Xu, Liming ; Sun, Fanyue ; Feng, Jianxin ; Wang, Chenghui ; Wang, Shaolin ; Wang, Baosen ; Li, Yan ; Zhu, Yaping ; Xue, Wei ; Zhao, Lan ; Wang, Jintu ; Gu, Ying ; Lv, Weihua ; Wu, Kejing ; Xiao, Jingfa ; Wu, Jiayan ; Zhang, Zhang ; Yu, Jun ; Sun, Xiaowen. / Genome sequence and genetic diversity of the common carp, Cyprinus carpio. In: Nature Genetics. 2014 ; Vol. 46, No. 11. pp. 1212-1219.
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AU - Kuang, Youyi

AU - Xu, Jian

AU - Zheng, Xianhu

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AU - Wang, Guoliang

AU - Zhang, Yan

AU - Huo, Linhe

AU - Zhao, Zixia

AU - Cao, Dingchen

AU - Lu, Cuiyun

AU - Li, Chao

AU - Zhou, Yi

AU - Liu, Zhanjiang

AU - Fan, Zhonghua

AU - Shan, Guangle

AU - Li, Xingang

AU - Wu, Shuangxiu

AU - Song, Lipu

AU - Hou, Guangyuan

AU - Jiang, Yanliang

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AU - Song, Lai

AU - Sun, Jing

AU - Ji, Peifeng

AU - Wang, Jian

AU - Li, Qiang

AU - Xu, Liming

AU - Sun, Fanyue

AU - Feng, Jianxin

AU - Wang, Chenghui

AU - Wang, Shaolin

AU - Wang, Baosen

AU - Li, Yan

AU - Zhu, Yaping

AU - Xue, Wei

AU - Zhao, Lan

AU - Wang, Jintu

AU - Gu, Ying

AU - Lv, Weihua

AU - Wu, Kejing

AU - Xiao, Jingfa

AU - Wu, Jiayan

AU - Zhang, Zhang

AU - Yu, Jun

AU - Sun, Xiaowen

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