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, Zsigmond 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: Contribution to journalArticle

291 Scopus citations

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 (US)
Pages (from-to)1212-1219
Number of pages8
JournalNature Genetics
Volume46
Issue number11
DOIs
StatePublished - Nov 5 2014
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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  • Cite this

    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., ... 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