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

• Published in: Nature genetics Vol. 46; no. 11; pp. 1212 - 1219
• Main Authors: 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, Zsigmond, 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
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.11.2014; Nature Publishing Group
• Subjects: 38/39; 45/22; 45/23; 45/77; 45/90; 45/91; 631/208/212; 631/208/514/1948; Agriculture; Animal Genetics and Genomics; Animals; Aquaculture products; Base Sequence; Biological diversity; Biomedicine; Cancer Research; Carp; Carps - genetics; Chromosome Mapping; Evolution, Molecular; Fish; Freshwater aquaculture; Gene Expression Profiling; Gene Function; Genes; Genetic diversity; Genetic research; Genetic Variation; Genome - genetics; Genome Components - genetics; Genomics; Human Genetics; Molecular Sequence Data; Sequence Analysis, DNA; Skin - metabolism; Species Specificity; Zebrafish
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/ng.3098

Xiaowen Sun and colleagues report the whole-genome sequencing of the common carp, Cyprinus carpio . They also resequenced 33 representative accessions from a worldwide collection and provide insights into population structure and evolution. 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 (2 n = 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.