The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation

作者：Yaping Wang, Ying Lü, Yong Zhang, Zemin Ning, Yan Li, Qiang Zhao, Hengyun Lu, Rong Huang, Xiao-Qin Xia, Qi Feng, Xu‐Fang Liang, Kunyan Liu, Lei Zhang, Tingting Lu, Tao Huang, Danlin Fan, Qijun Weng, Chuanrang Zhu, Yiqi Lu, Wenjun Li, Ziruo Wen, Congcong Zhou, Qilin Tian, Xiaojun Kang, Mijuan Shi, Wanting Zhang, Songhun Jang, Fukuan Du, Shan He, Lanjie Liao, Yongming Li, Bin Gui, Huihui He, Zhen Ning, Cheng Yang, Libo He, Lifei Luo, Rui Yang, Qiong Luo, Xiaochun Liu, Shuisheng Li, Wen Huang, Ling Xiao, Haoran Lin, Bin Han, Zuoyan Zhu · 发表于：Nature Genetics · 年份：2015 · DOI：10.1038/ng.3280 · 被引用次数：457 · 研究领域：Genetic diversity and population structure、Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities、interferon and immune responses

Bin Han and colleagues report the draft genome sequence of the grass carp Ctenopharyngodon idellus, a major commercially farmed species of freshwater fish. Analyses of the grass carp genome identify lineage-specific duplications that may have contributed to the adaptation of this species to a vegetarian diet. The grass carp is an important farmed fish, accounting for ∼16% of global freshwater aquaculture, and has a vegetarian diet. Here we report a 0.9-Gb draft genome of a gynogenetic female adult and a 1.07-Gb genome of a wild male adult. Genome annotation identified 27,263 protein-coding gene models in the female genome. A total of 114 scaffolds consisting of 573 Mb are anchored on 24 linkage groups. Divergence between grass carp and zebrafish is estimated to have occurred 49–54 million years ago. We identify a chromosome fusion in grass carp relative to zebrafish and report frequent crossovers between the grass carp X and Y chromosomes. We find that transcriptional activation of the mevalonate pathway and steroid biosynthesis in liver is associated with the grass carp's adaptation from a carnivorous to an herbivorous diet. We believe that the grass carp genome could serve as an initial platform for breeding better-quality fish using a genomic approach.