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Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation

文献类型： 外文期刊

作者： Jian, Jianbo 1 ; Yang, Liandong 1 ; Gan, Xiaoni 1 ; Wu, Bin 2 ; Gao, Li 2 ; Zeng, Honghui 1 ; Wang, Xuzhen 1 ; Liang, Zhi 1 ;

作者机构： 1.Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Hubei, Peoples R China

2.BGI Shenzhen, BGI Genom, Shenzhen, Peoples R China

3.Hunan Fisheries Sci Inst, Changsha, Peoples R China

4.Jianghan Univ, Hubei Engn Res Ctr Protect & Utilizat Special Bio, Sch Life Sci, Wuhan, Peoples R China

5.Chinese Acad Fishery Sci, Pearl River Fisheries Res Inst, Guangzhou, Peoples R China

6.Univ Wurzburg, Bioctr, Physiol Chem, Wurzburg, Germany

7.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming, Yunnan, Peoples R China

关键词： bighead carp; chromosome fusion; divergence; evolution; silver carp; speciation

期刊名称：MOLECULAR ECOLOGY RESOURCES （ 影响因子：7.09； 五年影响因子：8.745 ）

ISSN： 1755-098X

年卷期： 2021 年 21 卷 3 期

页码：

收录情况： SCI

摘要： The edible silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis), which are two of the "Four Domesticated Fish" of China, are cultivated intensively worldwide. Here, we constructed 837- and 845-Mb draft genome assemblies for the silver carp and the bighead carp, respectively, including 24,571 and 24,229 annotated protein-coding genes. Genetic maps, anchoring 71.7% and 83.8% of all scaffolds, were obtained for the silver and bighead carp, respectively. Phylogenetic analysis showed that the bighead carp formed a clade with the silver carp, with an estimated divergence time of 3.6 million years ago; the time of divergence between the silver carp and zebrafish was 50.7 million years ago. An East Asian cyprinid genome-specific chromosome fusion took place similar to 9.2 million years after this clade diverged from the clade containing the common carp and Sinocyclocheilus. KEGG and GO analyses indicated that the expanded gene families in the silver and bighead carp were associated with diseases, the immune system and environmental adaptations. Genomic regions differentiating the silver and bighead carp populations were detected based on the whole-genome sequences of 42 individuals. Genes associated with the divergent regions were associated with reproductive system development and the development of primary female sexual characteristics. Thus, our results provided a novel systematic genomic analysis of the East Asian cyprinids, as well as the evolution and speciation of the silver carp and bighead carp.

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