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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.

鲢鱼和ead鱼的全基因组测序为其进化和物种形成提供了新的视角。

  • 影响因子:0
  • DOI:10.1111/1755-0998.13297
  • 作者列表:"Jian J","Yang L","Gan X","Wu B","Gao L","Zeng H","Wang X","Liang Z","Wang Y","Fang L","Li J","Jiang S","Du K","Fu B","Bai M","Chen M","Fang X","Liu H","He S
  • 发表时间:2021-04-01
Abstract

: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 ~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.

摘要

: 我国 “四种家养鱼类” 中的两种,世界范围内集中养殖的食用鲢鱼和ead鱼。在这里,我们分别构建了鲢鱼和ead鱼的837和845 Mb草图基因组组装,包括24,571和24,229个注释的蛋白质编码基因。分别获得了银和ead鱼的遗传图谱,锚定了所有支架的71.7% 和83.8%。系统发育分析表明,ead鱼与鲢鱼形成了一条进化枝,估计其分化时间为360万年前; 鲢鱼与斑马鱼的分化时间为5070万年前。东亚鲤科鱼的基因组特异性染色体融合发生在这一分支从含有鲤鱼和辛环che的分支分化后约920万年。KEGG和GO分析表明,银和ead鱼中扩增的基因家族与疾病、免疫系统和环境适应有关。基于42个个体的全基因组序列检测区分银和ead鱼群体的基因组区域。与分歧区域相关的基因与生殖系统发育和女性主要性征的发育有关。因此,我们的结果提供了对东亚鲤鱼的新的系统基因组分析,以及鲢鱼和ead鱼的进化和物种形成。

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