Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success

Lin Chen, Chengyu Li, Bijun Li, Xiaofan Zhou, Yulin Bai, Xiaoqing Zou, Zhixiong Zhou, Qian He, Baohua Chen, Mei Wang, Yaguo Xue, Zhou Jiang, Jianxin Feng, Tao Zhou, Zhanjiang Liu, Peng Xu

Research output: Contribution to journalArticlepeer-review


Hybridization and polyploidization have made great contributions to speciation, heterosis, and agricultural production within plants, but there is still limited understanding and utilization in animals. Subgenome structure and expression reorganization and cooperation post hybridization and polyploidization are essential for speciation and allopolyploid success. However, the mechanisms have not yet been comprehensively assessed in animals. Here, we produced a high-fidelity reference genome sequence for common carp, a typical allotetraploid fish species cultured worldwide. This genome enabled in-depth analysis of the evolution of subgenome architecture and expression responses. Most genes were expressed with subgenome biases, with a trend of transition from the expression of subgenome A during the early stages to that of subgenome B during the late stages of embryonic development. While subgenome A evolved more rapidly, subgenome B contributed to a greater level of expression during development and under stressful conditions. Stable dominant patterns for homoeologous gene pairs both during development and under thermal stress suggest a potential fixed heterosis in the allotetraploid genome. Preferentially expressing either copy of a homoeologous gene at higher levels to confer development and response to stress indicates the dominant effect of heterosis. The plasticity of subgenomes and their shifting of dominant expression during early development, and in response to stressful conditions, provide novel insights into the molecular basis of the successful speciation, evolution, and heterosis of the allotetraploid common carp.

Original languageEnglish (US)
Pages (from-to)589-602
Number of pages14
JournalFundamental Research
Issue number3
StatePublished - May 2024


  • Allotetraploid
  • Environmental adaptation
  • Expression dominance shift
  • Homoeologous expression
  • Subgenome structural evolution

ASJC Scopus subject areas

  • General


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