TY - JOUR
T1 - Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success
AU - Chen, Lin
AU - Li, Chengyu
AU - Li, Bijun
AU - Zhou, Xiaofan
AU - Bai, Yulin
AU - Zou, Xiaoqing
AU - Zhou, Zhixiong
AU - He, Qian
AU - Chen, Baohua
AU - Wang, Mei
AU - Xue, Yaguo
AU - Jiang, Zhou
AU - Feng, Jianxin
AU - Zhou, Tao
AU - Liu, Zhanjiang
AU - Xu, Peng
N1 - Publisher Copyright:
© 2023
PY - 2024/5
Y1 - 2024/5
N2 - 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.
AB - 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.
KW - Allotetraploid
KW - Environmental adaptation
KW - Expression dominance shift
KW - Homoeologous expression
KW - Subgenome structural evolution
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U2 - 10.1016/j.fmre.2023.06.011
DO - 10.1016/j.fmre.2023.06.011
M3 - Article
AN - SCOPUS:85170081648
SN - 2096-9457
VL - 4
SP - 589
EP - 602
JO - Fundamental Research
JF - Fundamental Research
IS - 3
ER -