The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio

Peng Xu (), Jian Xu, Guangjian Liu, Lin Chen, Zhixiong Zhou, Wenzhu Peng, Yanliang Jiang, Zixia Zhao, Zhiying Jia, Yonghua Sun, Yidi Wu, Baohua Chen, Fei Pu, Jianxin Feng, Jing Luo, Jing Chai, Hanyuan Zhang, Hui Wang, Chuanju Dong, Wenkai Jiang and Xiaowen Sun
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Peng Xu: Chinese Academy of Fishery Sciences, Fengtai
Jian Xu: Chinese Academy of Fishery Sciences, Fengtai
Guangjian Liu: Novogene Bioinformatics Institute
Lin Chen: Xiamen University
Zhixiong Zhou: Xiamen University
Wenzhu Peng: Xiamen University
Yanliang Jiang: Chinese Academy of Fishery Sciences, Fengtai
Zixia Zhao: Chinese Academy of Fishery Sciences, Fengtai
Zhiying Jia: Chinese Academy of Fishery Sciences
Yonghua Sun: Chinese Academy of Sciences
Yidi Wu: Xiamen University
Baohua Chen: Xiamen University
Fei Pu: Xiamen University
Jianxin Feng: Henan Academy of Fishery Sciences
Jing Luo: Center for Life Sciences, Yunnan University
Jing Chai: Center for Life Sciences, Yunnan University
Hanyuan Zhang: Chinese Academy of Fishery Sciences, Fengtai
Hui Wang: Xiamen University
Chuanju Dong: Henan Normal University
Wenkai Jiang: Novogene Bioinformatics Institute
Xiaowen Sun: Chinese Academy of Fishery Sciences

Nature Communications, 2019, vol. 10, issue 1, 1-11

Abstract: Abstract Common carp (Cyprinus carpio) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid genome evolution in vertebrates. Here, we generate three chromosome-level reference genomes of C. carpio and compare to related diploid Cyprinid genomes. We identify a Barbinae lineage as potential diploid progenitor of C. carpio and then divide the allotetraploid genome into two subgenomes marked by a distinct genome similarity to the diploid progenitor. We estimate that the two diploid progenitors diverged around 23 Mya and merged around 12.4 Mya based on the divergence rates of homoeologous genes and transposable elements in two subgenomes. No extensive gene losses are observed in either subgenome. Instead, we find gene expression bias across surveyed tissues such that subgenome B is more dominant in homoeologous expression. CG methylation in promoter regions may play an important role in altering gene expression in allotetraploid C. carpio.

Date: 2019
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DOI: 10.1038/s41467-019-12644-1

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