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

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  • Peng Xu

    (Chinese Academy of Fishery Sciences, Fengtai
    Xiamen University
    Pilot National Laboratory for Marine Science and Technology
    Ningde Fufa Fisheries Company Limited)

  • 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
    Henan Normal University)

  • Chuanju Dong

    (Henan Normal University)

  • Wenkai Jiang

    (Novogene Bioinformatics Institute)

  • Xiaowen Sun

    (Chinese Academy of Fishery Sciences)

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.

Suggested Citation

  • 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 C, 2019. "The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-12644-1
    DOI: 10.1038/s41467-019-12644-1
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    Cited by:

    1. Li He & Yuàn Wang & Yi Wang & Ren-Gang Zhang & Yuán Wang & Elvira Hörandl & Tao Ma & Yan-Fei Mao & Judith E. Mank & Ray Ming, 2024. "Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. Anthony K. Redmond & Dearbhaile Casey & Manu Kumar Gundappa & Daniel J. Macqueen & Aoife McLysaght, 2023. "Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Heiner Kuhl & Kang Du & Manfred Schartl & Lukáš Kalous & Matthias Stöck & Dunja K. Lamatsch, 2022. "Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    4. Min-Rui-Xuan Xu & Zhen-Yang Liao & Jordan R. Brock & Kang Du & Guo-Yin Li & Zhi-Qiang Chen & Ying-Hao Wang & Zhong-Nan Gao & Gaurav Agarwal & Kevin H-C Wei & Feng Shao & Shuai Pang & Adrian E. Platts , 2023. "Maternal dominance contributes to subgenome differentiation in allopolyploid fishes," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    5. Adam M. Session & Daniel S. Rokhsar, 2023. "Transposon signatures of allopolyploid genome evolution," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    6. Liang Ma & Ke-Wei Liu & Zhen Li & Yu-Yun Hsiao & Yiying Qi & Tao Fu & Guang-Da Tang & Diyang Zhang & Wei-Hong Sun & Ding-Kun Liu & Yuanyuan Li & Gui-Zhen Chen & Xue-Die Liu & Xing-Yu Liao & Yu-Ting Ji, 2023. "Diploid and tetraploid genomes of Acorus and the evolution of monocots," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

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