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Maternal dominance contributes to subgenome differentiation in allopolyploid fishes

Author

Listed:
  • Min-Rui-Xuan Xu

    (Jiujiang University)

  • Zhen-Yang Liao

    (Chinese Academy of Agricultural Sciences)

  • Jordan R. Brock

    (Michigan State University)

  • Kang Du

    (Texas State University)

  • Guo-Yin Li

    (Zhoukou Normal University)

  • Zhi-Qiang Chen

    (Glbizzia Biosciences)

  • Ying-Hao Wang

    (Chinese Academy of Agricultural Sciences)

  • Zhong-Nan Gao

    (Jiujiang University)

  • Gaurav Agarwal

    (Michigan State University)

  • Kevin H-C Wei

    (University of California Berkeley
    University of British Columbia)

  • Feng Shao

    (Southwest University, School of Life Sciences)

  • Shuai Pang

    (Glbizzia Biosciences)

  • Adrian E. Platts

    (Michigan State University)

  • Jozefien Velde

    (Max Planck Institute for Plant Breeding Research)

  • Hong-Min Lin

    (Jiujiang University)

  • Scott J. Teresi

    (Michigan State University)

  • Kevin Bird

    (Michigan State University)

  • Chad E. Niederhuth

    (Michigan State University)

  • Jin-Gen Xu

    (Jiujiang Academy of Agricultural Sciences)

  • Guo-Hua Yu

    (Jiujiang University)

  • Jian-Yuan Yang

    (Jiujiang University)

  • Si-Fa Dai

    (Jiujiang University)

  • Andrew Nelson

    (Boyce Thompson Institute)

  • Ingo Braasch

    (Michigan State University)

  • Xiao-Gu Zhang

    (Jiujiang University)

  • Manfred Schartl

    (Texas State University
    University of Würzburg)

  • Patrick P. Edger

    (Michigan State University)

  • Min-Jin Han

    (Southwest University)

  • Hua-Hao Zhang

    (Jiujiang University)

Abstract

Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed ‘subgenome dominance’ remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations.

Suggested Citation

  • 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.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43740-y
    DOI: 10.1038/s41467-023-43740-y
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