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Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry

Author

Listed:
  • Chao Fang

    (Michigan State University)

  • Ning Jiang

    (Michigan State University
    Michigan State University AgBioResearch
    Michigan State University)

  • Scott J. Teresi

    (Michigan State University
    Michigan State University)

  • Adrian E. Platts

    (Michigan State University)

  • Gaurav Agarwal

    (Michigan State University)

  • Chad Niederhuth

    (Michigan State University
    Michigan State University AgBioResearch)

  • Patrick P. Edger

    (Michigan State University
    Michigan State University AgBioResearch
    Michigan State University)

  • Jiming Jiang

    (Michigan State University
    Michigan State University
    Michigan State University AgBioResearch)

Abstract

Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.

Suggested Citation

  • Chao Fang & Ning Jiang & Scott J. Teresi & Adrian E. Platts & Gaurav Agarwal & Chad Niederhuth & Patrick P. Edger & Jiming Jiang, 2024. "Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46861-0
    DOI: 10.1038/s41467-024-46861-0
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    1. Yuyun Zhang & Zijuan Li & Jinyi Liu & Yu’e Zhang & Luhuan Ye & Yuan Peng & Haoyu Wang & Huishan Diao & Yu Ma & Meiyue Wang & Yilin Xie & Tengfei Tang & Yili Zhuang & Wan Teng & Yiping Tong & Wenli Zha, 2022. "Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Yuannian Jiao & Norman J. Wickett & Saravanaraj Ayyampalayam & André S. Chanderbali & Lena Landherr & Paula E. Ralph & Lynn P. Tomsho & Yi Hu & Haiying Liang & Pamela S. Soltis & Douglas E. Soltis & S, 2011. "Ancestral polyploidy in seed plants and angiosperms," Nature, Nature, vol. 473(7345), pages 97-100, May.
    3. Weifeng Xu & Qian Zhang & Wei Yuan & Feiyun Xu & Mehtab Muhammad Aslam & Rui Miao & Ying Li & Qianwen Wang & Xing Li & Xin Zhang & Kang Zhang & Tianyu Xia & Feng Cheng, 2020. "The genome evolution and low-phosphorus adaptation in white lupin," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    4. Adam M. Session & Daniel S. Rokhsar, 2023. "Transposon signatures of allopolyploid genome evolution," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
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