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Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants

Author

Listed:
  • Panpan Zhang

    (Laboratory of Plant Genome and Development
    Laboratory of Plant Genome and Development
    University of Montpellier)

  • Assane Mbodj

    (Laboratory of Plant Genome and Development
    Laboratory of Plant Genome and Development)

  • Abirami Soundiramourtty

    (Laboratory of Plant Genome and Development
    University of Perpignan)

  • Christel Llauro

    (Laboratory of Plant Genome and Development
    Laboratory of Plant Genome and Development)

  • Alain Ghesquière

    (CIRAD)

  • Mathieu Ingouff

    (CIRAD)

  • R. Keith Slotkin

    (Donald Danforth Plant Science Center
    University of Missouri)

  • Frédéric Pontvianne

    (Laboratory of Plant Genome and Development)

  • Marco Catoni

    (University of Birmingham)

  • Marie Mirouze

    (Laboratory of Plant Genome and Development
    Laboratory of Plant Genome and Development)

Abstract

Abundant extrachromosomal circular DNA (eccDNA) is associated with transposable element (TE) activity. However, how the eccDNA compartment is controlled by epigenetic regulations and what is its impact on the genome is understudied. Here, using long reads, we sequence both the eccDNA compartment and the genome of Arabidopsis thaliana mutant plants affected in DNA methylation and post-transcriptional gene silencing. We detect a high load of TE-derived eccDNA with truncated and chimeric forms. On the genomic side, on top of truncated and full length TE neo-insertions, we detect complex structural variations (SVs) notably at a disease resistance cluster being a natural hotspot of SV. Finally, we serendipitously identify large tandem duplications in hypomethylated plants, suggesting that SVs could have been overlooked in epigenetic mutants. We propose that a high eccDNA load may alter DNA repair pathways leading to genome instability and the accumulation of SVs, at least in plants.

Suggested Citation

  • Panpan Zhang & Assane Mbodj & Abirami Soundiramourtty & Christel Llauro & Alain Ghesquière & Mathieu Ingouff & R. Keith Slotkin & Frédéric Pontvianne & Marco Catoni & Marie Mirouze, 2023. "Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41023-0
    DOI: 10.1038/s41467-023-41023-0
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    References listed on IDEAS

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    1. Jundong Zhuang & Yaoxin Zhang & Congcong Zhou & Danlin Fan & Tao Huang & Qi Feng & Yiqi Lu & Yan Zhao & Qiang Zhao & Bin Han & Tingting Lu, 2024. "Dynamics of extrachromosomal circular DNA in rice," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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