Jundong Zhuang

Shanghai Jiao Tong University

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Qi Feng

Chinese Academy of Sciences

Yan Zhao

Chinese Academy of Sciences

Tingting Lu

Guangxi University

Yiqi Lu

Chinese Academy of Sciences

Qiang Zhao

Chinese Academy of Sciences

Yaoxin Zhang

Center for Excellence in Molecular Plant Sciences

Congcong Zhou

Chinese Academy of Sciences

Danlin Fan

Center for Excellence in Molecular Plant Sciences

Bin Han

Shanxi Agricultural University

Tao Huang

Center for Excellence in Molecular Plant Sciences

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Chinese Academy of Sciences

National Center for Gene Research

Center for Excellence in Molecular Plant Sciences

Shanghai Institutes for Biological Sciences

Pyongyang University of Science and Technology

University of Lausanne

Central South University

University of Chinese Academy of Sciences

State Key Laboratory of Plant Genomics

Kim Il-sung University

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Dynamics of extrachromosomal circular DNA in rice

Nature Communications (2024)

Jundong Zhuang Yaoxin Zhang Congcong Zhou Danlin Fan Tao Huang

Abstract The genome’s dynamic nature, exemplified by elements like extrachromosomal circular DNA (eccDNA), is crucial for biodiversity and adaptation. Yet, the role of eccDNA in plants, particularly rice, remains underexplored. Here, we identify 25,598 eccDNAs, unveiling the widespread presence of eccDNA across six rice tissues and revealing its formation as a universal and random process. Interestingly, we discover that direct repeats play a pivotal role in eccDNA formation, pointing to a unique origin mechanism. Despite eccDNA’s prevalence in coding sequences, its impact on gene expression is minimal, implying its roles beyond gene regulation. We also observe the association between eccDNA’s formation and minor chromosomal deletions, providing insights of its possible function in regulating genome stability. Further, we discover eccDNA specifically accumulated in rice leaves, which may be associated with DNA damage caused by environmental stressors like intense light. In summary, our research advances understanding of eccDNA’s role in the genomic architecture and offers valuable insights for rice cultivation and breeding.

Extrachromosomal DNA

10.1038/s41467-024-46691-0

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