The Adaptational Dynamics of Extrachromosomal Circular DNA in Rice

The dynamic nature of the genome, exemplified by elements such as extrachromosomal circular DNA (eccDNA), plays a fundamental role in biodiversity and adaptation. However, our understanding of eccDNA in plants is still very limited. This study aims to bridge this gap by conducting a comprehensive investigation into eccDNA within the rice genome, a globally significant crop. We developed a reliable method and identified a total of 7532 highly confident eccDNAs from six tissues, revealing its formation as a universal, random event indicative of a shared mechanism across organisms. Importantly, we discovered a critical role for direct repeats in the genesis of eccDNA, unveiling a unique mechanism of eccDNA formation. Our results also demonstrated that the formation of eccDNA could result in minor chromosomal deletions, providing new insights into genome stability. Despite the significant presence of eccDNA in the coding sequences (CDS) of rice, its direct influence on gene expression appears to be limited, suggesting that the role of eccDNA might extend beyond the direct regulation of gene expression. Interestingly, we observed a tissue-specific proliferation of eccDNA in rice leaves, potentially associated with DNA damage induced by intense light exposure and radiation stress. In summary, our findings underscore the integral role of eccDNA in shaping the genomic landscape, thereby enhancing our understanding of genomic stability. These insights have broad implications for future advancements in rice cultivation and breeding strategies.