Unveiling eccDNA Dynamics in Rice: Insights into Adaptation to Nutritional Stress

Abstract

Extrachromosomal circular DNAs (eccDNAs) have been identified in various eukaryotic organisms and play a crucial role in genomic plasticity. However, in crop plants, the role of eccDNAs in responses to environmental cues, particularly nutritional stresses, remains unexplored. Rice (Oryza sativa ssp. japonica), a vital crop for more than half the world's population and an excellent plant model for genomic studies, faces numerous environmental challenges during growth. Therefore, we conducted comprehensive studies investigating the distribution, sequence information, and potential responses of rice eccDNAs to nutritional stresses. We described the landscape of rice eccDNAs during optimal growth phase change and identified the specific induction on gene-overlapped eccDNAs (ecGenes), Transposable Element-overlapped eccDNAs (ecTEs), and the full-length repeat units-overlapped eccDNAs (full-length ecRepeatUnits) in response to nitrogen (N) and phosphorus (P) deficiency. Furthermore, we analyzed multiple-fragment eccDNAs and proposed a TE-mediated homologous recombination mechanism as the origin of rice multiple-fragment eccDNAs. Our studies provide direct evidence of the role of eccDNAs in rice genome plasticity under nutritional stresses and highlight the significance of their abundance and specificity.