Ni Hanfang, Yong-Villalobos Lenin, Gu Mian, López-Arredondo Damar Lizbeth, Chen Min, Geng Liyan, Xu Guohua, Herrera-Estrella Luis Rafael
National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China.
MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China.
Nat Commun. 2025 May 4;16(1):4150. doi: 10.1038/s41467-025-59572-x.
Extrachromosomal circular DNAs (eccDNAs) have been identified in various eukaryotic organisms and are known to play crucial roles 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 over half the world's population and an excellent model plant for genomic studies, faces numerous environmental challenges during growth. Therefore, we conduct comprehensive studies investigating the distribution, sequence, and potential responses of rice eccDNAs to nutritional stresses. We describe the changes in the eccDNA landscape at various developmental stages of rice in optimal growth. We also identify eccDNAs overlapping with genes (ecGenes), transposable elements (ecTEs), and full-length repeat units (full-length ecRepeatUnits), whose prevalence responds to nitrogen (N) and phosphorus (P) deficiency. We analyze multiple-fragment eccDNAs and propose a potential TE-mediated homologous recombination mechanism as the origin of rice's multiple-fragment eccDNAs. We provide evidence for the role of eccDNAs in the rice genome plasticity under nutritional stresses and underscore the significance of their abundance and specificity.
染色体外环状DNA（eccDNA）已在多种真核生物中被鉴定出来，并且已知其在基因组可塑性中发挥关键作用。然而，在农作物中，eccDNA在应对环境线索，特别是营养胁迫方面的作用仍未得到探索。水稻（Oryza sativa ssp. japonica）是全球一半以上人口的重要粮食作物，也是基因组研究的优秀模式植物，在生长过程中面临众多环境挑战。因此，我们开展了全面研究，调查水稻eccDNA对营养胁迫的分布、序列及潜在反应。我们描述了水稻在最佳生长状态下不同发育阶段eccDNA图谱的变化。我们还鉴定出与基因（ecGenes）、转座元件（ecTEs）和全长重复单元（全长ecRepeatUnits）重叠的eccDNA，其丰度对氮（N）和磷（P）缺乏有反应。我们分析了多片段eccDNA，并提出了一种潜在的转座元件介导的同源重组机制作为水稻多片段eccDNA的起源。我们为营养胁迫下eccDNA在水稻基因组可塑性中的作用提供了证据，并强调了其丰度和特异性的重要性。
