Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress
Abstract 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. Ri...
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| Language: | English |
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Nature Portfolio
2025-05-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-59572-x |
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| author | Hanfang Ni Lenin Yong-Villalobos Mian Gu Damar Lizbeth López-Arredondo Min Chen Liyan Geng Guohua Xu Luis Rafael Herrera-Estrella |
| author_facet | Hanfang Ni Lenin Yong-Villalobos Mian Gu Damar Lizbeth López-Arredondo Min Chen Liyan Geng Guohua Xu Luis Rafael Herrera-Estrella |
| author_sort | Hanfang Ni |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-fa8c7ff24a1b4a54a9bc72e20454d657 |
| institution | DOAJ |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-fa8c7ff24a1b4a54a9bc72e20454d6572025-08-20T02:55:35ZengNature PortfolioNature Communications2041-17232025-05-0116111810.1038/s41467-025-59572-xAdaptive dynamics of extrachromosomal circular DNA in rice under nutrient stressHanfang Ni0Lenin Yong-Villalobos1Mian Gu2Damar Lizbeth López-Arredondo3Min Chen4Liyan Geng5Guohua Xu6Luis Rafael Herrera-Estrella7National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural UniversityDepartment of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech UniversityNational Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural UniversityDepartment of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech UniversityNational Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural UniversityNational Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural UniversityNational Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural UniversityDepartment of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech UniversityAbstract 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.https://doi.org/10.1038/s41467-025-59572-x |
| spellingShingle | Hanfang Ni Lenin Yong-Villalobos Mian Gu Damar Lizbeth López-Arredondo Min Chen Liyan Geng Guohua Xu Luis Rafael Herrera-Estrella Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress Nature Communications |
| title | Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress |
| title_full | Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress |
| title_fullStr | Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress |
| title_full_unstemmed | Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress |
| title_short | Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress |
| title_sort | adaptive dynamics of extrachromosomal circular dna in rice under nutrient stress |
| url | https://doi.org/10.1038/s41467-025-59572-x |
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