Elucidating long non-coding RNA networks in tomato plants in response to Funneliformis mosseae colonization and cucumber mosaic virus infection
Abstract Tomato plants face biotic challenges like infections by cucumber mosaic virus (CMV), a member of the Cucumovirus genus in the Bromoviridae family, as well as beneficial interactions, such as colonization by the symbiotic fungus Funneliformis mosseae, which belongs to the Glomeraceae family....
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BMC
2025-04-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-025-06515-9 |
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| author | Narjes Maleki Abozar Ghorbani Mahsa Rostami Solomon Maina |
| author_facet | Narjes Maleki Abozar Ghorbani Mahsa Rostami Solomon Maina |
| author_sort | Narjes Maleki |
| collection | DOAJ |
| description | Abstract Tomato plants face biotic challenges like infections by cucumber mosaic virus (CMV), a member of the Cucumovirus genus in the Bromoviridae family, as well as beneficial interactions, such as colonization by the symbiotic fungus Funneliformis mosseae, which belongs to the Glomeraceae family. While this symbiosis boosts nutrient uptake and stress tolerance, viral infections can reduce yield and quality. Understanding how tomatoes manage these interactions is vital for enhancing crop productivity. To explore the molecular mechanisms behind these interactions, this study focuses on long non-coding RNAs (lncRNAs), which play crucial roles in gene regulation, stress response, and plant metabolic pathways. Tomato RNA-seq data were analyzed to identify lncRNAs and their interactions with microRNAs (miRNAs) through de novo assembly, mapping, expression analysis, and localization prediction. In this study, 3210 lncRNAs were identified from 12 SRA datasets of tomato plants, including control, CMV-infected, F. mosseae-colonized, and co-infected samples. Among these, 3194 were novel lncRNAs and 16 were conserved. Expression analysis revealed significant differential expression patterns across treatments. Pathway analysis indicated that these lncRNAs are involved in key metabolic processes, such as carbon metabolism, amino acid biosynthesis, and secondary metabolite production, suggesting their role in enhancing disease resistance. Furthermore, we predicted interactions between identified lncRNAs and miRNAs, including miR160a, miR166a/b, miR167a, miR171a/b/c, miR1917, miR1918, and miR395a/b, thereby highlighting potential regulatory networks that could modulate stress responses. The subcellular localization of identified lncRNAs revealed a predominance in the cytoplasm, implying their involvement in post-transcriptional regulation. This study accentuates the significance of lncRNAs in tomato plant defense mechanisms and provides a foundation for future research focused on enriching resistance to viral infections and boosting stress resilience. |
| format | Article |
| id | doaj-art-cdb8489425894d0b991a13fe06d8aa3d |
| institution | OA Journals |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-cdb8489425894d0b991a13fe06d8aa3d2025-08-20T02:30:22ZengBMCBMC Plant Biology1471-22292025-04-0125111510.1186/s12870-025-06515-9Elucidating long non-coding RNA networks in tomato plants in response to Funneliformis mosseae colonization and cucumber mosaic virus infectionNarjes Maleki0Abozar Ghorbani1Mahsa Rostami2Solomon Maina3Department of Plant Protection, Faculty of Agriculture, University of ZanjanNuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI)Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI)New South Wales Department of Primary Industries and Regional Development, Agriculture and BiosecurityBiosecurity and Food Safety, Elizabeth Macarthur Agricultural InstituteAbstract Tomato plants face biotic challenges like infections by cucumber mosaic virus (CMV), a member of the Cucumovirus genus in the Bromoviridae family, as well as beneficial interactions, such as colonization by the symbiotic fungus Funneliformis mosseae, which belongs to the Glomeraceae family. While this symbiosis boosts nutrient uptake and stress tolerance, viral infections can reduce yield and quality. Understanding how tomatoes manage these interactions is vital for enhancing crop productivity. To explore the molecular mechanisms behind these interactions, this study focuses on long non-coding RNAs (lncRNAs), which play crucial roles in gene regulation, stress response, and plant metabolic pathways. Tomato RNA-seq data were analyzed to identify lncRNAs and their interactions with microRNAs (miRNAs) through de novo assembly, mapping, expression analysis, and localization prediction. In this study, 3210 lncRNAs were identified from 12 SRA datasets of tomato plants, including control, CMV-infected, F. mosseae-colonized, and co-infected samples. Among these, 3194 were novel lncRNAs and 16 were conserved. Expression analysis revealed significant differential expression patterns across treatments. Pathway analysis indicated that these lncRNAs are involved in key metabolic processes, such as carbon metabolism, amino acid biosynthesis, and secondary metabolite production, suggesting their role in enhancing disease resistance. Furthermore, we predicted interactions between identified lncRNAs and miRNAs, including miR160a, miR166a/b, miR167a, miR171a/b/c, miR1917, miR1918, and miR395a/b, thereby highlighting potential regulatory networks that could modulate stress responses. The subcellular localization of identified lncRNAs revealed a predominance in the cytoplasm, implying their involvement in post-transcriptional regulation. This study accentuates the significance of lncRNAs in tomato plant defense mechanisms and provides a foundation for future research focused on enriching resistance to viral infections and boosting stress resilience.https://doi.org/10.1186/s12870-025-06515-9MiRNA interactionMycorrhizal colonizationNon-coding RNAsPlant virusStress responseCucumber mosaic virus |
| spellingShingle | Narjes Maleki Abozar Ghorbani Mahsa Rostami Solomon Maina Elucidating long non-coding RNA networks in tomato plants in response to Funneliformis mosseae colonization and cucumber mosaic virus infection BMC Plant Biology MiRNA interaction Mycorrhizal colonization Non-coding RNAs Plant virus Stress response Cucumber mosaic virus |
| title | Elucidating long non-coding RNA networks in tomato plants in response to Funneliformis mosseae colonization and cucumber mosaic virus infection |
| title_full | Elucidating long non-coding RNA networks in tomato plants in response to Funneliformis mosseae colonization and cucumber mosaic virus infection |
| title_fullStr | Elucidating long non-coding RNA networks in tomato plants in response to Funneliformis mosseae colonization and cucumber mosaic virus infection |
| title_full_unstemmed | Elucidating long non-coding RNA networks in tomato plants in response to Funneliformis mosseae colonization and cucumber mosaic virus infection |
| title_short | Elucidating long non-coding RNA networks in tomato plants in response to Funneliformis mosseae colonization and cucumber mosaic virus infection |
| title_sort | elucidating long non coding rna networks in tomato plants in response to funneliformis mosseae colonization and cucumber mosaic virus infection |
| topic | MiRNA interaction Mycorrhizal colonization Non-coding RNAs Plant virus Stress response Cucumber mosaic virus |
| url | https://doi.org/10.1186/s12870-025-06515-9 |
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