Using Nanopore direct RNA sequencing, the study generated the first transcriptome-wide m5C methylome of tomato fruits under pathogen attack. The results showed that infection did not broadly change the overall level or regional pattern of m5C modification, but instead triggered highly specific changes at individual RNA sites. These changes were closely linked to altered expression of ethylene signaling and defense-related genes, suggesting that RNA epigenetic regulation may help coordinate tomato fruit resistance.
RNA modifications are increasingly recognized as important regulators of plant growth, development, stress responses, and gene expression. Among them, m5C modification has been studied in relation to root development, heat stress, oxidative stress, and RNA metabolism, but its role in plant responses to biotic stress remains poorly understood. Tomato is a major horticultural crop, yet postharvest fungal disease causes serious losses during production, transport, and storage. B. cinerea is especially destructive because it causes rapid fruit decay and gray mold, reducing both market value and shelf life. Although tomato defense involves transcription factors, hormone signaling, protein kinases, and other regulatory layers, how m5C RNA methylation contributes to this defense remains unclear.
A study (DOI:10.48130/ph-0026-0010) published in Plant Hormones on 14 May 2026 by Ying Gao’s & Leilei Zhou’s team, Chongqing University, reports that pathogen infection reshapes specific m5C sites in tomato fruit transcripts and may regulate defense by coordinating ethylene signaling and stress-response gene expression.
To investigate this RNA-level defense mechanism, the researchers inoculated mature green ‘Micro-Tom’ tomato fruits with B. cinerea and collected pericarp tissues 48 hours after infection. Mock-inoculated fruits served as controls. Total RNA was extracted from three independent biological replicates for each group, enriched for messenger RNA, and analyzed using Nanopore direct RNA sequencing, a technology that can read full-length RNA molecules and detect RNA modifications directly from electrical current signals. The sequencing data were aligned to the tomato reference genome, and high-confidence m5C sites were identified and compared between infected and control fruits. The analysis showed that m5C sites were mainly distributed in coding sequences (CDSs) and 3′ untranslated regions (3′ UTRs), while only a smaller fraction appeared in 5′ untranslated regions (5′ UTRs). This distribution pattern remained broadly stable after B. cinerea infection, indicating that the pathogen did not reshape the global architecture of m5C modification. However, the infection induced strong site-specific changes: 354 m5C sites were significantly upregulated and 341 were significantly downregulated, distributed across hundreds of gene transcripts. Most affected transcripts carried only one altered m5C site, suggesting localized regulation rather than transcript-wide modification shifts. By integrating m5C methylation profiles with transcript abundance data, the team found a generally negative relationship between m5C modification and gene expression. Transcripts with reduced m5C levels tended to show increased expression, while transcripts with elevated m5C levels were more often downregulated. Notably, several ethylene signaling genes, protein kinase genes, redox-related genes, and toxin-resistance genes showed coordinated decreases in m5C modification and increases in transcript levels. These genes are associated with hormone-mediated defense, pathogen signal transduction, reactive oxygen species regulation, and detoxification. The study also identified transcriptional changes in putative m5C regulators, including downregulation of the demethylase gene SlALKBH1 and upregulation of the reader protein gene SlALY4, pointing to possible components of the tomato m5C response system.
Overall, the study highlights m5C RNA methylation as a previously underexplored regulatory layer in tomato fruit defense against gray mold. Rather than acting through broad methylation changes, m5C appears to fine-tune selected transcripts involved in hormone signaling and defense activation. The work expands understanding of plant–pathogen interactions from the perspective of RNA epigenetics and lays a foundation for future research on how RNA modifications influence postharvest resistance. Further functional validation of key m5C-modified genes and m5C regulatory proteins could help identify new strategies for reducing fungal decay and extending the storage life of tomato fruits.
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References
DOI
10.48130/ph-0026-0010
Original Source URL
https://doi.org/10.48130/ph-0026-0010
Funding Information
This work was supported by the Fundamental Research Funds for the Central Universities of Chongqing University (Grant No. 2025CDJ-IAISYB-065) and the National Natural Science Foundation of China (Grant No. 32472403).
About Plant Hormones
Plant Hormones (e-ISSN 3067-221X) is an open access, online-only, academic journal publishing rigorously peer-reviewed original articles, reviews, break-through methods, editorials, and perspectives on broad aspects of plant hormone biosynthesis, signal transduction, and crosstalk. The journal primarily publishes fundamental research that represents significant advances or new insight into specialized areas of plant hormones, and review articles that provide comprehensive and critical review of current research areas and offer directions or perspectives for future research. The journal publishes applied research that has significant implications for the development of agriculture, horticulture, and forestry. Plant Hormones also provides a community forum by publishing editorials and perspective papers for expressing opinions on specific issues or new perspectives about existing research on particular topics. Plant Hormones is hosted by Chongqing University, and published by Maximum Academic Press.