Nanopore direct RNA sequencing reveals the m5C methylomes of tomato fruits in response to Botrytis cinerea

Résumé fourni par la source

RNA methylation, particularly 5-methylcytosine (m5C) modification, has emerged as a pivotal regulatory layer governing plant development and stress responses. However, the role of m5C in mediating the resistance of tomato (Solanum lycopersicum) fruit to the fungal pathogen Botrytis cinerea remains unclear. In this study, we utilized Nanopore direct RNA sequencing to generate the transcriptome-wide m5C methylomes in B. cinerea-infected tomato fruits. Our results revealed that m5C sites are preferentially enriched in coding sequences (CDSs) and 3' untranslated regions (3' UTRs). Notably, B. cinerea infection induced site-specific m5C changes without altering the global modification level. Integrated omics analysis identified a transcriptome-wide negative correlation between m5C modification and gene expression. Importantly, a large number of ethylene signaling pathway and defense-related genes exhibited reduced m5C levels, accompanied by significantly increased transcript abundance, implying that m5C may act as a novel regulator of fruit's resistance to B. cinerea by coordinating hormone signaling and defense response pathways. Furthermore, the putative m5C demethylase gene SlALKBH1 and the reader protein gene SlALY4 were transcriptionally downregulated and upregulated by B. cinerea infection, respectively. Collectively, this study establishes the first comprehensive m5C methylomes of tomato fruits upon B. cinerea infection and provides new insights into RNA-based epigenetic regulation of hormone signaling during plant–pathogen interactions.

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