Profiling of extracellular vesicle-associated microRNAs reveals a regulated response to potato virus Y infection in tomato

Plant extracellular vesicles (EVs) serve as critical mediators of intercellular communication during plant-pathogen interactions, particularly through their cargo of regulatory small RNAs, enabling the transport of miRNAs to distant tissues during biotic stress. Potato virus Y (PVY), one of the most economically damaging plant viruses globally, poses significant threats to solanaceous crop production. However, the landscape of EV-associated miRNAs and their regulatory roles in PVY infection remain largely unexplored. In this study, we isolated and characterized EV-associated particles from the apoplastic fluid of both PVY-infected and healthy tomato leaves using differential ultracentrifugation, followed by transmission electron microscopy, nanoparticle size analysis, and western blotting. High-throughput small RNA sequencing revealed 96 significantly differentially expressed miRNAs in EV-associated particles upon viral challenge. Bioinformatic prediction revealed that 80% of these dysregulated miRNAs potentially target multiple genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses demonstrated significant overrepresentation of predicted target genes in pathways associated with transcription, ta-siRNA biogenesis involved in RNA interference, protein binding, RNAi-mediated antiviral immune response, oxidative phosphorylation, mRNA surveillance pathway, and eukaryotic ribosome biogenesis. Our findings demonstrate that PVY infection selectively modulates the miRNA composition within tomato EV-associated particles. These EV-associated particles delivered miRNAs may contribute to a sophisticated antiviral defense mechanism by co-regulating host immunity. This study provides novel insights into the role of EV-associated particles mediated RNA communication in plant immunity and lays a theoretical foundation for developing innovative miRNA- and EV-based antiviral strategies for crop protection.