A Trichoderma microRNA-like RNA suppresses a chitinase gene in Solanum lycopersicum to escape host immunity during early root colonization

MicroRNAs play crucial roles in biological processes, but the function of microRNA-like RNAs (milRNAs) from Trichoderma remains elusive. In this study, we report that Tra-milR1 is transferred from Trichoderma to Solanum lycopersicum via extracellular vesicles (EVs). Tra-milR1 associates with Solanum lycopersicum Argonaute protein SlyAGO1 to suppress the expression of SlyChit4, a key immunity-related chitinase gene. Overexpression of Tra-milR1 in Trichoderma accelerated the colonization process. SlyChit4 loss of function enhanced susceptibility to Botrytis cinerea and facilitated Trichoderma colonization, while SlyChit4 overexpression had the reverse effect. Furthermore, recombinant SlyChit4 protein inhibited Trichoderma spore germination, blocked hyphal growth, and disrupted the fungal cell wall. Moreover, Tra-milR1 enabled Trichoderma DQ-1 to evade host immunity at the early stage of colonization (0 to 24 h post-inoculation [hpi]), while its elicitors stimulated the host plant's immunity at the late stage of colonization (24 to 96 hpi). These results highlight the mechanisms by which Trichoderma exerts precise temporal regulation of the immune response in tomato.