Fungal small RNA: unveiling the breakthroughs and promising applications

Small RNAs (sRNAs) are abundant endogenous non-coding RNAs in eukaryotic organisms that regulate gene expression by binding to their target mRNAs either completely or partially. The rapid advancements in fungal sRNA research in recent years have significantly expanded our understanding of their biogenesis, functional mechanisms, and roles in fungal biology. Unlike previous reviews that predominantly focus on the intracellular biogenesis and regulatory networks of fungal sRNAs within fungal cells, this review uniquely bridges fungal sRNA molecular biology with plant pathology by centering on the bidirectional cross-kingdom RNAi trafficking between fungi and plants. We provide a comprehensive overview of fungal sRNA types, especially novel subtypes identified in recent studies, the key protein factors involved in their biogenesis, and the molecular mechanisms governing their intracellular functions. Additionally, we conduct an in-depth analysis of the trafficking routes of fungal sRNAs into host plants, their targeted interference with plant immune signaling cascades, and the reciprocal regulation of fungal physiology by plant-derived sRNAs. Finally, we discussed the potential applications of fungal sRNAs in biotechnology and pathogen control, particularly in the development of host-induced gene silencing (HIGS)/spray-induced gene silencing (SIGS)-based crop protection strategies. This work not only serves as a valuable reference for future studies on fungal sRNAs but also highlights the translational potential of cross-kingdom RNAi in plant–fungal pathosystems, filling critical gaps in existing literature.