Small RNAs at the heart of the molecular tug-of-war between a plant and its fungal pathogen

A study published in Plant Direct, explores how small RNAs (sRNAs) shape the battle between the plant Arabidopsis thaliana and the fungal pathogen Colletotrichum higginsianum. The work formed part of the international ERA-CAPS project ‘Exosomes’, involving collaboration between scientists at the BIOGER unit and the University of California Davis, USA.

By sequencing sRNAs from both organisms across three different infection stages, namely appressoria on the plant surface and the biotrophic and necrotrophic phases, the researchers reveal how sRNA populations shift during host invasion.

Early in the infection, when host cells are still alive, the fungus produces abundant 29‑nt sRNAs, while the plant counters with a diverse set of sRNAs, including regulatory miRNAs with known roles in plant immunity and development. Several miRNAs, such as miR396, miR170_171, miR472, and miR858b, show stage‑specific changes, suggesting the plant rewires its gene regulation as infection advances.

During the necrotrophic phase, when the fungus extensively kills host cells, the sRNA landscape shifts dramatically. Fungal sRNAs decrease in size to a dominant 18‑nt population, consistent with enhanced RNA turnover and degradation, while the plant’s sRNAs shift towards a dominant 21‑nt population and its overall regulatory capacity weakens. Whereas fungal tRNA‑derived fragments (tRFs) decline, host tRFs increase, suggesting differences in RNA‑processing between host and pathogen during necrotrophy.

Overall, the work shows that infection is a molecular tug‑of‑war driven by rapidly changing sRNA populations. By mapping these dynamics, the study highlights RNA turnover and sRNA‑based regulation as key forces in plant-fungal interactions, with potential relevance for RNA‑guided disease resistance in crop plants.

Contact:  richard.oconnell@inrae.fr

Reference: CE Armijos, TTH Chu, RJ O’Connell, BC Meyers, P Baldrich (2026) Stage-Specific RNA Turnover Drives Small RNA Dynamics in Arabidopsis-Colletotrichum Interactions. Plant Direct; 10:e70172 https://doi.org/10.1002/pld3.70172