P-311 - Cross-kingdom RNA interference to control F. graminearum — Discovery and Application of Brachypodium-derived sRNAs via improved PARE and new computational Methods

Cross-kingdom RNA interference (ckRNAi) is a widespread phenomenon in which organisms from different clades exchange silencing signals. In plant-microbe-interactions the exchanged signal often has an antagonistic effect on the receiving organism. By utilizing naturally evolved small regulatory RNAs (sRNAs) robust, specific and highly effective crop protection can be achieved. Plant-derived ckRNAi-capable sRNAs can serve as a blueprint. To discover such sRNAs in the interaction of the monocot model plant Brachypodium distachyon (Bd) and the notorious pathogen Fusarium graminearum (Fg) a deep RNA-degradome (PARE), sRNAome and transcriptome sequencing was conducted. This data was analysed via a newly developed ckRNAi analysis pipeline. By simulating random degradome profiles for different sRNA classes – based on length and 5’-terminal nucleotides – and contrasting these with real world observations, robust statistical evidence for ckRNAi was generated. Highly stringent selection criteria identified 43 Bd-derived sRNAs that target fundamental conserved metabolic processes in Fg and are organized in several long non-coding RNA (lncRNA) genes. sRNAome data shows phasing in these lncRNAs indicating tasiRNA-like biogenesis. Spray-application of one of these sRNAs protects Bd against Fg with an exceptionally high effectivity. Additionally, while targeting a highly conserved region in a ubiquitous gene, this sRNA is predicted to target fungi exclusively.