Dual RNA-Seq analysis reveals the molecular dialogue between Monilinia fructicola and Prunus persica

Monilinia fructicola is the most aggressive pathogen among Monilinia species, causing heavy yield losses, particularly in stone fruits. A dual RNA-Seq approach was applied to investigate the infection dynamics in Prunus persica fruits, demonstrating its effectiveness in capturing a comprehensive molecular snapshot of host-pathogen interaction. A total of 1,003,651,968 next-generation sequencing reads (2 × 100 bp, Illumina technology) were generated from peach fruits, both inoculated and uninoculated, at 0, 12, and 24 hours post-inoculation. Row reads were mapped to the reference genomes of P. persica and M. fructicola, enabling a detailed comparative analysis that identified 1,996 differentially expressed genes (DEGs) in P. persica and 5,063 in M. fructicola (FC ≥ |2|, FDR ≤ 0.05). Functional analysis of peach DEGs revealed a strong activation of defence responses, including phytohormone signalling, glucosinolate and glutathione metabolism, fungal polysaccharide degradation, and cell wall macromolecule catabolism. In contrast, photosynthesis-related processes, such as light reactions, starch/sucrose metabolism, and photorespiration, were repressed. Notably, the mevalonate pathway, associated with sterol and terpenoid biosynthesis, was induced, while the non-mevalonate pathway, linked to photosynthetic isoprenoids, was repressed. Defence-related genes included berberine bridge enzyme-like proteins, pathogenesis-related proteins, antimicrobial biosynthetic genes, hydrolytic enzymes, transcription factors, receptor-like proteins, and disease-resistance proteins. In M. fructicola, the infection process promoted toxin biosynthesis, peptidase activity, cell wall-degrading enzymes, monooxygenases, dioxygenases, and oxidoreductases, while biosynthesis-related and mitotic processes were downregulated. The identification of candidate effectors, cell-death elicitors, fungal-specific transcription factors, and stress response proteins further highlighted key virulence strategies. This study not only provides new insights into the molecular interactions between M. fructicola and P. persica, shedding light on key processes involved in the infection process and potential targets for disease control strategies, but also highlights the power of dual RNA-Seq as a robust tool for obtaining a comprehensive view of molecular mechanisms in plant-pathogen interaction.