Gene expression dynamics in Monilinia fructicola and Prunus persica during the battle for infection revealed by dual RNA-Seq analysis

Monilinia fructicola is the most destructive pathogen among Monilinia species, causing significant yield losses mostly on stone fruits. In this study, the infection dynamics on Prunus persica fruits was explored by dual RNA-Seq. A total of 1,003,651,968 next-generation sequencing reads (2 x 100 bp, Illumina technology) were generated from peach fruits, inoculated or not with the pathogen, at 0, 12 and 24 hours post-inoculation and mapped to the reference genomes of P. persica and M. fructicola. By comparing inoculated vs uninoculated samples at different sampling times, 1,996 differentially expressed genes (DEGs) of P. persica and 5,063 DEGs of M. fructicola were identified (FC ≥ |2|, FDR ≤ 0.05). Functional analysis of peach DEGs showed induction of defence responses, phytohormone signalling, glucosinolate and glutathione metabolism, cell wall macromolecule catabolism, and fungal polysaccharide degradation. Photosynthesis light reaction, starch/sucrose metabolism, and photorespiration were repressed. The mevalonate pathway related to sterol and terpenoid biosynthesis was activated, while the non-mevalonate pathway associated with photosynthetic isoprenoids was repressed. Defence-related genes identified included berberine bridge enzyme-like proteins, pathogenesis-related proteins, key genes for biosynthesis of antimicrobial compounds, hydrolytic enzymes, transcription factors, receptor-like and disease-resistance proteins. In M. fructicola, infection-induced toxin biosynthesis, peptidase activity, cell-wall degrading enzymes, monoxygenases, dioxygenases, and oxidoreductases were upregulated, while biosynthetic and mitosis-related processes were downregulated. Candidate effectors, cell-death elicitors, fungal-specific transcription factors, stress response proteins, and other putative virulence factors were identified. This study provides insights into molecular interactions between M. fructicola and P. persica, highlighting potential targets for brown rot control.