Gene Expression Dynamics in Monilinia fructicola and Prunus persica During the Battle for Infection Revealed by Dual RNA-Seq Analysis

Abstract

Brown rot, caused by Monilinia fructicola, poses a significant threat to global peach production, but the molecular interactions underlying host defence and pathogen colonisation remain incompletely defined. In this study, we used dual RNA-Seq to simultaneously capture the gene expression profiles of Prunus persica and M. fructicola during early infection (12 and 24 h post-inoculation). High-depth sequencing enabled a detailed analysis of transcriptional dynamics in both organisms. P. persica displayed a delayed yet robust defence response with marked activation of immune signalling, oxidative burst, cell wall fortification, hormone signalling, and secondary metabolism at 24 hpi. M. fructicola initiated infection rapidly, first expressing cell wall-degrading enzymes, then upregulating protein synthesis, energy metabolism, effector proteins, phytotoxins, and stress adaptation genes. Integrated analysis revealed a tightly coordinated interplay between fungal virulence strategies and peach defence mechanisms, including cell wall modification and immune responses. These findings provide a comprehensive framework for host–pathogen dynamics, offering actionable insights for developing resistant peach cultivars for field cultivation and for targeted strategies to improve post-harvest disease management and fruit shelf-life.