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.

Cercospora beticola, the causal agent of Cercospora leaf spot (CLS), is a major pathogen affecting beet (Beta vulgaris) worldwide. Rapid and accurate detection is critical for effective disease control. This study validated a diagnostic framework combining portable quantitative PCR (qPCR) and laboratory-based digital droplet PCR (ddPCR) assays to detect and quantify C. beticola in leaves, seeds, and soil-associated crop residues. We used two portable qPCR systems (Biomeme Franklin^® Three9 and Hyris bCUBE^™) for in-field diagnostics, and ddPCR (Bio-Rad Laboratories) for laboratory analysis. Two rapid DNA extraction protocols, the Sigma-Aldrich REDExtract-N-Amp Plant PCR Kit (brief incubation at 95 °C) and the BN QuickPick Plant DNA Kit (magnetic-bead-based), were evaluated. The optimized portable qPCR assays achieved detection limits of 1 pg μL⁻¹, PCR efficiencies of 96–102%, and R² > 0.98. The ddPCR assay enabled accurate and absolute quantification even at low target concentrations and was resilient to common PCR inhibitors. Both methods proved robust in complex environmental matrices, with a detection threshold of 1% in infected residue soil. The framework’s sensitivity, specificity, and portability support timely on-site CLS diagnosis and informed management. This integrated approach advances portable molecular diagnostics and provides a platform for future field-ready disease surveillance and sustainable crop protection.