Comparative metabolomic profiling of the brown rot fungi Monilinia fructicola, Monilinia fructigena and Monilinia laxa

Brown rot, caused by Monilinia species, is a devastating disease of stone and pome fruits leading to yield losses in fruit orchards and even more in postharvest. This study investigated differences in the production of secondary metabolites among M. fructicola, M. fructigena, and M. laxa through genomic and metabolomic analyses. Genomic analysis using the antiSMASH prediction tool revealed varying numbers of biosynthetic gene clusters (BGCs) in the three species. Sixty-three orthologous BGCs were identified, with M. fructigena showing greater differences in the shared clusters. Nine clusters associated with siderophores, melanin, chloromonilinic acid, botcinic acid, solanapyrone, and retinal production were highlighted through annotation and literature review. Metabolomic analysis was conducted on five strains of each species to establish molecular fingerprints and identify differences in metabolomes. Two strains per each species were cultivated on various media to study BGC expression, linking metabolites with their corresponding gene clusters. Furthermore, M. fructicola was inoculated on nectarine fruits to explore secondary metabolite expression patterns during early stages of infection. Metabolomic analysis using UHPLC-MS/MS and bioinformatics tools (e.g. GNPS) identified several molecules associated with Monilinia species or other phytopathogenic fungi. Notable compounds included retinal, scytalone, solanapyrone, botcinic acid derivatives, and chloromonilinic acid, in line with the identified BGCs. Differences were observed in the presence of selected molecules among the three Monilinia species, with M. fructigena exhibiting the most significant variations. This research enhances our understanding of brown rot and provides knowledge on metabolites in Monilinia spp. and new potential targets to define effective disease management strategies. This study was carried out within the Agritech National Research Center and received funding from the European Union Next-GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) – MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 – D.D. 1032 17/06/2022, CN00000022). This manuscript reflects only the authors’ views and opinions, neither the European Union nor the European Commission can be considered responsible for them.