Omics approaches for characterization of the brown rot fungal pathogens Monilinia fructicola, Monilinia laxa and Monilinia fructigena.

Monilinia fructicola, Monilinia fructigena and Monilinia laxa are the main causal agents of blossom blight and brown rot, among the most important diseases on pome and stone fruits, responsible for heavy losses both in the field and in postharvest. Following the introduction of M. fructicola into Europe, the pathogen spread widely and rapidly and became prevalent over the native species M. laxa and M. fructigena. Multi-omics approaches were used to improve knowledge on biology, evolutionary history, and diversity of these important pathogens. High-quality reference genomes and transcriptomes of M. fructicola strain Mfrc123, M. fructigena strain Mfrg269 and M. laxa strain Mlax316 were de novo assembled and compared. The study was focused on several key areas: (i) phylogenomic and synthenic relationships between the Monilinia genomes and those of the closely related species Botrytis cinerea and Sclerotinia sclerotiorum; (ii) the abundance and evolutionary dynamics of transposable elements (TEs); (iii) the genetic basis of mating type and the genome-wide occurrence and extent of Repeat-Induced Point (RIP) mutations; (iv) the identification of common and species-specific effectors, carbohydrate-active enzymes (CAZymes) and secondary metabolite gene clusters (BGCs); and v) gene expression profiling under different cultural conditions. The results highlighted several differences that might explain host plants and organ preferences distinguishing the three Monilinia species. A metabolomic analysis was conducted on multiple strains of each species to establish molecular fingerprints and identify differences in metabolomes. Moreover, a shotgun metagenomic analysis was used to investigate the mycovirome of M. fructicola in a worldwide collection of isolates from different hosts and revealed a great abundance and diversity of mycoviruses infecting the fungus. A total of 32 +ssRNA viruses including a novel beny-like virus, the first one identified in Ascomycetes, and a new putative ssDNA mycovirus were identified and characterized.