New genetic resources for the causal agents of brown rot on stone fruits, Monilinia fructicola, Monilinia laxa and Monilinia fructigena.

Monilinia fructicola (MFRC), Monilinia laxa (MLAX) and Monilinia fructigena (MFRG) are the most important pathogens causing the brown rot disease of stone and pome fruits. The sources of genetic variation as well as genomic and transcriptomic data remain largely unexplored for the three fungal species. The molecular characterization of the MAT1 loci showed that MFRC, MLAX and MFRG have a bipolar heterothallic mating system, typical of other self-sterile Ascomycetes. Single isolates carry only one of two alternative idiomorphs, each containing a specific couple of genes (MAT1-1-1 and MAT1-1-5 in MAT1-1; MAT1-2-1 and MAT1-2-10 in MAT1-2). The populations of the three Monilinia species show a balanced distribution of mating types indicating a potential outcrossing in all the geographic areas in which the pathogens are present. ISSR markers suggested that asexual reproduction is prevalent, but that sexual recombination occurs in MFRC populations in Italy. The comple transcriptomes of MFRC, MLAX and MFRG was de novo assembled from Illumina sequence reads (about 70 million per species) and deposited in public database (https://www.ncbi.nlm.nih.gov/Traces/wgs; accessions GGAK00000000, GGAL00000000 and GGAM00000000). Comparative analyses among orthologous transcripts revealed transcripts over-expressed (FC≥8 and FDR≤0.05) or unique in MFRC (65), MLAX (30) or MFRG (31) that are involved in important biological and physiological processes, such as morphogenesis and development, pathogenesis, biosynthesis of secondary metabolites and detoxification systems. The obtained results will be useful to clarify aspects of their biology and physiology, including adaptability to different environmental conditions and plant-pathogen interactions, which can be of help for improving the disease management.