Gaining a better understanding of Colletotrichum species associated with apple diseases in Italy through integrated omic approach

Apple Bitter Rot (ABR) and Glomerella Leaf Spot (GLS), caused by Colletotrichum species, represent an emerging threat to apple production in Northern Italy and globally. In recent years, the incidence of these diseases has increased, and previous studies have reported the emergence of Colletotrichum species that were previously absent or only rarely detected in Europe, particularly members of the Gloeosporioides and Orchidearum species complexes. Although the species diversity of Colletotrichum associated with apple in Italy has been described, our understanding of their pathogenicity boundaries, molecular mechanisms, and population dynamics remains limited. This study aims to gain deeper insight into these mechanisms by integrating comparative genomics, transcriptomics, and population genetics. To clarify the boundaries of pathogenicity within major Colletotrichum lineages and across specific apple tissues, we developed a novel inoculation protocol. Preliminary results have revealed notable correlations between genetic background and pathogenic behaviour, shedding light on the mechanisms of host penetration. Several genomes, including those of C. chrysophilum and related species such as C. fructicola and C. nupharicola, have been sequenced using a combination of Oxford Nanopore and Illumina technologies. This genomic dataset forms the foundation for comprehensive comparative genomics and transcriptomic analyses aimed at identifying and characterizing pathogenicity-related genes and their expression dynamics during infection.