Genomic Insights into the Emergence of Colletotrichum chrysophilum: the Major Causal Agent of Apple Bitter Rot and Glomerella Leaf Spot

Apple Bitter Rot (ABR) and Glomerella Leaf Spot (GLS), caused by fungi of the Colletotrichum genus, represent an increasing threat to apple production in Europe and worldwide. Recent outbreaks have revealed a more complex Colletotrichum community than previously recognized, with species belonging to the Acutatum, Gloeosporioides, and Orchidearum complexes, including C. fioriniae, C. siamense, C. grossum, C. chrysophilum, and C. sojae. In Europe, the population structure closely mirrors global patterns and is dominated by C. chrysophilum, which represents about 60% of isolates and is commonly reported from both North and South America. This species has recently emerged as a relevant pathogen in Mediterranean orchards, raising questions about its introduction routes, ecological plasticity, and capacity for rapid host adaptation. Despite improved species delimitation, major gaps remain concerning the pathogenicity range, infection mechanisms, and population dynamics of Colletotrichum species affecting apple. Here, we highlight the need for an international collaborative framework to coordinate sampling, genome sequencing, and population genomics analyses of apple-associated Colletotrichum. Such efforts would enable comparative studies across continents and the development of shared genomic resources. Our work aims to integrate comparative genomics and population genetics to identify genomic determinants of virulence, trace introduction pathways, and uncover signals of host specialization in C. chrysophilum and related species.