Emergence of Neonectria ditissima in the Mid-Atlantic: Phylogenetics, Pathogenicity, Genomic Resources and Secondary Metabolite Gene Cluster Analysis

European canker, caused by the fungus Neonectria ditissima, represents one of the most destructive diseases threatening apple production across the globe. Our study documents the first confirmed case of N. ditissima causing European canker on apple in Virginia, confirming its emergence in a key apple-producing region of the Mid-Atlantic. To characterize these emergent isolates, we performed comprehensive pathogenicity assays on apple shoots and fruit and generated high-quality genomic resources for two virulent isolates using third-generation sequencing and RNA-seq-based annotation. Pathogenicity tests confirmed the ability of the isolates to cause canker and fruit rot, with virulence varying among strains. The genome assemblies we produced set a new standard for this species, achieving remarkable contiguity with N50 values exceeding 1.7 Mb. Mining these genomes for secondary metabolic biosynthetic gene clusters (BGCs) revealed that these isolates possess a large and diverse chemical arsenal, containing 47 to 48 BGCs. Critically, over 68% of these clusters appear to be novel. The characterized BGCs represent both intact and partial clusters, which have the potential to produce a wide range of bioactive compounds, including known mycotoxins (e.g., ACR toxin, ilicicolin), plant hormones (gibberellin), and other metabolites not previously associated with this pathogen, such as destruxin and swainsonine. These high-quality genomic resources and the discovery of uncharacterized secondary metabolites provide a critical foundation for future research into the virulence mechanisms of N. ditissima and the development of effective disease management strategies.