High-Quality Genomic and Phylogenetic Resources for <i>Neonectria ditissima</i> Isolates Obtained from Virginia Apple Orchards

European canker, caused by Neonectria ditissima, is a destructive disease of apple in cool and humid regions worldwide, yet its presence has not been previously documented in Virginia. The objectives of this study were to confirm the causal agent, assess pathogenicity on apple twigs and fruit, and generate high-quality genomic resources to support future investigations of this emerging pathogen in the Mid-Atlantic region. Isolates obtained from cankered branches were identified as N. ditissima based on morphology and multilocus phylogenetic analysis. Pathogenicity tests on apple twigs and fruit reproduced characteristic canker lesions and fruit rot, respectively, fulfilling Koch’s postulates. Two representative isolates were selected for de novo genome sequencing using Oxford Nanopore long-read data combined with RNA-seq–guided annotation. The resulting assemblies (45.6 – 46.1 Mb) were highly contiguous, with 19 – 21 chromosome-scale sequences assembled with &gt;96% BUSCO completeness scores. Genome mining revealed 47 – 48 putative secondary metabolite biosynthetic gene clusters, including clusters putatively associated with polyketide, nonribosomal peptide and terpene biosynthesis. Several clusters were previously reported to be transcriptionally active during growth on apple tissues, suggesting potential roles in host interaction. This study documents the first confirmed occurrence of N. ditissima in Virginia and provides improved genomic resources that expand current knowledge of this pathogen’s biology. These data establish a foundation for future work on population genomics, virulence mechanisms and host–pathogen interactions associated with European canker in the Mid-Atlantic U.S.A.