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ARS Home » Northeast Area » Kearneysville, West Virginia » Appalachian Fruit Research Laboratory » Innovative Fruit Production, Improvement, and Protection » Research » Publications at this Location » Publication #429054
Research Project: Superior Fruit Tree Cultivars for Orchard Resilience, Sustainability, and Consumer Appeal

Location: Innovative Fruit Production, Improvement, and Protection

Title: High-quality genomic and phylogenetic resources for Neonectria ditissima isolates obtained from Virginia apple orchards

Author
item BORBA, MAT - Virginia Tech
item Gottschalk, Christopher
item Jurick Ii, Wayne
item BRADSHAW, MICHAEL - North Carolina State University
item ACIMOVIC, SRDJAN - Virginia Tech

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/16/2026
Publication Date: 5/18/2026
Citation: Borba, M., Gottschalk, C.C., Jurick Ii, W.M., Bradshaw, M., Acimovic, S. 2026. High-quality genomic and phylogenetic resources for Neonectria ditissima isolates obtained from Virginia apple orchards. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-12-25-0142-R.
DOI: https://doi.org/10.1094/PHYTOFR-12-25-0142-R

Interpretive Summary: Apple fruit are a healthy, important part of American agriculture. A new fungus threatens apple tree fruit production in the mid atlantic region. This research reports the first finding of this emerging apple fruit pathogen. To help stave off the economic impact from this fungus, new research was performed to identify factors important for the fungus to cause disease. Having a genetic roadmap of the fungus will allow scientists and industry to track this pathogen and develop specific controls to limit its spread and impact.

Technical Abstract: 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 metabolite 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 are predicted to produce a 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.