The telomere-to-telomere genome and lifestyle transcriptome profiling of Discula destructiva Redlin provide modern molecular and genomic context to a historical epidemic

Abstract

Fungal pathogens have dramatically altered forests worldwide, yet the mechanisms underlying their virulence remain poorly understood. From the 1970s to the early 2000s, dogwood anthracnose, caused by Discula destructiva Redlin, devastated flowering and Pacific dogwoods (Cornus florida L. and C. nuttallii Aud., respectively). Despite the impacts of D. destructiva and other phytopathogens on forest ecosystems, genomic resources remain limited, hindering efforts to understand pathogenicity. The goal of this study was to evaluate the historical D. destructiva epidemic through a modern genomics lens by uncovering virulence- associated genes that likely contributed to its rapid spread across native dogwoods. We therefore utilized PacBio HiFi and Proximo Hi-C sequencing to assemble the first telomere-to-telomere, chromosome-scale genome for D. destructiva isolate AS111. The resulting 46.655 Mb assembly comprised eight chromosomes with an overall BUSCO completeness of 97.64%. We also identified 10,373 predicted gene models with an overall BUSCO completeness of 96.45%. To investigate gene expression across distinct life cycle phases, reproductive (sporulating) and vegetative (nonsporulating), we conducted RNA sequencing and identified 240 differentially expressed genes (padj < 0.05). GO enrichment revealed 162 upregulated genes during sporulation linked to plant cell wall degradation and sugar metabolism, whereas 78 downregulated genes were linked to electron carrier activity and redox balance. Among these 240 genes, 117 genes had predicted protein sequences that were also identified as a candidate virulence factor, including signal peptides, carbohydrate-active enzymes (CAZymes), and effectors, highlighting the role of sporulation-associated gene expression in D. destructiva virulence. Together, these findings suggest that the reproductive phase primes D. destructiva for host invasion and ecological persistence, which may influence its success as a forest pathogen. Author SummaryForest pathogens threaten ecosystems worldwide and cause extensive ecological and economic damage. Since the 1970s, native dogwood populations in North America have been devastated by dogwood anthracnose, caused by the exotic fungal pathogen Discula destructiva. Discula destructiva is just one of many destructive fungal pathogens in the order Diaporthales, which includes other noteworthy pathogens that cause chestnut blight (Cryphonectria parasitica) and butternut canker (Ophiognomonia clavigignenti-juglandacearum). Despite the widespread impact of fungal diseases, little is known about the genetic factors that drive their spread and severity. To help address this gap, we generated the first telomere-to-telomere, chromosome- scale genome assembly of D. destructiva and analyzed gene expression across distinct life cycle phases: reproductive (sporulating) and vegetative (nonsporulating) growth. Our findings revealed key sporulation-associated genes and virulence factors that may facilitate host infection and underscore the importance of sporulation in the pathogenicity of D. destructiva. These insights improve our understanding of the mechanisms that drive disease development, influence how fungal pathogens such as D. destructiva establish and persist in forest ecosystems, and provide a foundation for future comparative genomics among other devastating pathogens in Diaporthales.