New Genomic Resources for Understanding Old Pathogens: Lessons using Discula destructiva Redlin, the Causal Agent of Dogwood Anthracnose

Fungal pathogens of forest trees have dramatically altered forest biodiversity across North America. Understanding the genomic underpinnings of pathogenicity, e.g., evasion of host defenses or horizontal gene transfer, is crucial to predicting and preventing future epidemics, especially under anthropogenic climate change. Dogwood anthracnose, caused by the fungus, Discula destructiva Redlin, has decimated native flowering dogwood and pacific dogwood trees (Cornus florida L. and C. nuttallii Aud., respectively) in North America since the 1970s. This pathogen survives as an anamorphic hemibiotroph and is one of many notable pathogens of forest trees within the ascomycete order, Diaporthales. Despite the extensive impact of Diaporthalean pathogens on forest ecosystems, scant genomic resources (i.e., annotated, chromosome-scale reference genomes) exist to help understand traits that dictate pathogenicity. Thus, the overall goal of this research is to develop and characterize foundational genomic resources for D. destructiva, in the form of an annotated, chromosome-scale reference genome and transcriptome, thereby advancing our understanding of the pathogenic tendency within Diaporthales. Oak water agar and potato dextrose agar were found to promote abundant tissue growth necessary for DNA and RNA extractions. The first gapless, chromosome-scale genome of D. destructivaisolate AS111 yielded a 46.655 Mb assembly with eight chromosome-scale scaffolds and an overall genome completeness of 97.64%. There were 10,373 predicted genes identified with structural annotations. Functional annotation resulted in 10,505 predicted genes and a 17.202 Mb transcriptome assembly with an overall BUSCO completeness of 96.45%. There were 162 significantly upregulated and 78 significantly downregulated genes (adjusted P values < 0.05, respectively) identified for isolates under sporulation compared to non-sporulation. Gene Ontology (GO) Enrichment revealed that the significantly upregulated genes were involved in various processes targeting plant cell wall degradation such as hydrolase activity and carbohydrate and polysaccharide binding. Significantly downregulated genes were involved in various processes involving electron carrier activity and the binding of iron and heme. These novel genomic resources for D. destructiva will enable fine-scale profiling of virulence genes and facilitate comparative genomics with other Diaporthalean pathogens. Development of such resources is a critical first step to understanding historical epidemics to apply past lessons to novel pathogen invasions.