Phylogenomics of plant associated Botryosphaeriaceae species

The Botryosphaeriaceae is a fungal family including many destructive canker and dieback pathogens of woody plants. Seventeen species representing six genera (Botryosphaeria, Diplodia, Dothiorella, Lasiodiplodia, Neofusicoccum, and Neoscytalidium) were isolated from four symptomatic fruit and nut crops (apricot, grape, pistachio, and walnut). Of the 17 species, 15 are causal fungi of Botryosphaeria dieback of grape. Pathogenicity to potted grape plants was confirmed for all species, based on the presence of internal wood lesions after three months incubation in the greenhouse. Phylogenomic comparisons of the 17 species of wood-colonizing fungi revealed clade-specific expansion of gene families representing putative virulence factors (i.e., involved with toxin production and mobilization, wood degradation, and nutrient uptake): glycoside hydrolases, type I polyketide synthases, cytochrome P450s, and fungal peroxidases. Analyses revealed that secondary metabolism and transporter gene families in Lasiodiplodia have been enriched, whereas secreted CAZymes in Botryosphaeria and Neofusicoccum genomes have been enriched. In contrast, Diplodia, Dothiorella, and Neoscytalidium generally showed a contraction in the number of members of these gene families. Species with expansions of gene families, such as secreted CAZymes, glycoside hydrolases, secondary metabolism, and transporters, were the most virulent (i.e., were associated with the largest lesions), based on our pathogenicity tests and published reports. This study represents the first comparative phylogenomic investigation into the evolution of possible virulence factors from diverse, cosmopolitan members of the Botryosphaeriaceae.