Functional gene content of fungi in a pine needle disease system largely reflects their phylogeny

Gabriel Amorim de Albuquerque Silva , Temitope Folorunso, Lori Eckhardt, Janna R. Willoughby

Background: Fungi recovered from diseased host tissue can differ substantially in functional gene content, but interpreting that variation requires knowing how it relates to evolutionary history.

Results: We assembled and annotated genomes for 67 fungi cultured from pine needles with symptoms of brown spot needle blight and compared them with 13 reference genomes, including established pine pathogens. The isolates spanned four classes of Ascomycota. Functional gene content tracked phylogeny. Taxonomic class explained 21.4% of variation in carbohydrate-active enzyme family composition, and phylogenetic distance correlated with functional dissimilarity in every repertoire examined, most strongly for carbohydrate-active enzymes and least for predicted effectors. Comparisons pooling isolates and references across classes produced apparent lifestyle differences that did not persist within Dothideomycetes. Within that class, the needle pathogens Lecanosticta acicola and Dothistroma septosporum fell at the low end of the isolate distribution for cellulose- and pectin-associated enzyme genes, a reduction that persisted when enzyme families shared among substrate categories were excluded. Their biosynthetic gene cluster counts, secreted enzyme proportions, and predicted effector content fell within the isolate distributions.

Conclusions: These comparisons show that the positions of known pathogens depend on the functional repertoire examined and its evolutionary context. Because the ecological roles of the cultured fungi were not determined, their gene content cannot directly establish which contributed to disease. Outside plant cell wall degradation, the needle pathogens were not distinguishable from co-occurring fungi by gene content, and these genomes provide a comparative foundation for testing which fungi contribute to disease, and which functions are expressed during pine colonization.