Dirty Dianthus: A review of the Microbotryum-Dianthus plant pathogen system.

Microbotryum dianthorum is a species complex of smut fungi that act as biotrophic plant pathogens of Dianthus flowering plants. This group of pathogenic fungi are situated within a larger group of fungi that act as biotrophic plant pathogens, some of which are responsible for extensive crop loss in our agricultural system. These pathogens are distinct from other Microbotryum species in their ability to infect not only a single host, but multiple hosts. Their unique ability to parasitize several plant hosts may unlock potential clues about the potential for emergent infection disease in crop systems. Previous work has established that these pathogens leverage a suite of secreted proteins in their assault on their plant hosts and this will provide the framework and focus of this analysis. This dissertation seeks to understand generalist Microbotryum species through a combined approach of genome analysis to identify secreted proteins, expression analysis through several key fungal lifecycle stages, and a population genomics survey. Chapter 1 includes a review of the relevant accumulated literature on fungal plant pathogens and the Microbotryum model system. In chapter 2, we characterized the fungal secretome of Microbotryum intermedium through use of a pipeline to identify the collection of secreted proteins produced in this species. In chapter 3, we analyzed gene expression in the haploid, mating, and active infection lifecycle phases of both Microbotryum superbum and Microbotryum segueri. Finally, in chapter 4, we conducted a large-scale population genomics survey of 127 fungal genomes on various host species throughout Europe to see how secretomes vary across spaces and how they vary in unique local ecologies. This study found that there is a surprising degree of variation within populations but there is also a core set of secreted proteins that are shared between populations in Microbotyum on Dianthus hosts. This research contributes to the currently small but growing body of work on Microbotryum dianthorum and it also contributes 127 assembled and annotated genomes to a field of fungal biology that is sorely lacking this important resource.