Evolution of plant penetration strategies in pathogenic fungi

Fungal spores are responsible for initiation and propagation of the majority of biotic plant diseases. Yet the core and species-specific genetics of spore germination have not been comparatively analyzed in multiple fungal lineages. We performed comparative transcriptomics of spore germination among six fungi to determine how expression of orthologous genes has changed during evolution, and to predict genes whose knockouts will exhibit phenotypic differences in the spore germination and host penetration processes. We chose fungi representing different approaches to plant penetration, including penetration using melanized appressoria, penetration through natural openings, and direct penetration without melanization, and included Neurospora crassa as a comparison. To provide a uniform basis for comparison among species, we assayed transcriptional profiles during germination on a single defined medium as well as during germination on hosts. We estimated ancestral gene expression for orthologous genes, identifying genes that undergo species- or clade-specific transcriptional shifts during the spore germination process, as well as transcriptional shifts that are unique to different mechanisms of plant penetration. Functional assays of a subset of genes exhibiting species-specific and infection-type specific up-regulation were performed to determine the roles of these genes in conidial germination of these fungi. These assays revealed genes, not previously identified, which have important roles in conidial phenotypes, germination, and hyphal growth. These experiments contribute to our understanding of how shifts in gene expression drive the evolution of conidial germination in a wide range of fungi.