Genomics of fungal plant pathogens and adaptation to their host plants

We compared the genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum belong to the class of Dothideomycetes, are phylogenetically closely related, but have different lifestyles and infect different hosts. C. fulvum is a biotroph that infects tomato, while D. septosporum is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes but differ significantly in size, which is mainly due to the difference in repeat content. Repeat-rich areas in C. fulvum, which primarily consist of retrotransposons, were enriched for species-specific genes including those encoding secreted effector proteins. Several previously cloned effector genes from C. fulvum are present in D. septosporum and some of them (Ecp2 and Avr4) are recognized by tomato Cf resistance proteins and cause a Cf-mediated hypersensitive response. Some gene clusters encoding the dothistromin toxin, well studied in D. septosporum, are conserved in C. fulvum, although in this fungus some of the genes are pseudogenized or not expressed in planta. C. fulvum produces the species-specific enzyme a-tomatinase, absent in D. septosporum, that detoxifies a-tomatine present in high concentrations in tomato enabling it to colonize tomato. In the two fungi and other Dothideomycetes introner-like elements were identified; these are highly structured near-identical introns present in different genes that are multiplied by a yet unknown mechanism. Overall, comparison of the two genomes shows that closely related plant pathogens have adapted to different hosts and lifestyles by different mechanisms including gene innovations, pseudogenization and gene regulation.