The genome of the fungus Cladosporium fulvum suggests an ancestral host jump to tomato

Cladosporium fulvum is a Dothideomycete fungus pathogenic on tomato but its biotrophic lifestyle differs from most other members of this class of fungi. Its genome sequence is most related to Dothistroma septosporum, a hemi-biotrophic pathogen causing pine needle blight and producing the toxin dothistromin. The C. fulvum genome size is twice that of D. septosporum because of invasion by transposable elements that have strongly shaped its structure and likely the interaction with its host plant tomato. Although it is a biotroph, the C. fulvum genome contains many genes that are typically found in hemi-biotrophs and necrotrophs. In particular, its carbohydrate-degrading enzyme catalog comprises a large arsenal for pectin degradation and C. fulvum grows well on different complex carbohydrate substrates including lignin. Also 15 gene clusters for secondary metabolite biosynthesis are present in the genome, including the gene cluster responsible for dothistromin production. Strikingly, several of the genes involved in cell walldegradation and secondary metabolite production are not expressed in planta and others are pseudogenized. These phenomena are reminiscent of a jump by an ancestral D. septosporum-related fungal pathogen to tomato where it adapted to a biotrophic lifestyle by differentiation in gene content and gene regulation. Genes involved in adaptation to this lifestyle may encode not only small secreted effectors, but also structural proteins like hydrophobins and enzymes involved in degradation of antimicrobial saponins like a-tomatinase.