Comparative genomics of Dothideomycetes plant pathogens

The Dothideomycetes are one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops, whether for biofuel, food or feed. Eighteen genomes of fungi belonging to this group have currently been sequenced, allowing comparative genome analysis. Chromosome content of these organisms is highly conserved; however, rearrangements have taken place mostly within, rather than between, chromosomes. This is caused mostly by inversions, which can be observed between closely related species. In more distantly related species, these inversions have led to a re-shuffling within the individual chromosomes. Despite this re-shuffling, some gene clusters have remained intact during evolution. Effector genes (e.g. encoding small secreted proteins and proteins involved in secondary metabolism) are more numerous in plant pathogens than in non-pathogens. Repetitive DNA content (e.g. originating from transposable elements) varies widely among the Dothideomycetes. Effector genes are over-represented among the genes flanking these transposable elements. It has been suggested that this causes the Repeat Induced Point-mutation (RIP) machinery to target these effector genes, allowing for faster evolution of these genes and consequently faster evasion of the defenses of the host plant. In Mycosphaerella graminicola, several chromosomes have previously been identified as being dispensable. These chromosomes show a lower GC content and gene density, higher repeat content and an under-representation of proteins involved in metabolism and transcriptional regulation. Chromosomes with these properties have been identified for several other Dothideomycetes, suggesting dispensability. These results offer valuable insights into fungi of the class Dothideomycetes and their method of pathogenicity.