Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis

Fungi and comycetes are the casual agents of many of the most serious of plants. Here are report a detailed comparative analysis of the genome sequences of thirty six species of fungi and comycetes, including seven plant pathogenic species that aims to explore the common genetic features associated with plant disease-causing speceis. The predicted translational products of each genome have been clustered into groups of potential orthologies using Markov Chain Clustering and the data integrated into the e-Fungi object-oriented data warehouse (http://www.e-fungi.org.uk/). Analysis of the species distribution of members of these clusters has identified proteins that are specific to filamentous fungal species and a group of protiens found only in plant pathogens. By comparing the gene inventories of filamentous, ascomycetous phytopathogenic and free-living species of fungi, we have identified a set of gene families that appear to have expanded during the evolution of phytopathogens and may therefore serve important roles in plant disease. We have also characterised the predicted set of secreted proteins encoded by each genome and identified a set of protein families which are significantly over represented in the secretomes of plant pathogenic fungi, including putative effector proteins that might perturb host cell biology during plant infection. These results demonstrate the potential of comparative genome analysis for exploring the evolution of eukaryotic microbial pathogenesis.