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Comparative Study
. 2008 Jun 4;3(6):e2300.
doi: 10.1371/journal.pone.0002300.

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

Darren M Soanes  1 , Intikhab Alam, Mike Cornell, Han Min Wong, Cornelia Hedeler, Norman W Paton, Magnus Rattray, Simon J Hubbard, Stephen G Oliver, Nicholas J Talbot
Affiliations
Comparative Study

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

Darren M Soanes et al. PLoS One. .

Abstract

Fungi and oomycetes are the causal agents of many of the most serious diseases of plants. Here we report a detailed comparative analysis of the genome sequences of thirty-six species of fungi and oomycetes, including seven plant pathogenic species, that aims to explore the common genetic features associated with plant disease-causing species. The predicted translational products of each genome have been clustered into groups of potential orthologues 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 proteins 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. The results demonstrate the potential of comparative genome analysis for exploring the evolution of eukaryotic microbial pathogenesis.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Species tree of filamentous ascomycetes used in this study based on concatenated sequences from 60 universal fungal protein families.
Support values shown for each branch (based on 100 bootstraps). Phytopathogenic species are highlighted in bold type. A more detailed methodology has been described previously .
Figure 2
Figure 2. Bar chart showing the percentage of the total proteome that is predicted to be secreted in each fungal species.
The number of secreted proteins is indicated at the top of each bar.
See this image and copyright information in PMC

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