Joly et al. BMC Genomics 2010, 11:422 http://www.biomedcentral.com/1471-2164/11/422 proteins (CFEM = Common in Fungal Extracellular and Membrane). This particular domain is an eight cysteine- containing domain for which members are proposed to have important roles in fungal pathogenesis [48], and it was by far the most highly represented PFAM domain in the S+ dataset. CFEM-containing proteins could func- tion as cell-surface receptors, signal transducers, or adhesion molecules in host-pathogen interactions [48]. Moreover, five unisequences had significant similarity to gEgh16/gEgh16 H proteins from Blumeria graminis, a large family potentially involved in host-pathogen inter- actions [49]. An appressorium-specific expression pat- tern was described for numerous gEgh16/gEgh16 H homologues, including virulence genes GAS1 (MAS3) and GAS2 (MAS1) from Magnaporthe grisea. GAS1 or GAS2 deletion mutants had no defect in vegetative growth, conidiation or appressoria formation, but were reduced in appressorial penetration and lesion develop- ment [50]. The diverse ecological niches of fungal species are mirrored in their secretome, which includes gene families encoding various proteolytic and carbohydrate- Page 4 of 16 degrading enzymes known to act on the linkages found in plant cell walls and compatible with the array of nutritional sources they can exploit [47]. Consistent with the molecular function GO analysis (Figure 1), 36.56% and 47.88% of Melampsora secreted proteins with a GO assignment were involved in binding (GO:0005488) and catalytic activity (GO:0003824), respectively. Note that there was a trend towards con- centration of a distinct set of processes and functions in the group of proteins making up the Melampsora secre- tome. Significantly higher proportions of secreted pro- teins, relative to the entire dataset, were assigned to the following functions: carbohydrate and ion binding, and hydrolase and oxidoreductase activity (GO:0030246 and GO:0043167, and GO:0016787 and GO: 0016491). There also appeared to be enrichment of proteins involved in processes related to cell adhesion (GO:0007155), response to stimulus (GO:0050896), reg- ulation of molecular function (GO:0065009), carbohy- drate and lipid transport (GO:0008643 and GO:0006869), and primary metabolic process (GO:0044238), including oxygen and reactive oxygen Figure 1 Gene Ontology classification of the Melampsora unisequence dataset. For each main GO category (A: Biological process; B: Molecular function; and C: Cellular component), percentages were based on the total number of ontologies found for unisequences encoding putative secreted proteins (S+) or non-secreted proteins (NS) (see values in D). Note that individual GO categories can have multiple mappings resulting in percentage values higher than 100%. Underlined GO categories are overrepresented in S+ compared with NS (***: significant at the 0.1% level; **: significant at the 1% level; *: significant at the 5% level).