An Interspecies Comparative Analysis of the Predicted Secretomes of the Necrotrophic Plant Pathogens <i>Sclerotinia sclerotiorum</i> and <i>Botrytis cinerea</i>

<div><p>Phytopathogenic fungi form intimate associations with host plant species and cause disease. To be successful, fungal pathogens communicate with a susceptible host through the secretion of proteinaceous effectors, hydrolytic enzymes and metabolites. <i>Sclerotinia sclerotiorum</i> and <i>Botrytis cinerea</i> are economically important necrotrophic fungal pathogens that cause disease on numerous crop species. Here, a powerful bioinformatics pipeline was used to predict the refined <i>S</i>. <i>sclerotiorum</i> and <i>B</i>. <i>cinerea</i> secretomes, identifying 432 and 499 proteins respectively. Analyses focusing on <i>S</i>. <i>sclerotiorum</i> revealed that 16% of the secretome encoding genes resided in small, sequence heterogeneous, gene clusters that were distributed over 13 of the 16 predicted chromosomes. Functional analyses highlighted the importance of plant cell hydrolysis, oxidation-reduction processes and the redox state to the <i>S</i>. <i>sclerotiorum</i> and <i>B</i>. <i>cinerea </i> secretomes and potentially host infection. Only 8% of the predicted proteins were distinct between the two secretomes. In contrast to <i>S</i>. <i>sclerotiorum</i>, the <i>B</i>. <i>cinerea</i> secretome lacked CFEM- or LysM-containing proteins. The 115 fungal and oomycete genome comparison identified 30 proteins specific to <i>S</i>. <i>sclerotiorum</i> and <i>B</i>. <i>cinerea</i>, plus 11 proteins specific to <i>S</i>. <i>sclerotiorum</i> and 32 proteins specific to <i>B</i>. <i>cinerea</i>. Expressed sequence tag (EST) and proteomic analyses showed that 246 <i>S</i>. <i>sclerotiorum</i> secretome encoding genes had EST support, including 101 which were only expressed <i>in vitro</i> and 49 which were only expressed <i>in planta</i>, whilst 42 predicted proteins were experimentally proven to be secreted. These detailed <i>in silico</i> analyses of two important necrotrophic pathogens will permit informed choices to be made when candidate effector proteins are selected for function analyses <i>in planta</i>.</p>