S . sclerotiorum secretome prediction and analysis pipeline. (a) secretome analysis pipeline. We identified 745 predicted secreted proteins (yellow box) among which 486 showing experimental evidence for expression in planta (S. sclerotiorum secreted proteins expressed in p lanta, SPEPs). The number of proteins filtered out is indicated in grey with dotted arrows, the number of selected proteins is given within boxes, bioinformatics tools and resources used are indicated in blue. (b) Identification of effector candidates (ECs) based on sequence, motifs or protein domains conserved in fungal effectors. (c) Identification of ECs belonging to duplicated gene families and showing signatures of positive selection. (d) Identification of S. sclerotiorum-specific ECs of unknown function analogous to known protein folds. The results of analyses b, c and d are reported in tables and figures as indicated.