Figure 3

Sclerotinia effector candidates selected based on Ka/Ks ratio. (a) Distribution of Ka/Ks ratio for the 197 SPEP genes with orthologs in B. cinerea, calculated with Yn00 method on pairwise ortholog alignments. (b) Predicted 3D protein structure of SS1G_07749, a member of the glycoside hydrolase 11 xylanase family with global Ka/Ks = 2 in comparisons with B. cinerea orthologs. Residues of the 3D model are color-coded according to site-specific Ka/Ks ratios calculated using Bayesian inference with M8 model [28]. Residues with Ka/Ks > 1 are labeled on the structure. A putative Beta-D-Xylopyranose substrate molecule present in the 3b5l_B model, best structural analog of SS1G_07749, is shown as balls and sticks. The side chains of residues forming the predicted substrate binding site predicted by COFACTOR are show as sticks. The interface with plant xylanase inhibitors shown as a yellow dotted line was inferred from [53, 54] and the necrotizing peptide region shown as a grey dotted line was inferred from [9].