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Figure S1. Structure-based multiple sequence alignment of the NB-ARC domain of PM3CS with APAF-1, CED-4 and ten plant R proteins. The PM3CS sequence was added to the structure-based multiple sequence alignment published in van Ooijen et al. (2008), including gain- and loss-of-function positions in pink and yellow, respectively. Green stars mark amino-acid positions that are conserved within R proteins and APAF-1 at the ADP binding site. Amino acids that are polymorphic in the corresponding PM3B sequence are coloured in orange; those that are polymorphic in both PM3A and PM3B are in red. The secondary-structure prediction reveals that PM3CS carries the vast majority of the α-helices (blue) and β-stands (brown) present in APAF-1. Furthermore, the alignment indicates that the NB-ARC domain encoded by Pm3CS contains all motifs of the three subdomains NB, ARC1 and ARC2. Only the first motif, hhGRExE, seems to be absent in PM3CS.

Figure S2. Amino acid differences of the PM3A PM3G proteins. Polymorphic amino acids are indicated below the PM3CS sequence, which is identical to the consensus sequence of the seven functional PM3 proteins. The protein domains are indicated on the left. The predicted CC structure is underlined. Motifs conserved in the NB-ARC domains of NBS-LRR proteins are underlined and labelled on top. The x-positions of the LxxLxLxx motif are highlighted in red, and the conserved leucines or other hydrophobic residues are represented in bold. Residues of the ARC2 subdomain that form loops in the 3D model (Figure 5) are coloured in green, and side chains of polymorphic residues that point to the solvent are highlighted in light blue. The notional positions of the AflII, BclI and NsiI restriction sites in the corresponding DNA sequence used for constructing chimeric genes are indicated.

Table S1. Numbers of powdery mildew isolates with the different (a)virulence gene combinations for Pm3a/Pm3f (a) and Pm3b/Pm3c (b).

Table S2.P values of Student’s t-test on HI of constructs shown in Figure 3.

Table S3.P values of Student’s t-test on HI of constructs shown in Figure 4a.

Table S4.P values of Student’s t-test on HI of constructs shown in Figures 4a and 6a (virulent controls).

Table S5.P values of Student’s t-test on HI of constructs shown in Figure 4b.

Table S6.P values of Student’s t-test on HI of constructs shown in Figure 6a.

Table S7.P values of Student’s t-test on HI of constructs shown in Figure 6b.

Table S8.P values of Student’s t-test on HI of constructs shown in Figure 7.

Appendix S1. Supplementary text for Experimental Procedures.

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