PtoR

1. PtoR pim400 pim373 pim411 peru605 chi551 chi620 chi497 chi489 chi493 chi487 chi580 peru505 peru243 pim114 chmPto chm115 chm106 parv80 parv94 peru592 peru554 peru236 peru515 peru245 peru238 peru602 peru518 peru603 peru517 peru521 peru239 peru246 peru608 peru234 peru594 chi565 chi151 chi502 chi566 peru570 hir46 hir132 hir137 hir540 LhirPtoE hir183 hir186 S. ochranthum Pto parv72 parv79 parv90 chm103 chmPth3 chm116 chm112 chm114 Pth3R peru513 peru555 Pth3S peru562 peru506 peru345 peru557 100 75 Pto 78 89 94 96 Pth3 96 95 peru512 100 peru561 peru571 peru569 chi490 95 chi123 chi498 chi499 chi121 chi549 chi149 peru559 100 hir538 80 hir139 hir54 LhirPtoF chi552 chi600 peru563 peru520 100 100 chi124 Pth5 chmPth5 parv99 99 Pth5R peru519 78 hir536 peru507 99 penn544 penn64 86 penn203 99 penn542 chi122 chi548 hir541 99 hir168 hir134 100 hir47 84 hir58 hir140 91 penn543 penn545 100 100 penn68 Fen S. ochranthum Fen LhirPtoB 95 FenS FenR LhirPtoD 98 Pth2 Pth2R 100 81 Pth2S S. ochranthum Pth2 Pth2 Lyco S. berthaultii berDF1 parv73 chm117 99 chm101 peru508 100 84 parv84 83 hir178 parv85 100 penn63 Pth4 Pth4R Pth4S S. tuberosum tbrDI2 100 S. dulcamara S.sucrense scrDG4 Outgroup S. berthaultii berDF4 S. tuberosum tbrDI4 95 S. sucrense scrDG1 S. berthaultii berS1 S. berthaultii ber7A 5 changes

2. Supplemental Figure 1. Phylogeny based on nucleotide sequences of alleles of Pto gene family inferred by maximum parsimony analysis. The major clades were named according to the genes from the Pto locus from L. esculentum and L. pimpinellifolium (GenBank Acc. No. AF220603 and AF220602). These sequences are highlighted in orange. The suffix 'S' corresponds to the sequences from the cultivar 76S of L. esculentum, while 'R' corresponds to those from the cultivar 76R containing the Pto family introgressed from L. pimpinellifolium. Bootstrap frequencies greater than 75% are indicated above the branches. The tree is rooted as in Vleeshouwers (2001).