Supplementary Table 1 Primers Used in Real Time Quantitative RT-PCR Analysis

Supplementary Table 1 Primers used in Real time quantitative RT-PCR analysis

Probe set / Putative function / Primers sequences
AY049040 / 18S rRNA / Forward: 5’-CTGAGAAACGGCTACCACAT-3’
Reverse: 5’- CCCAAGGTCCAACTACGAG-3’
Ta.21342.1.S1_x_at / Chitinase 3 / Forward: 5’-GCCGTTCGCATAGTCAATC-3’
Reverse: 5’-CGCACCATTATTCGCTTGT-3’
Ta.25666.1.A1_at / MAP kinase homolog / Forward: 5’-CACTGGGTCGTGACACTTCT-3’
Reverse: 5’-CCTCCTCTTCCTTGTATGCTG-3’
Ta.9226.1.S1_at / Pathogenesis-related protein 4 / Forward: 5’-ACGGGATGCTGCCTTGTA-3’
Reverse: 5’-GATAACCCGTTTGGTCTTTTC-3’
Ta.169.1.S1_x_at / Germin-like protein / Forward: 5’-ACGAGCACAAACAGAAATAGGA-3’
Reverse: 5’-GAAGGAAGGAAGAGGAGGATG-3’
Ta.25053.1.S1_at / Thaumatin-like protein / Forward:5’-GACGACCAGACCAGCACCT-3’
Reverse: 5’-CCTTGTTCCTTATTGATCCCA-3’
Ta.28233.1.S1_at / Glutathione-S-transferase / Forward: 5’-TGTCGTTGGTGCTGGTCT-3’
Reverse: 5’-GTGTCCCTGTGGCATAAGTG-3’
Ta.28224.2.S1_x_at / Cyc07 / Forward:5’-GCTCGGTTTTATTGTGTGGC-3’
Reverse: 5’-TCTTGGACTTGGGATTCTATTTGT-3’
TaAffx.27263.1.S1_at / Vacuolar proton-inorganic pyrophosphatase / Forward: 5’-CAATGTATTCCTCTGCCCC-3’
Reverse: 5’- GAAACCTGTGAAAAACCGC-3’
TaAffx.120874.1.S1_x_at / 23kDa oxygen evolving protein of photosystem II / Forward: 5’-TCCACCTCCTGCTTCCTCC-3’
Reverse: 5’- GCCTCGTCATTCTTCTGCG-3’
Ta.13242.2.S1_x_at / Cdpk1 protein / Forward: 5’-TTCCTCGCTTCCTTTCTCC-3’
Reverse: 5’-ATCAAAACACACGGGCACA-3’
Ta.11386.2.S1_a_at / Ascorbate peroxidase / Forward: 5’-AGGGATTCTCGCTGGACGC-3’
Reverse: 5’-AACGAAGGGCTCTGGCTGTG-3’
Ta.2383.2.S1_x_at / HSP80 / Forward: 5’-TGGGCAATGTAAACGAGGG-3’
Reverse: 5’-AAAGGGGATTTGAGGCAGG-3’
Ta.881.1.S1_at / Cytosolic glyceraldehyde-3-phosphate dehydrogenase GAPDH / Forward: 5’-ACATCTTTCAGACCCGTTCA-3’
Reverse: 5’-TTTTTACAGTTCCTCCCACAG-3’
Ta.223.1.S1_at / Beta-1,3-glucanase precursor (Glb3) / Forward: 5’-AACGAGAACCAGAAGACAGGG-3’
Reverse:5’- CATTTAGAAAGTAACGGAGTAGGC-3’
Ta.8108.2.S1_x_at / Cold acclimation protein WCOR410c / Forward: 5’-TGGCTACCTCTCCTTGCTCA-3’
Reverse: 5’- CATTTTTTCCCTTGCTTGTG-3’
TaAffx.130064.4.S1_at / High-affinity phosphate transporter PT1 / Forward: 5’-CATTTCTCCCTGGCTTTGA-3’
Reverse: 5’-CGGTGACCCTCCTTGATT-3’
Ta.97.1.S1_at / WIR1 / Forward: 5’-ATCTCCCAGACACAATGCT-3’
Reverse: 5’-GGTGGTGCGTGACAGTAG-3’
Ta.1997.2.S1_a_at / Sec61p / Forward: 5’-CGCTGTTCTATGTGGTCTTCA-3’
Reverse: 5’-GATGTATCTTGTTCAACTCCCTCT-3’
Ta.28766.3.S1_at / Endotransglucosylase/hydrolase XTH5 / Forward: 5’-CGGAGATAGGGAAGATGGG-3’
Reverse: 5’-CGTGACAAGAAAAAGGAGCAAA-3’
Ta.2307.1.S1_at / phosphoglycerate kinase (AA1-480) / Forward: 5’-ATGCCCTGGACACAACACA-3’
Reverse: 5’-ATCAGCCACTCCCACCTTC-3’
Ta.2402.1.S1_at / S-adenosylmethionine decarboxylase precursor / Forward: 5’-CGATAGATTGGTTGATTGC-3’
Reverse: 5’-ATAACAGAGATTGTCAGAGGC-3’
Ta.1197.1.S1_at / alpha 1,4-glucan phosphorylase / Forward: 5’- AGTTTATCAGGAGTGGTGCT-3’
Reverse: 5’-GCCAACAAGGAAGTAGTCA-3’

Supplementary Table 2 Basal defense transcripts in two interactions

Functional category / Putative function / Probe set ID / Incompatible / Compatible
Fold change / P-Values / Fold Change / P-Values
Cell structure / Alpha-tubulin / Ta.28299.2.S1_at / 2.000000 / 0.000078 / 2.828427 / 0.000020
Cell structure / Alpha-tubulin / Ta.3596.1.S1_a_at / 2.640000 / 0.000020 / 3.249010 / 0.000020
Cell structure / Alpha-tubulin / Ta.3596.1.S1_x_at / 4.000000 / 0.000167 / 4.924578 / 0.000020
Cell structure / Beta-tubulin / Ta.28022.2.A1_at / 2.462289 / 0.000035 / 2.462289 / 0.000020
Cell structure / Protein H2A / Ta.29508.1.S1_at / 3.031433 / 0.000020 / 8.000000 / 0.000020
Cell structure / Protein H2A / Ta.29508.2.S1_a_at / 3.482202 / 0.000020 / 9.189587 / 0.000020
Cell structure / Protein H2A / Ta.29508.3.S1_a_at / 4.000000 / 0.000020 / 12.125730 / 0.000020
Cell structure / Protein H2A / Ta.14360.1.S1_a_at / 3.482202 / 0.000020 / 3.031433 / 0.000020
Cell structure / Protein H2A / Ta.14360.1.S1_x_at / 4.000000 / 0.000020 / 3.249010 / 0.000020
Disease/defence / Beta 1,3-glucanase / TaAffx.109595.1.S1_at / 2.000000 / 0.000078 / 4.594793 / 0.000020
Disease/defence / Beta 1,3-glucanase / Ta.303.3.S1_at / 6.062866 / 0.000020 / 9.189587 / 0.000020
Disease/defence / Beta 1,3-glucanase / Ta.303.3.S1_x_at / 3.031433 / 0.000078 / 4.924578 / 0.000020
Disease/defence / beta glucanase / Ta.10.1.S1_a_at / 5.656854 / 0.000020 / 3.031433 / 0.000020
Disease/defence / beta glucanase / Ta.10.1.S1_x_at / 4.000000 / 0.000020 / 3.031433 / 0.000020
Disease/defence / beta glucanase / Ta.10.2.S1_x_at / 4.000000 / 0.000020 / 2.297397 / 0.000020
Disease/defence / Beta-1,3-glucanase precursor (Glb3) / Ta.223.1.S1_at / 2.462289 / 0.000020 / 12.125730 / 0.000020
Disease/defence / Beta-D-glucan exohydrolase / Ta.23066.1.S1_s_at / 6.062866 / 0.000020 / 4.287094 / 0.000020
Disease/defence / Beta-D-glucan exohydrolase / Ta.6584.3.S1_a_at / 2.462289 / 0.000020 / 2.000000 / 0.000020
Disease/defence / Catalase / Ta.1055.2.S1_at / 3.732132 / 0.000020 / 2.143547 / 0.000020
Disease/defence / Catalase / Ta.1055.2.S1_x_at / 4.287094 / 0.000020 / 2.462289 / 0.000020
Disease/defence / Catalase / TaAffx.106322.1.S1_at / 10.556060 / 0.000020 / 8.000000 / 0.000020
Disease/defence / Chitinase 1 / Ta.30501.1.S1_at / 13.928810 / 0.000020 / 39.396620 / 0.000020
Disease/defence / chitinase 1 / Ta.2784.1.A1_at / 16.000000 / 0.000020 / 21.112130 / 0.000020
Disease/defence / chitinase 2 / Ta.2783.1.S1_at / 4.924578 / 0.000020 / 4.594793 / 0.000020
Disease/defence / chitinase 3 / Ta.21342.1.S1_x_at / 68.593500 / 0.000020 / 119.428200 / 0.000020
Disease/defence / chitinase IV precursor / Ta.224.1.S1_at / 4.287094 / 0.000020 / 4.000000 / 0.000020
Disease/defence / Cold acclimation protein WCOR410c / Ta.8108.2.S1_x_at / 6.498019 / 0.000088 / 42.224250 / 0.000020
Disease/defence / Cold acclimation protein WCOR410c / Ta.8108.2.S1_at / 18.379170 / 0.000030 / 32.000000 / 0.000020
Disease/defence / cold regulated protein / Ta.13183.1.S1_s_at / 4.594793 / 0.000020 / 9.189587 / 0.000020
Disease/defence / cold regulated protein / Ta.13183.1.S1_x_at / 4.594793 / 0.000020 / 9.849155 / 0.000020
Disease/defence / Cold shock domain protein 3 / Ta.27343.1.S1_at / 4.000000 / 0.000020 / 3.732132 / 0.000020
Disease/defence / Dehydroascorbate reductase / Ta.26922.1.S1_at / 2.828427 / 0.000492 / 4.287094 / 0.000046
Disease/defence / Dehydroascorbate reductase / Ta.5105.2.S1_a_at / 2.297397 / 0.000020 / 3.031433 / 0.000046
Disease/defence / germin protein precursor / Ta.22673.1.S1_s_at / 4.000000 / 0.000020 / 3.249010 / 0.000020
Disease/defence / Germin protein precursor / TaAffx.55270.1.S1_at / 2.000000 / 0.000692 / 2.297397 / 0.000130
Disease/defence / germin-like protein / Ta.169.1.S1_x_at / 84.448510 / 0.000020 / 84.448510 / 0.000020
Disease/defence / Germin-like protein / Ta.20563.1.S1_x_at / 10.556060 / 0.000023 / 12.125730 / 0.000189
Disease/defence / glutaredoxin / Ta.1071.1.S1_at / 2.297397 / 0.000027 / 2.462289 / 0.000020
Disease/defence / glutathione synthetase / Ta.5307.1.S1_at / 3.732132 / 0.000020 / 2.000000 / 0.000020
Disease/defence / glutathione synthetase / TaAffx.59101.1.S1_s_at / 4.287094 / 0.000020 / 3.482202 / 0.000046
Disease/defence / Glutathione transferase / Ta.28354.1.S1_at / 3.482202 / 0.000020 / 12.996040 / 0.000020
Disease/defence / Glutathione transferase / Ta.28219.1.A1_at / 8.000000 / 0.000438 / 4.594793 / 0.000865
Disease/defence / glutathione transferase / Ta.3679.1.S1_x_at / 9.189587 / 0.000020 / 12.125730 / 0.000020
Disease/defence / Glutathione transferase / TaAffx.82926.1.S1_s_at / 2.828427 / 0.000020 / 2.639016 / 0.000020
Disease/defence / glutathione transferase F5 / Ta.3418.1.S1_x_at / 3.249010 / 0.000046 / 2.462289 / 0.000020
Disease/defence / Glutathione transferase F5 / Ta.3418.2.S1_x_at / 3.249010 / 0.000030 / 3.031433 / 0.000023
Disease/defence / Glutathione-S-transferase / Ta.28233.1.S1_at / 21.112130 / 0.000020 / 97.005860 / 0.000020
Disease/defence / Glutathione-S-transferase / TaAffx.56524.1.S1_at / 2.462289 / 0.000030 / 4.000000 / 0.000020
Disease/defence / HSP70 / Ta.22628.1.S1_at / 10.556060 / 0.000020 / 8.000000 / 0.000020
Disease/defence / HSP70 / Ta.22628.1.S1_x_at / 9.189587 / 0.000020 / 8.574188 / 0.000030
Disease/defence / HSP80-2 / Ta.22817.2.S1_s_at / 4.924578 / 0.000020 / 3.482202 / 0.000020
Disease/defence / ice recrystallization inhibition protein 1 precursor / Ta.12663.1.S1_at / 2.297397 / 0.000020 / 4.287094 / 0.000020
Disease/defence / Inducible phenylalanine ammonia-lyase / TaAffx.57491.1.S1_x_at / 2.462289 / 0.000020 / 2.828427 / 0.000020
Disease/defence / Lipid transfer protein 3 / Ta.4014.2.S1_at / 2.828427 / 0.000023 / 2.462289 / 0.000020
Disease/defence / Lipid transfer protein 3 / Ta.5890.1.A1_at / 9.849155 / 0.000167 / 5.278032 / 0.000114
Disease/defence / Lt1.1 protein / Ta.1683.1.S1_at / 2.639016 / 0.000020 / 2.462289 / 0.000023
Disease/defence / Lt1.1 protein / Ta.1683.1.S1_x_at / 3.249010 / 0.000020 / 2.462289 / 0.000020
Disease/defence / Lt1.1 protein / Ta.7479.1.S1_a_at / 12.996040 / 0.000020 / 24.251470 / 0.000020
Disease/defence / Lt1.1 protein / Ta.7479.2.S1_x_at / 14.928530 / 0.000020 / 24.251470 / 0.000020
Disease/defence / Lt1.1 protein / Ta.7479.3.S1_x_at / 16.000000 / 0.000273 / 22.627420 / 0.000273
Disease/defence / Metallothionein / TaAffx.110281.1.S1_s_at / 3.482202 / 0.000020 / 2.297397 / 0.000020
Disease/defence / Non-specific lipid transfer protein 1 precursor / Ta.5810.1.S1_at / 238.856400 / 0.000027 / 45.254830 / 0.000147
Disease/defence / Non-specific lipid transfer protein 1 precursor / TaAffx.55684.1.S1_at / 2.462289 / 0.000020 / 5.278032 / 0.000020
Disease/defence / Non-specific lipid transfer protein 1 precursor / TaAffx.55684.1.S1_x_at / 2.639016 / 0.000020 / 5.278032 / 0.000020
Disease/defence / Non-specific lipid transfer protein 1 precursor / Ta.9255.1.S1_a_at / 4.000000 / 0.000020 / 2.828427 / 0.000020
Disease/defence / Non-specific lipid transfer protein 1 precursor / Ta.9255.1.S1_at / 3.031433 / 0.000020 / 2.828427 / 0.000020
Disease/defence / Oxalate oxidase precursor / Ta.24553.1.A1_at / 6.964405 / 0.000052 / 4.000000 / 0.000035
(continued on next page)

Fold Change cut-off of ≥2.0

P-values threshold ≤0.001

Supplementary Table 2(continued from proceeding page)

Functional category / Putative function / Probe set ID / Incompatible / Compatible
Fold change / P-Values / Fold Change / P-Values
Disease/defence / pathogenesis-related protein 1 / Ta.278.1.S1_at / 5.278032 / 0.000020 / 68.593500 / 0.000020
sease/defence / pathogenesis-related protein 1 / Ta.278.1.S1_x_at / 4.594793 / 0.000020 / 194.011700 / 0.000020
Disease/defence / pathogenesis-related protein 4 / Ta.9226.1.S1_at / 724.077300 / 0.000020 / 90.509670 / 0.000020
Disease/defence / Pathogenesis-related protein 4 / TaAffx.116570.1.S1_at / 3.249010 / 0.000552 / 16.000000 / 0.000046
Disease/defence / Pathogenesis-related protein 4 / TaAffx.116570.1.S1_x_at / 4.924578 / 0.000060 / 19.698310 / 0.000023
Disease/defence / pathogenisis-related protein 1.1 / Ta.62.1.S1_x_at / 3.732132 / 0.000020 / 51.984150 / 0.000020
Disease/defence / Peroxidase / Ta.21505.1.S1_at / 4.594793 / 0.000020 / 10.556060 / 0.000020
Disease/defence / Peroxidase / Ta.22564.1.S1_at / 103.968300 / 0.000030 / 315.173000 / 0.000020
Disease/defence / Peroxidase / Ta.22564.2.S1_a_at / 362.038700 / 0.000241 / 1448.155000 / 0.000346
Disease/defence / Peroxidase / Ta.22564.2.S1_x_at / 222.860900 / 0.000273 / 630.345900 / 0.000307
Disease/defence / Peroxidase / Ta.22593.2.S1_at / 2.639016 / 0.000552 / 6.498019 / 0.000023
Disease/defence / peroxidase / Ta.24715.1.S1_at / 59.714110 / 0.000020 / 1024.000000 / 0.000020
Disease/defence / peroxidase / Ta.4876.1.A1_x_at / 48.502930 / 0.000020 / 13.928810 / 0.000052
Disease/defence / peroxidase / Ta.5385.1.S1_at / 157.586500 / 0.000020 / 1024.000000 / 0.000020
Disease/defence / peroxidase / Ta.82.1.S1_at / 39.396620 / 0.000020 / 415.873200 / 0.000020
Disease/defence / Peroxidase / Ta.21505.2.S1_x_at / 7.464264 / 0.000052 / 8.574188 / 0.000040
Disease/defence / Peroxidase / Ta.22593.1.A1_at / 5.656854 / 0.000020 / 8.574188 / 0.000020
Disease/defence / Peroxidase / Ta.24710.1.S1_at / 68.593500 / 0.000147 / 111.430500 / 0.000060
Disease/defence / phenylalanine ammonia lyase / Ta.1465.1.S1_at / 5.656854 / 0.000020 / 5.278032 / 0.000020
Disease/defence / phenylalanine ammonia lyase / Ta.20429.1.S1_at / 2.000000 / 0.000020 / 3.031433 / 0.000023
Disease/defence / pSBGer1 protein / Ta.87.1.S1_at / 13.928810 / 0.000020 / 6.062866 / 0.000035
Disease/defence / pSBGer1 protein / Ta.87.1.S1_x_at / 12.996040 / 0.000023 / 6.062866 / 0.000035
Disease/defence / pSBGer1 protein / Ta.24723.1.S1_x_at / 9.849155 / 0.000020 / 5.278032 / 0.000020
Disease/defence / Putative xylanase inhibitor / Ta.13818.1.S1_at / 10.556060 / 0.000027 / 17.148380 / 0.000114
Disease/defence / Putative xylanase inhibitor / Ta.8574.2.A1_at / 34.296750 / 0.000020 / 25.992080 / 0.000020
Disease/defence / Senescence-associated protein / Ta.5224.3.S1_a_at / 2.462289 / 0.000020 / 3.732132 / 0.000020
Disease/defence / Senescence-associated protein / Ta.5224.3.S1_x_at / 2.462289 / 0.000078 / 3.031433 / 0.000214
Disease/defence / senescence-associated protein / TaAffx.499.1.A1_at / 2.639016 / 0.000020 / 2.143547 / 0.000020
Disease/defence / thaumatin-like protein / Ta.24501.1.S1_at / 9.849155 / 0.000020 / 51.984150 / 0.000020
Disease/defence / thaumatin-like protein / Ta.25053.1.S1_at / 103.968300 / 0.000020 / 222.860900 / 0.000020
Disease/defence / thaumatin-like protein / Ta.27762.1.S1_x_at / 12.996040 / 0.000020 / 73.516690 / 0.000020
Disease/defence / thaumatin-like protein / Ta.959.1.S1_at / 6.062866 / 0.000020 / 68.593500 / 0.000020
Disease/defence / Type 1 non-specific lipid transfer protein precursor / Ta.1337.1.S1_x_at / 2.143547 / 0.000020 / 16.000000 / 0.000020
Disease/defence / Type 1 non-specific lipid transfer protein precursor / Ta.1337.2.S1_x_at / 8.574188 / 0.000020 / 48.502930 / 0.000020
Disease/defence / Type 1 non-specific lipid transfer protein precursor / Ta.13751.1.S1_at / 2.462289 / 0.000020 / 4.924578 / 0.000020
Disease/defence / Wali2 protein / TaAffx.104648.1.S1_at / 45.254830 / 0.000020 / 19.698310 / 0.000020
Disease/defence / Wali2 protein / Ta.16472.1.S1_s_at / 4.924578 / 0.000101 / 4.287094 / 0.000692
Disease/defence / Wali3 protein / Ta.105.1.S1_at / 4.287094 / 0.000020 / 78.793240 / 0.000020
Disease/defence / wali3 protein / Ta.21267.1.S1_s_at / 90.509670 / 0.000040 / 73.516690 / 0.000020
Disease/defence / wali5 protein / Ta.21350.1.S1_x_at / 3.482202 / 0.000020 / 14.928530 / 0.000020
Disease/defence / Wali5 protein / TaAffx.27893.1.S1_x_at / 6.062866 / 0.000052 / 6.964405 / 0.000046
Disease/defence / wali6 protein / Ta.5024.1.S1_x_at / 32.000000 / 0.000020 / 55.715240 / 0.000020
Disease/defence / Wgluc5 protein / Ta.8584.1.S1_at / 8.574188 / 0.000020 / 55.715240 / 0.000020
Disease/defence / Wgluc5 protein / Ta.24427.1.S1_at / 3.031433 / 0.000060 / 2.000000 / 0.000052
Disease/defence / WIR1, pathogen defense protein / Ta.13.1.S1_at / 29.857060 / 0.000020 / 25.992080 / 0.000020
Disease/defence / wrsi5-1 protein / Ta.30711.1.S1_x_at / 97.005860 / 0.000020 / 59.714110 / 0.000020
Disease/defence / xylanase inhibitor protein I / Ta.1200.1.S1_at / 3.732132 / 0.000020 / 11.313710 / 0.000020
Disease/defence / xylanase inhibitor protein I / Ta.1200.1.S1_x_at / 3.249010 / 0.000020 / 11.313710 / 0.000020
Disease/defence / xylanase inhibitor TAXI-III / Ta.21262.1.A1_at / 9.849155 / 0.000030 / 4.594793 / 0.000020
Disease/defence / xylanase inhibitor TAXI-III / Ta.21262.1.A1_x_at / 8.574188 / 0.000078 / 4.594793 / 0.000020
Energy / Beta amylase / Ta.23322.1.S1_s_at / 11.313710 / 0.000052 / 21.112130 / 0.000052
Energy / ald protein / Ta.304.1.S1_at / 8.000000 / 0.000020 / 4.000000 / 0.000027
Energy / ald protein / Ta.304.1.S1_x_at / 4.287094 / 0.000027 / 2.639016 / 0.000020
Energy / Beta amylase / Ta.23322.2.S1_at / 19.698310 / 0.000020 / 4.000000 / 0.000020
Energy / Beta amylase / Ta.23322.3.S1_at / 4.000000 / 0.000020 / 68.593500 / 0.000052
Energy / Chlorophyll a/b-binding protein WCAB precursor / Ta.2538.1.S1_at / 2.000000 / 0.000020 / 2.639016 / 0.000020
Energy / Chlorophyll a/b-binding protein WCAB precursor / Ta.2538.2.S1_at / 2.297397 / 0.000023 / 2.143547 / 0.000020
Energy / formate dehydrogenase / Ta.28325.1.S1_x_at / 3.249010 / 0.000060 / 2.143547 / 0.000020
Energy / glucan endo-1,3-beta-D-glucosidase / Ta.28.1.S1_at / 45.254830 / 0.000040 / 445.721900 / 0.000020
Energy / Glucan endo-1,3-beta-D-glucosidase / TaAffx.15327.1.S1_at / 32.000000 / 0.000020 / 157.586500 / 0.000020
Energy / Glucan endo-1,3-beta-D-glucosidase / TaAffx.24475.1.S1_at / 78.793240 / 0.000023 / 5.278032 / 0.000020
Energy / Glucan endo-1,3-beta-D-glucosidase / TaAffx.24475.1.S1_x_at / 25.992080 / 0.000020 / 36.758350 / 0.000020
Energy / glucose-6-phosphate dehydrogenase / Ta.706.1.S1_s_at / 5.656854 / 0.000020 / 3.482202 / 0.000023
Energy / phosphoenolpyruvate carboxylase / Ta.81.1.S1_at / 2.828427 / 0.000023 / 2.297397 / 0.000027
Energy / phosphoglycerate mutase / Ta.605.1.S1_at / 2.462289 / 0.000020 / 2.639016 / 0.000020
Energy / phosphoglycerate mutase / TaAffx.7147.1.S1_at / 2.462289 / 0.000035 / 4.924578 / 0.000020
Energy / phosphomannomutase / Ta.29895.1.A1_s_at / 2.297397 / 0.000020 / 2.297397 / 0.000020
Energy / Phosphomannomutase / Ta.3539.1.S1_x_at / 2.000000 / 0.000035 / 2.000000 / 0.000020
(continued on next page)

Supplementary Table 2 (continued from proceeding page)

Functional category / Putative function / Probe set ID / Incompatible / Compatible
Fold Change / P-Values / Fold Change / P-Values
Energy / Ribulose-1,5-bisphosphate carboxylase activase / Ta.5210.2.S1_a_at / 6.498019 / 0.000020 / 2.462289 / 0.000020
Energy / Ribulose-1,5-bisphosphate carboxylase activase / Ta.3094.2.S1_at / 3.249010 / 0.000046 / 2.639016 / 0.000020
Energy / Ribulose-1,5-bisphosphate carboxylase activase / Ta.3094.2.S1_x_at / 2.143547 / 0.000046 / 2.828427 / 0.000020
Energy / Ribulose-1,5-bisphosphate carboxylase activase / Ta.5210.1.S1_at / 4.594793 / 0.000438 / 3.249010 / 0.000214
Energy / Ribulose-1,5-bisphosphate carboxylase activase / Ta.5210.3.S1_at / 7.464264 / 0.000027 / 7.464264 / 0.000023
Energy / Ribulose-1,5-bisphosphate carboxylase activase / TaAffx.113489.1.S1_at / 2.828427 / 0.000020 / 2.639016 / 0.000023
Energy / Ribulose-1,5-bisphosphate carboxylase activase / TaAffx.113489.1.S1_s_at / 3.482202 / 0.000020 / 3.482202 / 0.000020
Energy / Ribulose-1,5-bisphosphate carboxylase activase / TaAffx.113489.3.S1_at / 2.828427 / 0.000027 / 2.462289 / 0.000023
Energy / Ribulose-1,5-bisphosphate carboxylase activase / TaAffx.120014.1.S1_at / 2.297397 / 0.000046 / 2.000000 / 0.000101
Energy / uncoupling protein / Ta.48.1.S1_at / 3.249010 / 0.000023 / 2.297397 / 0.000865
Membrane and transport / delta tonoplast intrinsic protein TIP2;3 / Ta.1082.1.S1_x_at / 6.498019 / 0.000020 / 4.924578 / 0.000020
Membrane and transport / delta-type tonoplast intrinsic protein / Ta.1082.3.S1_at / 10.556060 / 0.000068 / 4.594793 / 0.000023
Membrane and transport / delta-type tonoplast intrinsic protein / Ta.1082.3.S1_x_at / 8.000000 / 0.000023 / 4.000000 / 0.000030
Membrane and transport / Delta-type tonoplast intrinsic protein / Ta.1082.2.S1_x_at / 6.062866 / 0.000023 / 3.482202 / 0.000030
Membrane and transport / delta-type tonoplast intrinsic protein /// delta tonoplast intrinsic protein TIP2;2 /// delta tonoplast intrinsic protein TIP2;3 / Ta.1082.1.S1_a_at / 5.278032 / 0.000020 / 4.924578 / 0.000020
Membrane and transport / Gamma-type tonoplast intrinsic protein / TaAffx.124475.1.A1_at / 2.639016 / 0.000052 / 4.594793 / 0.000052
Membrane and transport / Plasma membrane intrinsic protein 1 (PIP1) / Ta.1013.1.S1_at / 2.000000 / 0.000020 / 3.249010 / 0.000020
Membrane and transport / Plasma membrane intrinsic protein 3 / Ta.4950.2.S1_s_at / 2.462289 / 0.000307 / 12.996040 / 0.000023
Membrane and transport / Plasma membrane intrinsic protein 3 / Ta.23833.3.S1_x_at / 2.000000 / 0.000020 / 2.639016 / 0.000020
Membrane and transport / Plasma membrane intrinsic protein 3 / Ta.28728.1.S1_at / 4.594793 / 0.000020 / 3.482202 / 0.000020
Membrane and transport / Plasma membrane intrinsic protein 3 / Ta.28728.1.S1_x_at / 4.594793 / 0.000046 / 4.000000 / 0.000020
Membrane and transport / Plasma membrane intrinsic protein 3 / Ta.9372.1.S1_at / 4.594793 / 0.000020 / 2.639016 / 0.000020
Membrane and transport / Plasma membrane intrinsic protein 3 / Ta.9372.1.S1_x_at / 4.924578 / 0.000020 / 3.031433 / 0.000020
Membrane and transport / Sec61p / Ta.1997.1.S1_at / 13.928810 / 0.000020 / 13.928810 / 0.000020
Membrane and transport / Sec61p / Ta.1997.2.S1_a_at / 16.000000 / 0.000020 / 21.112130 / 0.000020
Membrane and transport / sugar transporter protein / Ta.4365.1.S1_at / 2.462289 / 0.000020 / 3.031433 / 0.000020
Membrane and transport / Voltage dependent anion channel (VDAC) / Ta.16669.1.S1_x_at / 3.482202 / 0.000189 / 6.062866 / 0.000346
Metabolism / cytosolic acetyl-CoA carboxylase / Ta.187.1.S1_at / 2.639016 / 0.000020 / 2.000000 / 0.000035
Metabolism / fatty acyl coA reductase / Ta.14149.1.S1_at / 3.031433 / 0.000020 / 4.000000 / 0.000020
Metabolism / Fatty acyl coA reductase / Ta.9528.1.A1_at / 3.732132 / 0.000020 / 5.278032 / 0.000030
Metabolism / Glutamine-dependent asparagine synthetase / Ta.2690.1.S1_at / 14.928530 / 0.000020 / 29.857060 / 0.000020
Metabolism / ornithine/acetylornithine aminotransferase / Ta.4834.1.S1_at / 12.996040 / 0.000020 / 21.112130 / 0.000020
Metabolism / Plastid glutamine synthetase isoform GS2a / TaAffx.54250.1.S1_at / 6.964405 / 0.000020 / 14.928530 / 0.000020
Metabolism / Putative 1,3-beta-glucan synthase 2 / TaAffx.92872.1.S1_at / 2.462289 / 0.000147 / 2.639016 / 0.000114
Metabolism / Putative 1,3-beta-glucan synthase 8 / Ta.1995.3.S1_a_at / 2.828427 / 0.000020 / 2.462289 / 0.000020
Metabolism / Starch branching enzyme 2 / Ta.3412.2.S1_a_at / 2.143547 / 0.000035 / 2.000000 / 0.000020
Protein destination and storage / aspartic proteinase / Ta.24959.1.S1_at / 2.828427 / 0.000020 / 2.297397 / 0.000020
Protein destination and storage / cathepsin B / Ta.11.2.S1_a_at / 3.249010 / 0.000020 / 3.031433 / 0.000020
Protein destination and storage / cathepsin B / Ta.11.3.S1_a_at / 2.297397 / 0.000020 / 2.143547 / 0.000020
Protein destination and storage / protein disulfide isomerase / Ta.796.1.S1_x_at / 4.924578 / 0.000030 / 3.732132 / 0.000030
Protein destination and storage / protein disulfide isomerase 2 precursor / Ta.74.1.S1_at / 6.062866 / 0.000020 / 4.924578 / 0.000020
Protein destination and storage / RUB1-conjugating enzyme / TaAffx.16897.1.A1_s_at / 2.828427 / 0.000020 / 2.462289 / 0.000020
Protein synthesis / Acidic ribosomal protein / Ta.14467.2.S1_a_at / 2.828427 / 0.000020 / 2.462289 / 0.000020
Protein synthesis / Acidic ribosomal protein / Ta.14467.3.S1_a_at / 3.249010 / 0.000020 / 3.732132 / 0.000020
Protein synthesis / Acidic ribosomal protein P2 / Ta.4035.3.S1_at / 2.639016 / 0.000020 / 3.732132 / 0.000020
Protein synthesis / QM / Ta.7999.1.S1_at / 2.462289 / 0.000020 / 3.031433 / 0.000020
Protein synthesis / QM / Ta.7999.2.S1_a_at / 2.639016 / 0.000020 / 2.639016 / 0.000020
Protein synthesis / QM / Ta.9113.1.S1_a_at / 3.249010 / 0.000020 / 2.639016 / 0.000020
Protein synthesis / QM / Ta.9113.3.S1_at / 3.249010 / 0.000020 / 2.297397 / 0.000060
Protein synthesis / QM / Ta.9113.3.S1_x_at / 3.249010 / 0.000060 / 2.828427 / 0.000020
Protein synthesis / Reversibly glycosylated polypeptide / Ta.135.2.S1_at / 2.143547 / 0.000040 / 3.482202 / 0.000020
Protein synthesis / Ribosomal protein L10A / Ta.28207.1.S1_at / 2.143547 / 0.000346 / 2.297397 / 0.000052
Protein synthesis / Ribosomal protein L3 (RPL3) mRNA, RPL3-A2 allele / Ta.13160.1.S1_at / 73.516690 / 0.000088 / 6.062866 / 0.000020
Protein synthesis / Ribosomal protein L3 (RPL3) mRNA, RPL3-A2 allele / Ta.28337.2.S1_x_at / 5.278032 / 0.000020 / 8.574188 / 0.000020
Protein synthesis / Ribosomal protein L3 (RPL3) mRNA, RPL3-A2 allele / Ta.29640.1.S1_x_at / 8.000000 / 0.000040 / 6.062866 / 0.000020
Protein synthesis / Ribosomal protein L39 / Ta.20974.1.S1_x_at / 2.143547 / 0.000023 / 2.000000 / 0.000020
Protein synthesis / Translation elongation factor 1 alpha-subunit / Ta.8304.1.S1_a_at / 9.189587 / 0.000020 / 2.143547 / 0.000020
Secondary metabolism / Allene oxide synthase / Ta.13362.1.S1_at / 2.143547 / 0.000273 / 9.189587 / 0.000020
Secondary metabolism / caffeic acid O-methyltransferase / Ta.336.1.S1_x_at / 3.031433 / 0.000020 / 5.278032 / 0.000020
Secondary metabolism / CCoAMT protein / Ta.9320.1.S1_at / 4.924578 / 0.000214 / 27.857620 / 0.000020
Secondary metabolism / CCoAMT protein / Ta.9320.1.S1_x_at / 8.000000 / 0.000023 / 34.296750 / 0.000020
Secondary metabolism / Phosphoethanolamine methyltransferase / TaAffx.86898.1.S1_at / 18.379170 / 0.000027 / 29.857060 / 0.000020
Secondary metabolism / S-adenosylmethionine decarboxylase precursor / Ta.2631.1.S1_at / 2.639016 / 0.000020 / 3.249010 / 0.000020
Secondary metabolism / S-adenosylmethionine decarboxylase precursor / Ta.3706.1.S1_at / 3.031433 / 0.000020 / 2.297397 / 0.000020
Signal transduction / Adenine phosphoribosyltransferase / Ta.570.1.A1_at / 2.462289 / 0.000020 / 2.639016 / 0.000020
Signal transduction / ADP-glucose pyrophosphorylase / Ta.4366.1.A1_at / 4.594793 / 0.000035 / 4.594793 / 0.000030
(continued on next page)

Supplementary Table 2(continued from proceeding page)

Functional category / Putative function / Probe set ID / Incompatible / Compatible
Fold change / P-Values / Fold change / P-Values
Signal transduction / ADP-glucose pyrophosphorylase / Ta.4366.2.S1_at / 3.732132 / 0.000020 / 3.732132 / 0.000020
Signal transduction / Calreticulin-like protein / Ta.22317.1.S1_at / 2.462289 / 0.000020 / 2.828427 / 0.000020
Signal transduction / calreticulin-like protein / Ta.22317.1.S1_s_at / 3.732132 / 0.000020 / 4.594793 / 0.000020
Signal transduction / Calreticulin-like protein / Ta.3324.1.S1_at / 2.828427 / 0.000020 / 2.462289 / 0.000020
Signal transduction / Cdpk1 protein / TaAffx.7177.1.S1_s_at / 2.297397 / 0.000020 / 6.062866 / 0.000020
Signal transduction / Cdpk1 protein / Ta.27751.5.S1_at / 18.379170 / 0.000020 / 19.698310 / 0.000020
Signal transduction / Cdpk1 protein / Ta.30790.1.S1_a_at / 3.031433 / 0.000020 / 2.462289 / 0.000020
Signal transduction / Cdpk1 protein / Ta.30790.2.S1_at / 3.031433 / 0.000020 / 2.462289 / 0.000020
Signal transduction / Cdpk1 protein / Ta.6371.1.A1_at / 3.031433 / 0.000189 / 2.639016 / 0.000020
Signal transduction / Cdpk1 protein / TaAffx.7177.1.S1_x_at / 3.031433 / 0.000020 / 4.924578 / 0.000020
Signal transduction / Guanylyl cyclase / Ta.5098.1.S1_a_at / 8.574188 / 0.000020 / 8.574188 / 0.000020
Signal transduction / Guanylyl cyclase / Ta.5098.1.S1_at / 2.297397 / 0.000130 / 3.732132 / 0.000020
Signal transduction / Guanylyl cyclase / Ta.5098.2.A1_at / 10.556060 / 0.000020 / 6.062866 / 0.000020
Signal transduction / MAP kinase homolog / Ta.25666.1.A1_at / 12.996040 / 0.000027 / 9.849155 / 0.000020
Signal transduction / MAP kinase homolog / Ta.25666.1.A1_x_at / 8.000000 / 0.000020 / 6.964405 / 0.000020
Signal transduction / MAP kinase homolog / TaAffx.67941.1.S1_at / 3.249010 / 0.000020 / 4.924578 / 0.000040
Signal transduction / Mitogen-activated protein kinase / Ta.12668.1.A1_at / 2.143547 / 0.000020 / 2.000000 / 0.000020
Signal transduction / Multiple inositol polyphosphate phosphatase PhyIIa1 / Ta.5140.1.S1_at / 3.732132 / 0.000027 / 3.249010 / 0.000020
Signal transduction / protein kinase / Ta.2551.1.S1_at / 4.594793 / 0.000241 / 4.594793 / 0.000020
Signal transduction / Rab protein / TaAffx.128555.1.S1_at / 5.278032 / 0.000101 / 34.296750 / 0.000030
Signal transduction / Wpk4 protein kinase / Ta.12517.1.S1_at / 2.143547 / 0.000020 / 2.143547 / 0.000020
Transcription / Cold-responsive protein / Ta.18487.1.S1_x_at / 4.287094 / 0.000020 / 6.498019 / 0.000020
Transcription / cold-responsive protein / Ta.2148.1.S1_x_at / 6.062866 / 0.000020 / 6.062866 / 0.000020
Transcription / DEAD-box ATPase-RNA-helicase / Ta.9622.2.S1_x_at / 2.000000 / 0.000101 / 2.000000 / 0.000088
Transcription / High mobility group protein / Ta.4508.3.S1_at / 2.639016 / 0.000020 / 5.278032 / 0.000020
Transcription / High mobility group protein / Ta.6247.2.S1_at / 5.278032 / 0.000068 / 2.000000 / 0.000020
Transcription / High mobility group protein / Ta.6247.3.S1_x_at / 4.924578 / 0.000020 / 2.143547 / 0.000020
Transcription / High mobility group protein / Ta.21335.1.S1_a_at / 2.462289 / 0.000020 / 3.732132 / 0.000020
Transcription / High mobility group protein / Ta.21335.1.S1_at / 5.656854 / 0.000020 / 4.287094 / 0.000492
Transcription / High mobility group protein / Ta.21335.2.A1_x_at / 5.278032 / 0.000020 / 6.964405 / 0.000020
Transcription / High mobility group protein / Ta.4508.1.S1_a_at / 2.639016 / 0.000020 / 2.143547 / 0.000020
Transcription / High mobility group protein / Ta.4508.3.S1_a_at / 2.462289 / 0.000020 / 2.639016 / 0.000020
Transcription / High mobility group protein / Ta.6247.1.A1_x_at / 3.031433 / 0.000020 / 2.462289 / 0.000389
Transcription / High mobility group protein / TaAffx.119486.1.S1_at / 2.462289 / 0.000020 / 4.287094 / 0.000020
Transcription / Putative high mobility group protein / TaAffx.80336.2.S1_x_at / 16.000000 / 0.000020 / 48.502930 / 0.000020
Transcription / Putative high mobility group protein / Ta.15042.1.A1_at / 7.464264 / 0.000046 / 11.313710 / 0.000060
Unclassified / AML15 / Ta.622.1.S1_at / 4.287094 / 0.000020 / 2.143547 / 0.000020
Unclassified / AML15 / Ta.622.3.S1_a_at / 4.000000 / 0.000020 / 2.828427 / 0.000020
Unclassified / gigantea / Ta.10215.1.S1_at / 2.000000 / 0.000020 / 3.031433 / 0.000020
Unclassified / S-adenosyl-L-homocysteine hydrolase / Ta.1258.2.S1_x_at / 2.143547 / 0.000020 / 2.297397 / 0.000020
Unclassified / S-adenosyl-L-homocysteine hydrolase / TaAffx.26191.1.S1_at / 4.000000 / 0.000307 / 2.297397 / 0.000307
Unclassified
Unclassified / secretory protein
secretory protein / Ta.231.1.S1_at
Ta.231.1.S1_x_at / 8.000000
14.928530 / 0.000023
0.000020 / 16.000000
7.464264 / 0.000020
0.000020

Supplementary Table 3 Incompatible-specific transcripts induced by Blumeria graminis f.sp. tritici

Functional category / Putative function / Probe set ID / Fold change / P-Values
Cell growth/division / Cyc07 / Ta.19321.1.S1_at / 2.639016 / 0.000114
Cell structure / Actin / Ta.1868.2.A1_at / 2.297397 / 0.000068
Cell structure / Actin-like protein / Ta.23142.9.S1_at / 2.000000 / 0.000147
Cell structure / beta-tubulin 5 / Ta.214.1.S1_at / 2.143547 / 0.000020
Cell structure / beta-tubulin 5 / Ta.214.1.S1_x_at / 2.297397 / 0.000068
Cell structure / Beta-tubulin 5 / Ta.214.2.A1_at / 3.732132 / 0.000241
Cell structure / Histone H2B / Ta.10189.3.S1_a_at / 2.000000 / 0.000346
Cell structure / histone H1 WH1B.1 / Ta.27790.1.S1_s_at / 3.249010 / 0.00002
Cell structure / Protein H2A / Ta.10329.23.S1_at / 3.031433 / 0.000214
Cell structure / Protein H2A / Ta.10329.40.S1_x_at / 2.828427 / 0.000114
Cell structure / Protein H2A / Ta.28400.1.S1_at / 2.462289 / 0.000027
Cell structure / Protein H2A / Ta.28400.1.S1_x_at / 2.639016 / 0.000023
Cell structure / Protein H2A / Ta.3455.1.S1_at / 2.639016 / 0.000273
Cell structure / Protein H2B-8 / Ta.6467.2.A1_at / 2.639016 / 0.00013
Cell structure / Protein H2B-8 / Ta.7378.2.S1_x_at / 4.000000 / 0.000438
Cell structure / Protein H2B-8 / Ta.7378.30.S1_x_at / 3.249010 / 0.000214
Cell structure / Protein H2A / TaAffx.55592.1.S1_at / 2.000000 / 0.000389
Cell structure / Protein H2B-8 / TaAffx.64770.1.A1_at / 2.828427 / 0.000214
Cell structure / Similar to histone H1 mRNA sequence / Ta.24171.1.S1_s_at / 2.143547 / 0.000088
Disease/defence / alternative oxidase / Ta.233.1.S1_at / 2.828427 / 0.000088
Disease/defence / Alternative oxidase / Ta.28131.1.S1_at / 3.732132 / 0.000020
Disease/defence / Alternative oxidase / Ta.28131.1.S1_x_at / 4.000000 / 0.000020
Disease/defence / alternative oxidase / Ta.3379.1.S1_at / 4.000000 / 0.000020
Disease/defence / Beta 1,3-glucanase / Ta.303.1.S1_x_at / 2.000000 / 0.000040
Disease/defence / Beta-1,3-glucanase / Ta.225.1.S1_at / 3.732132 / 0.000078
Disease/defence / Dehydroascorbate reductase / Ta.5105.1.S1_at / 2.297397 / 0.000020
Disease/defence / gamma-glutamylcysteine synthetase / Ta.5796.3.S1_a_at / 3.732132 / 0.000030
Disease/defence / Germin protein precursor / Ta.27477.1.S1_at / 4.000000 / 0.000020
Disease/defence / Germin protein precursor / Ta.27477.1.S1_x_at / 4.287094 / 0.000020
Disease/defence / Germin-like protein / Ta.18878.1.S1_at / 25.992080 / 0.000438
Disease/defence / glutaredoxin / Ta.1071.1.S1_x_at / 2.297397 / 0.000020
Disease/defence / Glutathione transferase / Ta.26230.1.S1_at / 6.062866 / 0.000189
Disease/defence / Glutathione transferase / Ta.26230.1.S1_x_at / 16.000000 / 0.000618
Disease/defence / Glutathione transferase / Ta.26230.2.S1_at / 3.482202 / 0.000389
Disease/defence / Glutathione transferase / Ta.3418.2.S1_at / 3.031433 / 0.000020
Disease/defence / glutathione synthetase / Ta.4355.1.S1_at / 2.000000 / 0.000618
Disease/defence / Glutathione-S-transferase 28e45 / Ta.24948.1.S1_at / 4.924578 / 0.000071
Disease/defence / Heat shock protein 16.9 / Ta.6262.2.S1_a_at / 2.639016 / 0.000020
Disease/defence / Heat shock protein 16.9 / Ta.6262.2.S1_x_at / 3.031433 / 0.000023
Disease/defence / HSP80-2 / Ta.11148.1.S1_at / 3.249010 / 0.000023
Disease/defence / Lipid transfer protein 3 / Ta.13693.1.S1_x_at / 5.656854 / 0.000214
Disease/defence / Lipid transfer protein 3 / Ta.3851.1.S1_a_at / 2.000000 / 0.000023
Disease/defence / Lipid transfer protein 3 / Ta.3851.1.S1_x_at / 2.143547 / 0.000020
Disease/defence / Lipid transfer protein 3 / Ta.3851.2.A1_at / 2.143547 / 0.000030
Disease/defence / Lipid transfer protein 3 / Ta.9064.1.S1_x_at / 4.594793 / 0.000130
Disease/defence / Lipid transfer protein 3 / Ta.9064.2.S1_s_at / 2.143547 / 0.000078
Disease/defence / Lipid transfer protein 3 / Ta.9644.1.S1_at / 2.000000 / 0.000020
Disease/defence / Lipid transfer protein 3 / TaAffx.111465.1.S1_at / 2.143547 / 0.000046
Disease/defence / Metallothionein-like protein / Ta.28750.1.S1_x_at / 2.000000 / 0.000241
Disease/defence / Metallothionein-like protein / Ta.6642.3.S1_a_at / 2.000000 / 0.000020
Disease/defence / N-1 mRNA for cytochrome P450 / Ta.174.1.S1_at / 2.000000 / 0.000030
Disease/defence / oxalate oxidase / Ta.24453.1.S1_s_at / 3.031433 / 0.000346
Disease/defence / Pathogenisis-related protein 1.2 / Ta.14437.1.S1_at / 2.639016 / 0.000020
Disease/defence / Pathogenisis-related protein 1.2 / TaAffx.31943.1.S1_at / 2.000000 / 0.000035
Disease/defence / polyphenol oxidase / TaAffx.115935.1.S1_x_at / 3.249010 / 0.000346
Disease/defence / pSBGer2 protein / Ta.28782.1.S1_x_at / 4.924578 / 0.000438
Disease/defence / pSBGer3 protein / Ta.27750.1.S1_at / 5.656854 / 0.000020
Disease/defence / pSBGer4 protein / Ta.22967.1.S1_x_at / 3.249010 / 0.000020
Disease/defence / thioredoxin H / Ta.1251.1.S1_at / 2.297397 / 0.000020
Disease/defence / Thiosulfate transferase / Ta.2761.1.S1_at / 2.143547 / 0.000035
Disease/defence / Type 1 non-specific lipid transfer protein precursor / Ta.1385.3.S1_x_at / 2.297397 / 0.000020
Disease/defence / Type 1 non-specific lipid transfer protein precursor / Ta.1385.4.S1_at / 3.249010 / 0.000020
Disease/defence / Type 1 non-specific lipid transfer protein precursor / Ta.1385.4.S1_x_at / 2.828427 / 0.000020
Disease/defence / upregulated following infection by Puccinia (rust) species / Ta.18775.1.S1_at / 2.639016 / 0.000030
Disease/defence / Upregulated following infection by Puccinia (rust) species / Ta.9136.3.S1_a_at / 2.297397 / 0.000068
Disease/defence / Wali7 protein / Ta.6652.1.S1_at / 2.639016 / 0.000020
Disease/defence / Wali7 protein / Ta.6652.2.A1_a_at / 2.297397 / 0.000027
Disease/defence / Wgluc5 protein / Ta.3828.2.S1_x_at / 2.297397 / 0.000492
Disease/defence / Wgluc5 protein / Ta.3828.3.A1_a_at / 2.828427 / 0.000020
Disease/defence / wgluc5 protein / Ta.3828.3.A1_x_at / 2.639016 / 0.000020
(continued on next page)

Fold Change cut-off of ≥2.0

P-values threshold ≤0.001

Supplementary Table 3 (continued from proceeding page)

Functional category / Putative function / Probe set ID / Fold change / P-Values
Disease/defence / Winv2 protein / Ta.5539.3.A1_x_at / 3.031433 / 0.000020
Disease/defence / xylanase inhibitor TAXI-I / Ta.20434.2.S1_x_at / 2.000000 / 0.000088
Energy / Ald protein / Ta.12733.1.S1_at / 2.297397 / 0.000023
Energy / Ald protein / Ta.304.2.S1_x_at / 2.000000 / 0.000020
Energy / Ald protein / Ta.304.3.S1_at / 3.249010 / 0.000020
Energy / Ald protein / Ta.304.3.S1_x_at / 3.249010 / 0.000020
Energy / Ald protein / Ta.304.4.S1_at / 2.462289 / 0.000020
Energy / Cytosolic glyceraldehyde-3-phosphate dehydrogenase GAPDH / Ta.10508.2.S1_a_at / 2.000000 / 0.000023
Energy / ferredoxin / Ta.2794.1.S1_at / 2.639016 / 0.000020
Energy / Fructan:fructan 1-fructosyltransferase / Ta.6008.3.S1_a_at / 2.000000 / 0.000023
Energy / HBP-1b / Ta.24199.1.S1_a_at / 10.556060 / 0.000027
Energy / hemoglobin Hb1 / Ta.5610.1.S1_at / 6.964405 / 0.000273
Energy / methylmalonate semialdehyde dehydrogenase / Ta.2907.1.S1_at / 3.732132 / 0.000020
Energy / Ribulose-1,5-bisphosphate carboxylase activase / Ta.21403.3.S1_a_at / 2.000000 / 0.000060
Energy / Ribulose-1,5-bisphosphate carboxylase activase / Ta.5210.2.S1_at / 6.964405 / 0.000020
Energy / Small subunit / Ta.20195.1.S1_at / 2.000000 / 0.000167
Energy / Small subunit / Ta.20195.1.S1_x_at / 2.639016 / 0.000214
Energy / Small subunit / Ta.22882.2.A1_at / 2.297397 / 0.000020
Energy / Small subunit / Ta.9789.1.S1_a_at / 2.000000 / 0.000114
Energy / sucrose synthase type I / Ta.92.1.S1_s_at / 4.594793 / 0.000020
Energy / sucrose-phosphate synthase 9 / Ta.20568.1.S1_at / 2.143547 / 0.000020
Membrane andtransport / Plasma membrane protein / Ta.8193.1.A1_at / 3.031433 / 0.000052
Membrane and transport / ammonium transporter AMT2.1 / Ta.27506.1.S1_at / 2.462289 / 0.000020
Membrane and transport / glucose-6-phosphate/phosphate translocator / Ta.7450.1.S1_at / 2.297397 / 0.000020
Membrane and transport / Glucose-6-phosphate/phosphate translocator / Ta.7450.1.S1_x_at / 2.297397 / 0.000020
Membrane and transport / Voltage dependent anion channel (VDAC) / Ta.22.1.S1_at / 2.000000 / 0.000020
Metabolism / Cytosolic acetyl-CoA carboxylase / Ta.9549.2.S1_s_at / 2.828427 / 0.000020
Metabolism / Cytosolic acetyl-CoA carboxylase / Ta.9549.3.S1_x_at / 2.462289 / 0.000078
Metabolism / Delta1-pyrroline-5-carboxylate synthetase / Ta.24918.1.S1_at / 2.828427 / 0.000020
Metabolism / Fertility relative protein RF1 / Ta.5541.2.S1_at / 2.143547 / 0.000023
Metabolism / Fertility relative protein RF1 / Ta.5541.2.S1_x_at / 2.000000 / 0.000214
Metabolism / proline-rich protein / Ta.14168.1.S1_at / 2.828427 / 0.000020
Metabolism / Putative 1,3-beta-glucan synthase 8 / Ta.1995.1.S1_at / 2.828427 / 0.000020
Metabolism / Putative 1,3-beta-glucan synthase 2 / Ta.6775.2.A1_a_at / 2.639016 / 0.000030
Metabolism / pyrroline-5-carboxylate reductase / Ta.591.1.S1_at / 2.828427 / 0.000068
Metabolism / Root abundant protein / Ta.1397.1.A1_at / 2.143547 / 0.000052
Metabolism / triacylglycerol lipase / Ta.9162.1.S1_at / 2.000000 / 0.000020
Protein destination and storage / 20S proteasome beta 5 subunit / Ta.14579.1.S1_at / 2.143547 / 0.000052
Protein destination and storage / Alpha/beta-gliadin precursor / Ta.3840.1.S1_at / 2.462289 / 0.000774
Protein destination and storage / Cathepsin B / Ta.11.2.S1_x_at / 2.297397 / 0.000966
Protein destination and storage / Immature spike ubiquitin-conjugating enzyme 2 / Ta.28850.1.S1_at / 2.000000 / 0.000020
Protein destination and storage / peptidylprolyl isomerase / Ta.639.1.S1_at / 9.189587 / 0.000035
Protein destination and storage / Pre-alpha-/beta-gliadin A-II / Ta.6111.1.S1_at / 3.249010 / 0.000020
Protein destination and storage / Pre-alpha-/beta-gliadin A-II / Ta.6111.1.S1_x_at / 3.031433 / 0.000020
Protein destination and storage / Ubiquitin activating enzyme E1 (UBA1) gene / Ta.1905.2.A1_x_at / 2.000000 / 0.000023
Protein destination and storage / Ubiquitin carrier protein / Ta.5314.1.S1_x_at / 2.000000 / 0.000030
Protein destination and storage / Ubiquitin carrier protein / Ta.5314.2.S1_a_at / 2.462289 / 0.000035
Protein destination and storage / Ubiquitin carrier protein / Ta.5314.3.S1_a_at / 2.000000 / 0.000068
Protein destination and storage / Ubiquitin-conjugating enzyme / Ta.9458.3.S1_x_at / 2.462289 / 0.000035
Protein synthesis / 40S ribosomal protein S9 / Ta.28748.1.S1_at / 2.143547 / 0.000020
Protein synthesis / 40S ribosomal protein S9 / Ta.28748.2.A1_at / 2.000000 / 0.000030
Protein synthesis / 40S ribosomal protein S9 / Ta.28748.3.S1_a_at / 2.828427 / 0.000020
Protein synthesis / 40S ribosomal protein S9 / Ta.28748.3.S1_x_at / 2.639016 / 0.000020
Protein synthesis / 5a2 protein / Ta.2022.2.S1_at / 2.297397 / 0.000020
Protein synthesis / Acidic ribosomal protein / Ta.14467.2.S1_at / 2.639016 / 0.000060
Protein synthesis / Elongation factor-1 alpha / Ta.28827.1.S1_at / 4.287094 / 0.000273
Protein synthesis / Ribosomal protein L10A / Ta.15844.1.S1_at / 2.828427 / 0.000966
Protein synthesis / Ribosomal protein S7 / Ta.5131.1.S1_at / 2.297397 / 0.000020
Protein synthesis / Translation elongation factor 1 alpha-subunit / Ta.8304.1.S1_x_at / 6.964405 / 0.000020
Protein synthesis / Translationally controlled tumor protein / Ta.28433.1.S1_at / 2.143547 / 0.000020
Secondary metabolism / betaine-aldehyde dehydrogenase / Ta.435.1.S1_at / 2.297397 / 0.000147
Secondary metabolism / delta-24-sterol methyltransferase / Ta.2251.1.S1_at / 2.462289 / 0.000020
Secondary metabolism / gibberellin 20-oxidase / Ta.141.1.S1_at / 16.000000 / 0.000618
Secondary metabolism / gibberellin 20-oxidase / Ta.141.1.S1_x_at / 13.928810 / 0.000035
Secondary metabolism / Obtusifoliol 14-demehylase (cyp51 gene) / Ta.19603.1.S1_s_at / 2.462289 / 0.000020
Secondary metabolism / Obtusifoliol 14-demehylase (cyp51 gene) / Ta.9296.2.S1_a_at / 2.297397 / 0.000020
Secondary metabolism / Phosphoethanolamine methyltransferase / Ta.24118.1.S1_at / 2.462289 / 0.000020
Signal transduction / 14-3-3 protein / Ta.22434.1.S1_at / 2.297397 / 0.000020
Signal transduction / 14-3-3 protein / Ta.22434.1.S1_x_at / 2.143547 / 0.000020
Signal transduction / Cdpk1 protein / Ta.30790.1.S1_at / 2.828427 / 0.000020
Signal transduction / CesA protein / Ta.9507.2.S1_at / 8.574188 / 0.000044
(continued on next page)

Supplementary Table 3(continued from proceeding page)

Functional category / Putative function / Probe set ID / Fold change / P-Values
Signal transduction / Geranylgeranylated protein ATGP1 / Ta.7765.1.A1_at / 9.849155 / 0.000692
Signal transduction / Isopentenyl pyrophosphate:dimethyllallyl pyrophosphate isomerase-like mRNA, partial sequence / Ta.14572.1.S1_at / 2.143547 / 0.000020
Signal transduction / Phosphoglycerate kinase (AA 1 - 401) / TaAffx.3058.1.S1_at / 3.732132 / 0.000865
Signal transduction / Small GTP-binding protein / Ta.6227.1.S1_at / 2.297397 / 0.000020
Signal transduction / Tousled-like protein kinase / TaAffx.120000.2.S1_s_at / 2.639016 / 0.000020
Signal transduction / YRK1 / Ta.22638.1.A1_at / 3.249010 / 0.000035
Signal transduction / zmMKP1 protein / Ta.14820.1.S1_at / 2.297397 / 0.000046
Transcription / BHLH transcription factor / Ta.497.1.S1_x_at / 2.000000 / 0.000027
Transcription / dehydration responsive element binding protein / Ta.5298.1.A1_at / 3.482202 / 0.000307
Transcription / EREBP/AP2 type transcription factor / Ta.12741.1.S1_s_at / 3.732132 / 0.000020
Transcription / Ethylene-responsive element binding protein 2 / Ta.8281.1.S1_at / 2.639016 / 0.000078
Transcription / High mobility group protein / Ta.23402.1.S1_at / 2.000000 / 0.000023
Transcription / High mobility group protein / Ta.27589.1.S1_at / 2.000000 / 0.000020
Transcription / histone acetyltransferase HAT1 / Ta.5414.1.S1_at / 2.000000 / 0.000020
Transcription / MRNA transport factor / Ta.5125.1.S1_at / 3.482202 / 0.000060
Transcription / MRNA transport factor / Ta.5125.2.A1_at / 2.297397 / 0.000147
Transcription / MRNA transport factor / Ta.5125.3.S1_at / 11.313710 / 0.000101
Unclassified / amylogenin / Ta.134.1.S1_at / 2.000000 / 0.000020
Unclassified / At1G21900 protein / Ta.22817.4.S1_at / 2.462289 / 0.000020
Unclassified / O-acetylserine (thiol) lyase / Ta.1053.2.S1_x_at / 2.297397 / 0.000273
Unclassified / p0552F09.19 protein / Ta.29618.1.S1_at / 2.297397 / 0.000052
Unclassified / Profilin / Ta.28625.1.A1_at / 2.828427 / 0.000052
Unclassified / S-adenosyl-L-homocysteine hydrolase / Ta.20449.3.S1_a_at / 2.143547 / 0.000020

Supplementary Table 4 Compatible-specific transcripts infected by Blumeria graminis f.sp. tritici