Supplementary Table1 List of Newly Cloned Tomato ACE Fragments Isolated Using Cdna-AFLP

Supplementary Table1 List of newly cloned tomato ACE fragments isolated using cDNA-AFLP

AFLP Frag-ment / GenBank Accession Number / Size (bp) / Matching AFLP Fragment Type I a / Matching AFLP Fragment Type II b / Matching ART Fragments c / HR-induced
or -repressed d / Functional Class / Top Homology (DFCI/SGN/NCBI) e / E value
(DFCI/
SGN Blastn
/NCBI
Blastx) / Length
of sequence match (%) / Identities (%) between the matched sequences
Avr9/Cf9 / Avr4/Cf4
147 / EL645744 / 111 / ＋＋＋ / ＋＋＋ / Metabolism / Hexose transporter (TC169872) / 1.2e-16 / 111/111
(100%) / 106/111 (95%)
157 / EL645745 / 154 / ＋＋ / ＋＋ / Miscellaneous / ATP-dependent Clp protease ATP-binding subunit clpAhomologue CD4A, chloroplast precursor (TC170921) / 2.9e-28 / 154/154
(100%) / 153/154 (99%)
160 / EL645746 / 162 / ＋＋＋ / ＋＋＋ / Metabolism / Prephenate dehydrogenase family protein (Arogenatedehydrogenase isoform 2)(EC1.3.1.43)(TC173005) / 5.9e-31 / 162/162
(100%) / 160/162 (98%)
161 / EL645747 / 228 / ＋＋ / ＋＋＋ / ns / Ns
171 / EL645748 / 171 / 172 / ＋＋＋＋ / ＋＋＋＋ / Transcription factor / Ethylene-responsive ER33 protein/BHLH transcription
factor (TC172024) / 9.5e-32 / 171/171
(100%) / 167/171 (97%)
172 / EL645749 / 170 / 171 / ＋＋＋ / ＋＋＋ / Transcription factor / Ethylene-responsive ER33 protein/BHLH transcription
factor (TC172024) / 8.7e-33 / 169/170
(99%) / 168/169 (99%)
186 / EL645750 / 125 / 498 / ＋ / ＋＋ / Defense-related / Acidic β-1,3-glucanase (β-1,3-endoglucanaseA)
(TC173376) / 1.0e-22 / 125/125
(100%) / 124/125 (99%)
187 / EL645751 / 127 / ＋＋ / ＋＋＋ / Defense-related / Pathogenesis-related protein P2
precursor (TC172742) / 5.2e-23 / 126/127
(99%) / 125/126 (99%)
210 / EL645752 / 250 / 350、209 / －－－ / －－－ / Metabolism / Short-chain dehydrogenase/reductase (SDR) family
protein /Alcohol dehydrogenase (TC170009) / 6.7e-50 / 250/250
(100%) / 246/250 (98%)
251 / EL645753 / 189 / － / －－－ / Photosynthesis / Magnesium-protoporphyrin IX monomethylester
[oxidative] cyclase chloroplast
precursor (TC186231) / 1.2e-27 / 187/189
(99%) / 182/190 (95%)
252a / EL645754 / 213 / 352 / ＋ / ＋＋＋ / Unknown / Expressed protein (SGN-U343506) / 5e-92 / 213/213
(100%) / 206/218 (94%)
258a / EL645755 / 207 / 358a / ＋ / ＋＋＋ / Protein synthesis / Chloroplast 30S ribosomal protein S8 (TC156596) / 7.6e-41 / 207/207
(100%) / 204/207 (98%)
259 / EL645756 / 280 / 328、330、357 / 292 / － / － / Photosynthesis / Ribulose bisphosphate carboxylase (RuBisCO) small
subunit 2A, chloroplast precursor (LESS5) (TC188927) / 2.4e-57 / 280/280
(100%) / 278/280 (99%)
261a / EL645757 / 221 / 261b / ＋ / ＋＋＋ / Defence-related / Xyloglucan-specific fungal endoglucanase inhibitor
protein /extracellular dermal glycoprotein
EDGP precursor-like(TC169927) / 1.7e-43 / 221/221
(100%) / 218/222 (98%)
261b / EL645758 / 225 / 261a / ＋ / ＋＋ / Defence-related / Xyloglucan-specific fungal endoglucanase inhibitor
protein / extracellular dermal glycoprotein EDGP
precursor-like (TC169927) / 2.8e-42 / 224/225
(99%) / 219/225 (97%)
263a / EL645759 / 390 / ＋＋ / ＋＋ / Unknown / Expressed protein (TC190719 ) / 6.3e-50 / 250/390
(64%) / 247/250 (98%)
264 / EL645760 / 152 / ＋＋ / ＋ / Miscellaneous / Tubby-like F-box protein (Tub family)
(SGN-U268337) / 5e-42 / 94/152
(61%) / 92/94 (97%)
266 / EL645761 / 109 / ＋ / ＋＋＋ / Defence-related / Polyphenol oxidase (TC176041) / 1.5e-19 / 109/109 (100%) / 109/109 (100%)
267 / EL645762 / 224 / ＋ / ＋＋＋ / Membrane fusion and secretion / Syntaxin 132 (AtSYP132)-like (TC181574) / 2.4e-44 / 223/224
(99%) / 220/223 (98%)
268 / EL645763 / 187 / ＋ / ＋＋＋ / Metabolism / Auxin and ethylene responsive GH3-like protein
(SGN-U323982) / 1e-100 / 187/187
(100%) / 186/187 (99%)
271 / EL645764 / 256 / 306、324、336、335、341、356 / ＋＋ / ＋ / Signalling-related / GTP binding protein family (SGN-U322215) / 1e-123 / 255/256
(99%) / 250/255 (98%)
272 / EL645765 / 304 / ＋ / ＋＋＋ / Metabolism / Acetyl-CoA synthetase (EC 6.2.1.1) (TC145533) / 8.9e-58 / 292/304
(96%) / 284/292 (97%)
273 / EL645766 / 298 / ＋＋ / ＋＋ / Membrane trafficking / Coatomer protein complex beta prime
(beta'-COP protein)(TC170440 ) / 1.8e-61 / 298/298
(100%) / 296/298 (99%)
274 / EL645767 / 223 / 314 / ＋ / ＋＋＋ / Unknown / Similar to GB|AAR92278.1|40823359|BT011242
At4g22580 [Arabidopsis thaliana] (TC146644 ) / 0.0051 / 186/223
(83%) / 119/194 (61%)
276 / EL645768 / 187 / ＋ / ＋＋＋ / Protein synthesis / 40S ribosomal protein S8 (TC172900) / 7.6e-37 / 185/187
(99%) / 185/185 (100%)
277 / EL645769 / 222 / ＋＋＋ / ＋＋ / Metabolism / 4-hydroxy-3-methylbut-2-en-1-yldiphosphate synthase
GcpE-like (TC185482) / 1.9e-44 / 222/222
(100%) / 222/223 (99%)
280 / EL645770 / 93 / ＋ / ＋＋＋ / Protein synthesis / Tomato 25S ribosomal RNA gene (TC5659 ) / 1.2e-14 / 93/93
(100%) / 90/93 (96%)
281 / EL645771 / 122 / ＋＋ / ＋＋＋ / Miscellaneous (Transporter) / Proton-dependent peptide transport family protein /
putative nitrate transporter NRT1-3 [Glycine max]
(SGN-U322832) / 6e-44 / 93/122
(76%) / 92/93 (98%)
283 / EL645772 / 206 / 285a / ＋＋＋＋ / ＋＋＋＋ / Defence-related / Acidic 26 kDa endochitinase precursor
(EC 3.2.1.14) (TC175574) / 3.4e-41 / 206/206
(100%) / 205/206 (99%)
284 / EL645773 / 275 / ＋＋＋ / ＋＋ / Unknown / EST of unknown function (tobacco|DV158104) / 2.8e-15 / 267/275
(97%) / 182/274 (66%)
285a / EL645774 / 209 / 283 / ＋ / ＋ / Defence-related / Acidic 26 kDa endochitinase precursor
(EC 3.2.1.14)(TC175574) / 8.7e-41 / 209/209
(100%) / 206/209 (98%)
285b / EL645775 / 169 / － / －－ / Miscellaneous (membrane targeting) / Putative C2 domain-containing protein (TC171387) / 6.4e-33 / 169/169
(100%) / 168/169 (99%)
286 / EL645776 / 243 / 307、315、320、231 / ＋ / ＋＋ / Transcriptional regulator / Zinc finger (C2H2 type) family DNA/RNA
binding protein(TC176057) / 1.2e-48 / 241/243
(99%) / 239/241 (99%)
288 / EL645777 / 272 / 295 / ＋＋ / ＋＋ / Unknown / EST of unknown function (pepper|BM061442) / 1.3e-43 / 272/272
(100%) / 246/274 (89%)
289 / EL645778 / 134 / －－－ / －－－ / Stress-responsive / A protein with weak
similarity GB|AAF61626.1|7384980|AF133717
stress enhanced protein 2
{Arabidopsis thaliana}(TC175900) / 4.8e-25 / 133/134
(99%) / 133/133 (100%)
290 / EL645779 / 225 / －－－ / －－－ / Metabolism / Glyceraldehyde-3-phosphate
dehydrogenase B subunit (TC184042) / 1.1e-45 / 225/225
(100%) / 224/225 (99%)
291 / EL645780 / 191 / －－－ / －－－ / Miscellaneous / Chaperone protein dnaJ-related
protein (SGN-U337301) / 3e-99 / 190/191
(99%) / 188/190 (98%)
292 / EL645781 / 231 / －－－ / －－－ / Metabolism / Nicotianamine synthase (S-adenosyl-L
-methionine:S-adenosyl-L-methionine:
S-adenosyl-methionine 3-amino-3-
carboxypropyltransferase) (Chloronerva)
(TC178772) / 6.4e-13 / 182/231
(79%) / 135/188 (71%)
295 / EL645782 / 271 / 288 / 288 / －－－ / －－－ / Unknown / EST of unknown function (pepper|BM061442) / 3.9e-47 / 271/271
(100%) / 250/271 (92%)
303 / EL645783 / 213 / －－－－ / －－－－ / Photosynthesis / Photosystem II reaction centre J protein-like
(potato|TC145009) / 4.2e-23 / 143/213 (67%) / 135/144 (93%)
304 / EL645784 / 180 / － / － / Photosynthesis / Photosystem I reaction centre subunit IX (PSI-J)
(TC190427 ) / 6.2e-12 / 84/180
(47%) / 82/85 (96%)
305 / EL645785 / 268 / － / － / Transcription / RNA polymerase beta subunit (TC169864) / 6.9e-54 / 268/268 (100%) / 266/268 (99%)
306 / EL645786 / 254 / 324、336、335、341、356、271 / －－ / －－ / Signalling-related / GTP binding protein-like (SGN-U322215) / 1e-129 / 253/254
(99%) / 250/253 (98%)
307 / EL645787 / 244 / 286、315、320、231 / － / － / Transcriptional regulator / Zinc finger (C2H2 type) family DNA/RNA
binding protein (TC176057) / 1.2e-48 / 241/244
(99%) / 239/241 (99%)
309 / EL645788 / 355 / －－ / －－－ / Metabolism / 2-oxoacid-dependentoxidase/
putativeflavonolsynthase-like protein
[Euphorbia esula] (SGN-U320189) / 0.0 / 355/355 (100%) / 355/355 (100%)
310 / EL645789 / 412 / 228 / 448、284 / －－ / －－－ / Protein synthesis / Solanum nigrum chloroplast tRNA-Ala, tRNA-Ile,
16S rRNA, tRNA-Val, rps12, rps7, ndhB genes
(TC147710) / 5.8e-85 / 412/412
(100%) / 407/414 (98%)
311 / EL645790 / 242 / －－－ / －－ / Transcription / RNA polymerase alpha subunit
(TC183795) / 2.7e-49 / 241/242
(99%) / 240/241 (99%)
314 / EL645791 / 223 / 274 / －－－ / －－－ / Unknown / Protein of unknown function
(TC140211 ) / 0.012 / 158/223
(71%) / 101/161 (62%)
315 / EL645792 / 244 / 286、307、320、231 / －－ / －－－ / Transcriptional regulator / Zinc finger (C2H2 type) family DNA/RNA
binding protein (TC176057) / 1.2e-48 / 241/244
(99%) / 239/241 (99%)
318 / EL645793 / 200 / 211、219、201b、220 / －－ / － / Defence-related / Carbonic anhydrase (EC 4.2.1.1)
(TC175780 ) / 3.2e-36 / 200/200
(100%) / 193/200 (96%)
320 / EL645794 / 239 / 286、307、315、231 / －－ / －－－ / Transcriptional regulator / Zinc finger (C2H2 type) family
DNA/RNA binding protein(TC176057) / 6.7e-44 / 236/239
(98%) / 233/242 (96%)
321a / EL645795 / 289 / －－ / －－－ / Signalling-related / Nodulin MtN21 family protein
(TC180584 )shuititongdaodanbai / 1.7e-59 / 288/289
(99%) / 286/288 (99%)
321b / EL645796 / 288 / －－ / －－－ / Miscellaneous (protein folding and transport) / FKBP-type peptidyl-prolyl cis-trans isomerase /
Trigger factor type chaperone family protein
[Arabidopsis thaliana] (TC184206) / 2.6e-58 / 287/288
(99%) / 283/287 (98%)
322a / EL645797 / 254 / 322c / －－ / －－ / Photosynthesis / Photosystem I assembly protein ycf4 (TC175491) / 1.3e-47 / 253/254 (99%) / 249/253 (98%)
322c / EL645798 / 245 / 322a / －－ / －－ / Photosynthesis / Photosystem I assembly protein ycf4 (TC175491) / 3.6e-45 / 244/245
(99%) / 241/252 (95%)
324 / EL645799 / 245 / 271、306、335、336、341、356 / －－ / －－－ / Signalling-related / GTP binding protein-related [Arabidopsis thaliana]
(SGN-U322215) / 1e-114 / 238/245
(97%) / 237/246 (96%)
325 / EL645800 / 71 / 81 / 18 / －－－ / －－－ / HR/Cell death-related / Hin1-like protein (TC174697) / 2.7e-08 / 71/71
(100%) / 70/74 (94%)
327 / EL645801 / 212 / －－－ / －－－ / Photosynthesis / Photosystem II reaction centre 6.1KD protein
(At2g30570/T6B20.8) (TC175602) / 1.5e-42 / 211/212
(99%) / 211/211 (100%)
328 / EL645802 / 285 / 357、330、259 / 292 / －－－ / －－－ / Photosynthesis / Ribulose bisphosphate carboxylase (RuBisCO)
small subunit 2A chloroplast precursor (TC188927) / 5.4e-57 / 284/285
(99%) / 279/284 (98%)
329 / EL645803 / 169 / －－－ / －－－ / Photosynthesis / Chlorophyll a-b binding protein 7 chloroplast
precursor(LHCI type II CAB-7) (TC173972) / 3.3e-33 / 169/169
(100%) / 169/169 (100%)
330 / EL645804 / 284 / 357、259、328 / 292 / －－－ / －－－ / Photosynthesis / Ribulose bisphosphate carboxylase (RuBisCO)
smallsubunit 2A chloroplast precursor (TC188927) / 6.7e-59 / 284/284
(100%) / 283/284 (99%)
331 / EL645805 / 368 / －－－ / －－－ / Transcriptional regulator / DEAD-box RNA helicase-like protein (TC185652) / 9.2e-78 / 368/368
(100%) / 366/368 (99%)
332 / EL645806 / 240 / －－－－ / －－－－ / Photosynthesis / Photosystem I reaction centre subunit IV A
chloroplast precursor (PSI-E A) (TC181349) / 1.8e-48 / 240/240
(100%) / 239/240 (99%)
333 / EL645807 / 332 / －－ / －－－－ / Metabolism / FAD-binding domain-containing protein, reticuline
oxidaseprecursor, Nectarin 5-like protein (SGN-U338453) / 1e-160 / 332/332
(100%) / 320/332 (96%)
334 / EL645808 / 349 / －－－ / －－－－ / Photosynthesis (thylakoid biogenesis) / PspA/IM30 family protein / membrane-associated
30 kDaprotein, chloroplast precursor (TC180402) / 2.7e-72 / 347/349 (99%) / 347/350 (99%)
335 / EL645809 / 253 / 271、306、324、336、341、356 / －－－－ / －－－－ / Signalling-related / GTP binding protein-related (SGN-U322215) / 1e-135 / 250/253
(99%) / 248/250 (99%)
336 / EL645810 / 254 / 271、306、324、335、341、356 / －－－ / －－－ / Signalling-related / GTP binding protein-related (SGN-U322215) / 1e-131 / 251/254 (98%) / 248/251 (98%)
337 / EL645811 / 236 / －－ / －－ / Unknown / Protein At3g15840 (TC171717) / 1.4e-47 / 236/236
(100%) / 235/237 (99%)
339 / EL645812 / 173 / －－－ / －－－ / Miscellaneous / Clp protease proteolytic subunit (TC137424) / 6.8e-32 / 173/173
(100%) / 167/173 (96%)
340 / EL645813 / 286 / －－－ / －－－ / Miscellaneous / ABC transporter ATPase (TC181255) / 2.1e-59 / 286/286
(100%) / 285/286 (99%)
341 / EL645814 / 247 / 271、306、324、335、336、356 / －－－ / －－－ / Signalling-related / GTP-binding family protein (SGN-U322215) / 1e-111 / 245/247
(99%) / 241/252 (95%)
342a / EL645815 / 220 / 342b / －－－ / －－－ / Photosynthesis / Photosystem I reaction centre subunit VI (PSI-H),
chloroplast precursor (SGN-U312346) / 6e-94 / 211/220
(96%) / 210/221 (95%)
342b / EL645816 / 231 / 342a / －－ / －－ / Photosynthesis / Photosystem I reaction centre subunit VI (PSI-H),
chloroplast precursor (SGN-U312346) / 1e-111 / 231/231
(100%) / 226/231 (97%)
343 / EL645817 / 249 / 454 / －－ / －－ / Miscallaneous (ATP synthesis coupled proton transport) / ATP synthase CF1 beta subunit (TC156713) / 5.3e-51 / 248/249
(99%) / 247/248 (99%)
344 / EL645818 / 156 / －－ / －－ / Defence-related / Methionine-rich arabinogalactan protein
(SGN-U313314) / 2e-32 / 156/156
(100%) / 144/156 (92%)
345 / EL645819 / 257 / －－－ / －－－ / Photosynthesis / Sulphur/Magnesium-chelatasesubunit
chlI chloroplastprecursor (Mg-protoporphyrin
IX chelatase) (TC178577) / 1.7e-52 / 257/257
(100%) / 255/257 (99%)
346 / EL645820 / 285 / 361a / ＋＋ / ＋＋ / Protein synthesis / Plastid ribosomal protein S10 precursor (TC172162) / 1.5e-58 / 285/285
(100%) / 283/285 (99%)
347 / EL645821 / 304 / －－ / －－－ / Protein synthesis / Chloroplast 30S ribosomal protein S20 (TC175570) / 1.4e-63 / 304/304 (100%) / 304/304 (100%)
348 / EL645822 / 184 / －－－ / －－－ / Photosynthesis / Tetratricopeptide repeat (TPR) domain containing
ferredoxin-like protein (TC181010) / 5.9e-36 / 184/184
(100%) / 183/184 (99%)
350 / EL645823 / 254 / 210、209 / －－－ / －－－ / Metabolism (respiration) / Short-chain dehydrogenase/reductase (SDR)
family protein, similar to 3-beta-hydroxysteroidde
hydrogenase GI:15983819from (Digitalis lanata)
/ putative alcoholdehydrogenase(SGN-U315454) / 1e-114 / 252/254
(99%) / 245/252 (97%)
351 / EL645824 / 244 / － / －－－ / Photosynthesis / Ferredoxin-1 chloroplast precursor (TC173805) / 6.0e-47 / 244/244
(100%) / 237/244 (97%)
352 / EL645825 / 218 / 252a / ＋ / ＋＋＋ / Unknown / Expressed protein (SGN-U343506) / 1e-108 / 218/218
(100%) / 213/218 (97%)
356 / EL645826 / 264 / 271、306、324、335、336、341 / －－－ / －－－ / Signalling-related / GTP binding protein-like (SGN-U322215) / 3e-90 / 263/264
(99%) / 244/264 (92%)
357 / EL645827 / 285 / 330、259、328 / 292 / －－ / －－－ / Photosynthesis / Ribulose bisphosphate carboxylase (RuBisCO)
small subunit 2A chloroplast precursor (TC188927) / 4.1e-59 / 285/285
(100%) / 284/285 (99%)
358a / EL645828 / 208 / 258a / －－－ / －－－ / Protein synthesis / Chloroplast 30S ribosomal protein S8 (TC156596) / 2.2e-40 / 208/208
(100%) / 204/208 (98%)
358b / EL645829 / 226 / －－－ / －－－ / Metabolism / Chloroplast inorganic pyrophosphatase (EC 3.6.1.1)
(TC181468) / 1.4e-45 / 225/226
(99%) / 224/225 (99%)
361a / EL645830 / 287 / 346 / －－ / －－ / Protein synthesis / Plastid ribosomal protein S10 precursor (TC172162) / 1.2e-57 / 287/287
(100%) / 283/287 (98%)
361b / EL645831 / 181 / －－ / －－ / Signalling-related / Putative calcium-binding EF hand family protein
(TC188643) / 4.0e-35 / 180/181
(99%) / 179/180 (99%)
366 / EL645832 / 149 / 106 / ＋＋＋ / ＋＋＋ / Metabolism / 6-phosphogluconate dehydrogenase (EC 1.1.1.44)
(TC143974) / 2.7e-26 / 147/149
(99%) / 142/147 (96%)
a Fragments matching directly with the ACE fragments analyzed by DNAstar SeqMan II software (assembling parameter, match size 25, Minimum matching percentage 85%)
b Fragments matching with the same TC/SGN sequence(s) analyzed by DNAstar SeqMan II software (assembling parameter, match size 25, Minimum matching percentage 85%)
c ART fragments matching either directly with ACE or ACE-matching TC/SGN sequence(S) analyzed by DNAstar SeqMan II software (assembling parametre, match size 25, Minimum matching percentage 85%)
d Induction or repression of gene expression by Avr9/Cf-9- or Avr4/Cf-4-dependent HR is shown as + and －, respectively. More + or －indicates stronger induction or repression
e Accession numbers of either GenBank or DFCI (TC number) or SGN (SGN number) of AFLP fragment homologues are included in parentheses. Note that gene polymorphism occurring in the two types of Avr/Cf seedlings is not included since only the ACE fragments from a single Avr/Cf interaction (the Avr4/Cf-4 interaction unless the ACE fragment showed a higher expression level in the Avr9/Cf-9 interaction) have been sequenced. ns: no similar sequence to the AFLP fragment is found in the databases (E-value>0.05)
ns: no similar sequence to the AFLP fragment is found in the databases (E-value>0.05)