Table I.
Genes preferentially expressed in the exocarp
| Clone IDb
|
Accession No.
|
SGNa
|
Annotationc
|
Fold Change E/Ld
|
Adjusted P Valuee
|
|
|---|---|---|---|---|---|---|
| Identifier | E Value | |||||
| Cell cycle and DNA processing: DNA processing | ||||||
| LE12CB04 | AJ785151 | No hit | – | Helicase SKI2W | 1.96 | 9.57E-04 |
| Cell fate: growth regulators/regulation of cell size | ||||||
| LE12CD10 | AJ785177 | U212786 | 0.0 | 1-Aminocyclopropane-1-carboxylic acid (ACC) oxidase | 3.44 | 2.68E-04 |
| LE08DC03 | AJ784658 | U212955 | 0.0 | S-adenosyl-l-Met (SAM) synthetase | 3.42 | 2.67E-04 |
| LE08CF02 | AJ784613 | U212956 | 0.0 | SAM synthetase | 2.73 | 4.64E-04 |
| LE12AA11 | AJ785011 | U214814 | 0.0 | 12-Oxophytodienoate reductase 3 | 3.55 | 2.25E-05 |
| Cell rescue defense and virulence: detoxification | ||||||
| Cat1 | M93719 | U212687 | 0.0 | Catalase1 | 2.94 | 1.72E-04 |
| LE08DF09 | AJ784688 | U232447 | 0.0 | Metallothionein | 4.95 | 5.39E-07 |
| Cell rescue defense and virulence: disease, virulence, and defense | ||||||
| LE08CE03 | AJ784607 | U215854 | 0.0 | Glucan endo-1-3-β-d-glucosidase | 4.10 | 1.53E-04 |
| LE12CG12 | AJ785203 | U213405 | 0.0 | Chitinase-like protein 1 | 2.38 | 4.32E-04 |
| LE12DD01 | AJ785237 | U212849 | 7.0E-59 | Disease resistant gene (Mi-copy2) | 2.38 | 2.61E-04 |
| Cell rescue defense and virulence: stress response | ||||||
| LEEGp6-1 | AJ832090 | U213745 | 2.0E-100 | Dehydrin | 4.61 | 2.08E-03 |
| LE08EE11 | AJ784748 | U228119 | 0.0 | Snakin | 9.87 | 1.09E-06 |
| LE12CE01 | AJ785180 | U214534 | 0.0 | Late embryogenesis-like protein | 5.08 | 4.73E-04 |
| LE08ED02 | AJ784732 | U220274 | 0.0 | DnaJ domain-containing unknown protein | 2.04 | 1.94E-03 |
| Cellular communication/signal transduction mechanism: intracellular signaling | ||||||
| LE08BE10 | AJ784545 | U213537 | 1.0E-132 | Zinc-finger protein | 1.73 | 1.15E-03 |
| LE15CD10 | AJ785473 | U216752 | 0.0 | Zinc finger protein LSD1 | 2.19 | 6.84E-04 |
| cLEN7J4 | AW222373 | U220143 | 0.0 | WRKY-type DNA binding protein | 4.52 | 1.66E-06 |
| cLED26N22 | AI897173 | U215853 | 0.0 | WRKY transcription factor Nt-SubD48 | 1.75 | 3.99E-04 |
| LE15CC02 | AJ785459 | U217026 | 0.0 | DNA-binding protein 3 | 6.17 | 8.36E-05 |
| LE15CD02 | AJ785467 | U213644 | 0.0 | Transcription factor JERF1 | 2.42 | 1.32E-03 |
| LE08AA01 | AJ784436 | U216050 | 0.0 | EREBP-3 | 4.52 | 5.65E-05 |
| LE15BB06 | AJ785382 | U224784 | 0.0 | DNA-binding protein remorin 2 | 1.64 | 5.68E-04 |
| LE15CA07 | AJ785446 | U213060 | 0.0 | 14-3-3 Protein | 8.35 | 3.53E-07 |
| LE08BE05 | AJ784542 | U212855 | 0.0 | Calmodulin | 2.56 | 1.88E-04 |
| LE12DD02 | AJ785238 | U221514 | 0.0 | Protein kinase APK1B | 4.72 | 1.40E-06 |
| LE15DB05 | AJ785520 | U235596 | 0.0 | Phospholipase | 5.96 | 7.09E-06 |
| Classification not yet clear | ||||||
| LE12CB08 | AJ785155 | U213254 | 0.0 | Allergen-like Ole | 2.87 | 1.19E-03 |
| LE12BF02 | AJ785113 | U212552 | 0.0 | Calcium-binding allergen Ole | 3.26 | 7.48E-05 |
| LE15DH09 | AJ785563 | U228352 | 3.3E-37 | Nodulin MtN3 | 6.01 | 1.95E-06 |
| LE12CH08 | AJ785209 | U214871 | 0.0 | Adhesion of calyx edges protein ACE | 1.99 | 4.24E-03 |
| LE08ED10 | AJ784740 | No hit | – | Coat protein | 2.80 | 2.60E-05 |
| LEEBp6-3 | AJ832081 | U216997 | 1.0E-102 | N-acetylethanolamine amidohydrolase | 2.08 | 4.95E-04 |
| cLEF3K1 | AW220963 | U215001 | 0.0 | Dehydration-responsive protein RD22 | 6.80 | 3.35E-05 |
| LE15BE03 | AJ785406 | U219000 | 1.0E-163 | SelT-like protein precursor | 2.03 | 6.40E-04 |
| Control of cellular organization: cell wall | ||||||
| cLES7E1 | AI779074 | U230830 | 0.0 | Extensin HRGP class II | 2.32 | 3.83E-05 |
| LE15DB11 | AJ785525 | No hit | – | Endo-β-1,4-glucanase | 1.73 | 2.82E-03 |
| LE15AG01 | AJ785355 | U222669 | 0.0 | Polygalacturonase inhibitor | 2.35 | 5.14E-06 |
| LE15DA02 | AJ785508 | U216941 | 0.0 | Pectate lyase | 1.95 | 2.34E-04 |
| LE15CA05 | AJ785445 | U213493 | 0.0 | Pectinesterase-like protein | 5.52 | 2.64E-04 |
| Development (systemic): plant development | ||||||
| LE08EF05 | AJ784752 | U215919 | 0.0 | TDR6 transcription factor | 4.97 | 2.64E-05 |
| LE12BF03 | AJ785114 | U220043 | 0.0 | Nam-like protein 2 | 3.72 | 3.13E-05 |
| Energy: electron transport and membrane-associated energy conservation | ||||||
| LE15AC06 | AJ785322 | U225169 | 0.0 | Cytochrome p450 77A2 | 3.80 | 1.46E-04 |
| mo5-10G1-11 | AJ270962 | U220531 | 0.0 | Ferredoxin | 2.23 | 9.68E-04 |
| Energy: fermentation | ||||||
| cLEI5L19 | AW648630 | U220098 | 0.0 | Aldehyde dehydrogenase (NAD+) | 2.13 | 1.59E-03 |
| Energy: glycolysis and gluconeogenesis | ||||||
| cLED19J22 | AI487966 | U228562 | 0.0 | Fructokinase-like protein | 3.78 | 4.46E-05 |
| LE15BB10 | AJ785385 | U213349 | 0.0 | Fructose-1-6-bisphosphate aldolase | 2.42 | 1.32E-03 |
| cLEC35N5 | AW032455 | U213624 | 0.0 | Pyruvate decarboxylase-1 | 5.02 | 1.53E-05 |
| cLET2D18 | AW037934 | U213321 | 0.0 | Ga3PDH-NADP | 2.43 | 1.37E-06 |
| cLES3M17 | AI777819 | U213529 | 0.0 | Triose-P isomerase (cytosolic) | 1.93 | 2.02E-05 |
| LDH1 | Y08887 | U214667 | 0.0 | LDH1 | 1.72 | 1.30E-03 |
| LE12BF10 | AJ785120 | U213348 | 0.0 | Fructose-bisphosphate aldolase (cytosolic) | 2.63 | 6.67E-04 |
| LE08BF04 | AJ784551 | U212825 | 0.0 | Ethylene-responsive enolase | 1.86 | 1.36E-03 |
| Energy: tricarboxylicacid pathway (citrate cycle, Krebs cycle, and tricarboxylic acid cycle) | ||||||
| cLES10I3 | AI780076 | U241915 | 0.0 | 2-Oxoglutarate dehydrogenase E1 component | 37.20 | 3.71E-06 |
| cLEN9B13 | AW222820 | U214866 | 0.0 | Succinyl CoA ligase | 1.63 | 1.67E-05 |
| Metabolism | ||||||
| LE08DC12 | AJ784665 | U213436 | 0.0 | Dehydrogenase | 3.33 | 7.22E-04 |
| Metabolism: amino acid metabolism | ||||||
| cLEC34J20 | AW035240 | U212562 | 0.0 | Glu decarboxylase | 1.69 | 1.47E-03 |
| cLED3A23 | AI484867 | U214486 | 0.0 | His decarboxylase | 2.37 | 6.56E-04 |
| LE08CH07 | AJ784635 | U213162 | 0.0 | Pro oxidase (mitochondrial) | 2.61 | 3.59E-04 |
| LE08DD05 | AJ784669 | U212637 | 0.0 | Adenosylmethionine decarboxylase | 2.93 | 1.35E-05 |
| LE08EC07 | AJ784725 | U215899 | 0.0 | Thr dehydratase/deaminase (chloroplastic) | 1.67 | 1.98E-03 |
| LE15CF04 | AJ785488 | U212948 | 0.0 | Arg decarboxylase | 3.77 | 2.87E-05 |
| LE15DB01 | AJ785516 | U213123 | 0.0 | Arg decarboxylase | 4.72 | 9.66E-05 |
| LE08EB11 | AJ784721 | U215839 | 0.0 | d-3-phosphoglycerate dehydrogenase (chloroplastic) | 2.57 | 1.25E-05 |
| Metabolism: biosynthesis of phenylpropanoids | ||||||
| LE12DH06 | AJ785275 | U212958 | 0.0 | Phe ammonia-lyase | 2.05 | 2.22E-03 |
| cLED8N18 | AI486371 | E213155 | 0.0 | Flavanone 3-hydroxylase | 3.14 | 5.51E-04 |
| LE15DH12 | AJ785566 | U214961 | 0.0 | Flavonol synthase | 12.41 | 1.35E-05 |
| Metabolism: compound and carbohydrate metabolism | ||||||
| LE08EA10 | AJ784713 | U213927 | 0.0 | dTDP-Glc 4 to 6-dehydratase-like protein | 2.92 | 9.78E-04 |
| LE08CG06 | AJ784625 | U222042 | 0.0 | β-Phosphoglucomutase | 1.63 | 2.78E-03 |
| Susy | AJ011319 | U213119 | 0.0 | Sucrose synthase | 4.58 | 6.36E-04 |
| Metabolism: lipid, fatty acid, and isoprenoid metabolism | ||||||
| LE08BH05 | AJ784564 | U212736 | 0.0 | Lipid transfer protein 2 | 28.34 | 1.46E-07 |
| LE15AG03 | AJ785357 | U222218 | 0.0 | Nonspecific lipid transfer protein | 14.93 | 4.55E-06 |
| LE12DB10 | AJ785227 | U217603 | 2.0E-128 | Acetyl-CoA C-acyltransferase | 5.75 | 1.39E-05 |
| LE08BB02 | AJ784516 | U213809 | 0.0 | GDSL-motif lipase/acylhydrolase | 16.64 | 3.03E-06 |
| Metabolism: metabolism of vitamins, cofactors, and prosthetic groups | ||||||
| LE15CH11 | AJ785507 | U212885 | 0.0 | Thiazole biosynthesis enzyme (chloroplastic) | 18.70 | 8.35E-05 |
| LE08BF03 | AJ784550 | U213063 | 0.0 | S-adenosyl-l-homo-Cys hydrolase | 1.86 | 1.07E-03 |
| LE12CF02 | AJ785189 | U213366 | 0.0 | GDP-Man pyrophosphorylase | 3.47 | 2.07E-06 |
| cLED13C20 | AI487366 | U223434 | 0.0 | SRG1-like protein [Fe(II)/ascorbate oxidase] | 3.04 | 9.22E-05 |
| Metabolism: nucleotide metabolism | ||||||
| LE12CB05 | AJ785152 | U214294 | 0.0 | Nucleotide sugar epimerase-like protein | 2.02 | 3.91E-03 |
| LE12BH04 | AJ785132 | U213290 | 0.0 | Guanylate kinase | 2.24 | 4.45E-03 |
| cLED6H5 | AI486997 | U214173 | 0.0 | Nucleoside diphosphate kinase 3 (mitochondrial) | 1.67 | 4.30E-04 |
| Metabolism: secondary metabolism | ||||||
| LE12CH04 | AJ785206 | U214174 | 0.0 | 4-Coumarate-CoA ligase 1 | 2.59 | 2.08E-05 |
| LE15BG09 | AJ785428 | U219467 | 0.0 | (R)-mandelonitrile lyase | 13.46 | 1.95E-06 |
| LE08AB07 | AJ784451 | U231541 | 1.0E-130 | Cinnamoyl CoA reductase | 3.26 | 2.26E-06 |
| Protein fate (folding, modification, and destination) | ||||||
| PBV1F07 | AJ006376 | U212604 | 0.0 | Subtilisin-like protease | 3.36 | 3.51E-05 |
| cLED19K24 | AI488034 | U215432 | 0.0 | Ubiquitin fusion-degradation protein | 5.56 | 4.55E-06 |
| Protein synthesis: ribosome biogenesis | ||||||
| LE15CG03 | AJ785496 | U213690 | 0.0 | 40S ribosomal protein S16 | 2.63 | 1.13E-03 |
| Protein synthesis: translation | ||||||
| LE12CC10 | AJ785166 | U214373 | 0.0 | Eukaryotic translation initiation factor 5A-3 | 1.77 | 1.36E-03 |
| Subcellular localization: cell wall | ||||||
| LE12AA02 | AJ785006 | U213588 | 0.0 | Pro-rich protein (PRP) | 3.17 | 1.00E-03 |
| LE12CB12 | AJ785159 | U216661 | 0.0 | Expansin precursor | 3.85 | 3.03E-06 |
| LE12DG11 | AJ785269 | U213725 | 0.0 | Expansin precursor | 2.89 | 1.74E-07 |
| cLEX3C8 | AW219178 | U220662 | 0.0 | Fasciclin-like arabinogalactan-protein 9 (FLA) | 2.05 | 6.92E-04 |
| Subcellular localization: cytoskeleton | ||||||
| LE12DG01 | AJ785262 | U212624 | 0.0 | β-tubulin | 1.99 | 1.31E-03 |
| LE15AA04 | AJ785298 | U220529 | 0.0 | Actin-depolymerizing factor | 1.75 | 3.98E-04 |
| cLER5G18 | AI773090 | U214141 | 0.0 | Profilin | 2.02 | 4.23E-05 |
| Systemic regulation of/interaction with environment | ||||||
| LE12CD01 | AJ785169 | U217735 | 0.0 | ERD3 protein | 4.72 | 3.48E-06 |
| LE12CC08 | AJ785164 | U214085 | 0.0 | Auxin growth promotor protein | 2.14 | 1.03E-03 |
| LEEbH9-1 | AJ832104 | U214511 | 2.3E-49 | Ethylene-responsive factor 2 | 3.21 | 6.96E-05 |
| LE15AE01 | AJ785335 | U215501 | 0.0 | Gast1 | 6.13 | 3.88E-07 |
| Transcription | ||||||
| LE15AB07 | AJ785312 | U214908 | 0.0 | Splicing factor | 3.03 | 2.12E-03 |
| LE15AF11 | AJ785354 | U219133 | 0.0 | RNA-binding protein | 1.62 | 2.71E-03 |
| Transport facilitation | ||||||
| cLER2E16 | AI772312 | U229995 | 0.0 | Hexose transporter | 5.50 | 3.57E-06 |
| cLER19B17 | AI776698 | U221086 | 0.0 | Hexose transporter | 9.04 | 1.71E-06 |
| cLER20L10 | AI777293 | U225438 | 0.0 | Sugar transporter | 11.58 | 1.86E-05 |
| LE15CF12 | AJ785494 | U214673 | 0.0 | Vacuolar ATP synthase subunit D | 1.60 | 2.00E-04 |
| LE15CD07 | AJ785470 | U213604 | 0.0 | Vacuolar-type H+-pyrophosphatase | 3.96 | 5.15E-04 |
| cLER16K11 | AI775644 | U222562 | 0.0 | Inorganic pyrophosphatase | 1.83 | 2.11E-03 |
| LE08AH02 | AJ784494 | U216601 | 0.0 | Ca2+-transporting ATPase | 2.16 | 2.93E-04 |
| LE12BD07 | AJ785099 | U213108 | 0.0 | Triose phosphate/phosphate translocator (chloroplastic) | 1.84 | 1.76E-03 |
| LE12AA06 | AJ785010 | U215083 | 0.0 | ABC transporter ATP-binding protein | 2.19 | 8.53E-05 |
| Protein of unknown function | ||||||
| LE15AH03 | AJ785367 | U214454 | 0.0 | Unknown function | 10.72 | 2.94E-06 |
| LE12AD05 | AJ785036 | U222930 | 1.0E-156 | Unknown function | 6.29 | 1.83E-05 |
| LE15DB10 | AJ785524 | U213279 | 1.0E-177 | Unknown function | 5.13 | 1.37E-04 |
| LE12BF04 | AJ785115 | U216056 | 0.0 | Unknown function | 4.44 | 1.00E-05 |
| LE15BB08 | AJ785384 | U213736 | 0.0 | Unknown function | 4.31 | 4.00E-03 |
| LE08DG12 | AJ784697 | U213845 | 0.0 | Unknown function | 4.14 | 1.49E-05 |
| LE08EE06 | AJ784743 | U218676 | 0.0 | Unknown function | 3.42 | 2.14E-05 |
| LE12AH12 | AJ785073 | U217816 | 1.0E-153 | Unknown function | 3.27 | 1.35E-05 |
| LE08BC03 | AJ784524 | U224283 | 0.0 | Unknown function | 3.16 | 2.07E-06 |
| LE08BG02 | AJ784557 | U216056 | 0.0 | Unknown function | 2.95 | 6.50E-06 |
| LE08ED04 | AJ784734 | U218910 | 3.0E-145 | Unknown function | 2.93 | 4.73E-04 |
| LE15BH05 | AJ785435 | U216284 | 0.0 | Unknown function | 2.87 | 3.04E-06 |
| cLED38D5 | AI899252 | U216929 | 0.0 | Similar to Fw2.2 | 2.78 | 2.69E-04 |
| LE08DA11 | AJ784646 | U213772 | 0.0 | Unknown function | 2.41 | 1.96E-04 |
| LE08ED08 | AJ784738 | U216703 | 1.0E-135 | Unknown function | 2.31 | 4.86E-03 |
| LE08EA06 | AJ784710 | U215330 | 0.0 | Unknown function | 2.17 | 6.88E-06 |
| LE15AF07 | AJ785351 | U214933 | 0.0 | Unknown function | 1.79 | 2.04E-04 |
| LE15CB12 | AJ785458 | U218795 | 2.0E-97 | Unknown function | 1.69 | 2.97E-04 |
| LE12CG03 | AJ785197 | U216761 | 0.0 | Unknown function | 1.65 | 8.65E-04 |
| Hypothetical protein | ||||||
| LE12AD06 | AJ785037 | U224304 | 0.0 | Hypothetical protein | 3.40 | 1.81E-04 |
| LE12AE11 | AJ785051 | U217497 | 0.0 | Hypothetical protein | 3.27 | 3.59E-06 |
| LE15CA09 | AJ785448 | U216598 | 0.0 | Hypothetical protein | 3.18 | 1.00E-05 |
| LE15BF08 | AJ785417 | U215214 | 0.0 | Hypothetical protein | 2.88 | 1.37E-04 |
| LE08AE08 | AJ784472 | U219916 | 0.0 | Hypothetical protein | 2.44 | 3.72E-04 |
| LE15DF09 | AJ785548 | U216065 | 0.0 | Hypothetical protein | 2.41 | 1.46E-07 |
| LE15BD01 | AJ785395 | U218211 | 0.0 | Hypothetical protein | 1.94 | 4.12E-03 |
| LE15AE06 | AJ785340 | U222115 | 0.0 | Hypothetical protein | 1.83 | 3.70E-03 |
| LE12AB02 | AJ785014 | U218329 | 0.0 | Hypothetical protein | 1.72 | 1.35E-04 |
| LE15BD04 | AJ785398 | U226333 | 0.0 | Hypothetical protein | 1.70 | 6.71E-04 |
| LE15DD10 | AJ785536 | U231906 | 0.0 | Hypothetical protein | 1.62 | 8.08E-05 |
| LE15CD06 | AJ785469 | U217504 | 0.0 | Hypothetical protein | 1.61 | 2.60E-04 |
| No homology | ||||||
| LE08BA12 | AJ784514 | No hit | – | – | 8.97 | 6.11E-06 |
| LE08DA06 | AJ784641 | No hit | – | – | 2.05 | 4.90E-06 |
a
SGN identification number of the best BLAST hit in the SGN tomato EST database, if any, and corresponding expect value.
b
Clone ID in the EMBL or TIGR tomato EST databases.
c
Putative function and classification into functional categories according to Munich Information Center for Protein Sequences (MIPS; http://www.mips.biochem.mpg.de/).
d
Mean ratio of the normalized data between exocarp (E) and locular tissue (L).
e
Probability of the t test.