Table 1 A total of 86 differentially expressed proteins identified in resistant and susceptible tomato cultivars after TYLCV infection

 1

gi|407970998

Chlorophyll a-b binding protein 4, Solanum lycopersicum

135

13

2

28.98/5.33

0.31^* ± 0.15

0.45^* ± 0.35

0.22^* ± 0.13

0.18^* ± 0.09

 2

gi|115813

Chlorophyll a-b binding protein 8, Solanum lycopersicum

212

15

5

29.34/8.96

1.09 ± 0.22

0.45^* ± 0.35

0.25^* ± 0.06

0.90 ± 0.33

 3

gi|460405507

Chlorophyll a-b binding protein 8, Solanum lycopersicum

81

4

1

29.26/8.65

1.34 ± 0.25

1.78 ± 0.30

0.46^* ± 0.03

0.36^* ± 0.13

 4

gi|460375240

Oxygen-evolving enhancer protein 1, Solanum lycopersicum

273

10

2

35.15/5.91

0.84 ± 0.07

0.18^* ± 0.01

0.31^* ± 0.04

1.49 ± 0.38

 5

gi|460372520

Oxygen-evolving enhancer protein 1, Solanum lycopersicum

99

19

2

35.48/5.84

1.93 ± 0.19

0.18^* ± 0.01

2.21^* ± 0.44

10.57^* ± 0.52

 6

gi|460408969

Rubisco accumulation factor 1, Solanum lycopersicum

119

9

3

50.46/5.10

5.36^* ± 0.28

1.85 ± 0.28

0.77 ± 0,29

2.18^* ± 0.39

 7

gi|460401823

Ribulose bisphosphate carboxylase/oxygenase activase 1, Solanum lycopersicum

56

3

1

49.05/8.15

0.09^* ± 0.04

0.57 ± 0.12

6.75^* ± 0.18

1.07 ± 0.29

 8

gi|723739979

Ribulose bisphosphate carboxylase/oxygenase activase, Solanum lycopersicum

285

11

3

50.97/8.76

0.88 ± 0.20

0.38^* ± 0.30

0.07^* ± 0.05

0.16^* ± 0.01

 9

gi|1778414

Ribulose 1,5-bisphosphate carboxylase/oxygenase activase, Oryza sativa

126

7

2

48.06/5.85

0.39^* ± 0.04

0.78 ± 0.16

3.45^* ± 0.40

1.73 ± 0.01

 10

gi|100380

Ribulose bisphosphate carboxylase activase, Nicotiana tabacum

103

7

1

26.08/5.01

0.05^* ± 0.01

0.03^* ± 0.02

3.25^* ± 0.44

5.57^* ± 0.43

 11

gi|488453358

Ribulose 1,5-bisphosphate carboxylase, Solanum lycopersicum

171

6

3

48.57/6.71

1.22 ± 0.14

43.48^* ± 0.38

0.04^* ± 0.01

0.01^* ± 0,01

 12

gi|488453358

Ribulose 1,5-bisphosphate carboxylase, Solanum lycopersicum

313

13

5

48.57/6.71

1.58 ± 0.11

23.71^* ± 0.28

0.06^* ± 0.01

0.02^* ± 0.01

13

gi|488453358

Ribulose 1,5-bisphosphate carboxylase, Solanum lycopersicum

62

4

2

48.57/6.71

1.37 ± 0.22

4.53^* ± 0.25

0.05^* ± 0.01

0.05^* ± 0.01

 14

gi|488453358

Ribulose 1,5-bisphosphate carboxylase, Solanum lycopersicum

124

8

3

48.57/6.71

0.83 ± 0.15

1.89 ± 0.20

0.09^* ± 0.01

0.04^* ± 0.01

 15

gi|1293000

Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit, Cheirodendron trigynum

200

6

3

52.90/6.31

0.63 ± 0.04

1.18 ± 0.20

0.10^* ± 0.05

0.06^* ± 0.01

 16

gi|168282

Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit, Lactoris fernandeziana

281

16

4

44.16/6.33

0.19^* ± 0.02

0.28^* ± 0.02

2.60^* ± 0.39

1.76 ± 0.24

 17

gi|21069067

Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit, Asplenium jahandiezii

60

4

1

39.38/7.31

1.00 ± 0.26

0.29^* ± 0.10

0.02^* ± 0.01

0.09^* ± 0.08

 18

gi|460379814

RubisCO large subunit-binding protein subunit beta, Solanum lycopersicum

203

10

4

64.53/5.46

5.11^* ± 0.34

2.87^* ± 0.15

1.26 ± 0.06

2.24^* ± 0.19

 19

gi|460366131

RubisCO large subunit-binding protein subunit beta, Solanum lycopersicum

53

4

2

63.24/5.72

1.15 ± 0.36

2.81^* ± 0.25

0.69 ± 0.08

0.28^* ± 0.09

 20

gi|92087012

Ribulose bisphosphate carboxylase large chain OS, Solanum lycopersicum

65

6

3

53.43/6.55

0.77 ± 0.12

10.02^* ± 0.24

0.09^* ± 0.01

0.01^* ± 0.01

 21

gi|92087012

Ribulose bisphosphate carboxylase large chain OS, Solanum lycopersicum

121

14

6

53.43/6.55

1.18 ± 0.07

32.57^* ± 0.19

0.08^* ± 0.01

0.01^* ± 0.01

 22

gi|460375527

Ferredoxin–NADP reductase, leaf-type isozyme, Solanum lycopersicum

118

13

3

40.90/8.67

0.28^* ± 0.07

0.93 ± 0.47

0.42^* ± 0.10

0.14^* ± 0.02

 23

gi|460373374

FerredoxinvNADP reductase, leaf-type isozyme, Solanum lycopersicum

299

20

5

40.77/8.37

0.82 ± 0.07

0.61 ± 0.07

0.48^* ± 0.02

0.65 ± 0.05

 24

gi|350537679

Carbonic anhydrase, Solanum lycopersicum

278

17

4

34.85/6.67

1.45 ± 0.12

3.21^* ± 0.27

0.85 ± 0.12

0.38^* ± 0.05

 25

gi|350537679

Carbonic anhydrase, Solanum lycopersicum

98

5

1

34.85/6.67

0.65 ± 0.15

0.35^* ± 0.03

1.53 ± 0.18

2.81^* ± 0.23

 26

gi|460389468

Protein TIC 62, Solanum lycopersicum

313

13

5

52.96/7.66

1.02 ± 0.14

0.20^* ± 0.11

0.13^* ± 0.04

0.70 ± 0.17

 27

gi|460372959

Peptidyl-prolyl cis-trans isomerase CYP38, Solanum lycopersicum

185

17

5

49.54/5.00

0.92 ± 0.12

1.61 ± 0.38

0.26^* ± 0.05

0.15^* ± 0.04

 28

gi|469517896

Glyceraldehyde-3-phosphate dehydrogenase, Atropa belladonna

101

10

4

34.16/6.04

0.88 ± 0.11

0.98 ± 0.29

0.46^* ± 0.03

0.44^* ± 0.13

 29

gi|460414390

ATP synthase delta chain, Solanum lycopersicum

166

6

4

27.32/8.90

0.49^* ± 0.17

1.62 ± 0.23

0.38^* ± 0.05

0.11^* ± 0.03

 30

gi|303279681

Aryl-al/cohol dehydrogenase related protein, Micromonas pusilla

54

3

1

41.07/8.65

0.53 ± 0.11

1.05 ± 0.21

2.49^* ± 0.35

1.28 ± 0.19

 31

gi|460397188

Thiamine thiazole synthase, Solanum lycopersicum

142

14

4

37.68/5.42

0.30^* ± 0.21

3.06^* ± 0.09

2.25^* ± 0.07

0.23^* ± 0.17

 32

gi|460365268

Biotin carboxylase 1, Solanum lycopersicum

413

13

6

59.08/6.52

0.68 ± 0.27

1.51 ± 0.26

0.82 ± 0.08

0.37^* ± 0.13

 33

gi|723747143

Aconitate hydratase, Solanum lycopersicum

218

5

4

107.83/6.52

67.86^* ± 0.19

3.13^* ± 0.22

0.26^* ± 0.02

5.77^* ± 0.85

 34

gi|350538543

Succinic semialdehyde reductase isofom 2, Solanum lycopersicum

123

7

2

38.94/8.50

2.01^* ± 0.26

2.52^* ± 0.10

1.24 ± 0.09

1.06 ± 0.93

 35

gi|460408278

Enolase-like, Solanum lycopersicum

207

11

4

48.21/5.99

3.37^* ± 0.29

4.38^* ± 0.04

1.49 ± 0.09

1.14 ± 0.14

 36

gi|460415839

Probable ATP synthase 24 kDa subunit, Solanum lycopersicum

78

5

1

27.75/8.69

0.44^* ± 0.08

0.49^* ± 0.12

1.31 ± 0.09

1.02 ± 0.28

 37

gi|460373820

ATP synthase gamma chain, Solanum lycopersicum

167

12

3

41.75/8.15

1.93 ± 0.33

3.80^* ± 0.24

0.09^* ± 0.01

0.05^* ± 0.01

 38

gi|460365435

Isocitrate dehydrogenase [NADP], Solanum lycopersicum

172

12

4

47.00/6.35

1.05 ± 0.22

0.27^* ± 0.12

0.21^* ± 0.03

0.86 ± 0.14

 39

gi|350535679

Cytosolic NADP-malic enzyme, Solanum lycopersicum

167

6

3

64.63/5.71

2.04^* ± 0.20

1.20 ± 0.14

0.48^* ± 0.07

0.49^* ± 0.20

 40

gi|31088232

Chitinase, Solanum lycopersicum

123

18

7

28.05/5.93

0.82 ± 0.11

0.30^* ± 0.03

1.51 ± 0.31

4.12^* ± 0.10

 41

gi|350535160

Wound-inducible carboxypeptidase precursor, Solanum lycopersicum

191

5

2

56.04/5.84

1.14 ± 0.07

0.78 ± 0.05

3.62^* ± 0.30

5.27^* ± 0.22

 42

gi|350535160

Wound-inducible carboxypeptidase precursor, Solanum lycopersicum

177

5

3

56.04/5.84

1.07 ± 0.17

0.48^* ± 0.02

2.72^* ± 0.19

6.05^* ± 0.30

 43

gi|350534564

26S protease regulatory subunit 6A homolog, Solanum lycopersicum

253

17

6

47.70/4.94

1.18 ± 0.05

0.78 ± 0.25

0.20^* ± 0.07

0.30^* ± 0.04

 44

gi|460393754

26S protease regulatory subunit 6B homolog, Solanum lycopersicum

198

7

2

46.80/5.63

1.24 ± 0.40

0.38^* ± 0.13

0.33^* ± 0.23

0.91 ± 0.34

 45

gi|460400419

Elongation factor G, Solanum lycopersicum

258

11

5

86.79/5.45

3.75^* ± 0.31

0.53 ± 0.02

0.47^* ± 0.01

3.29^* ± 0.39

 46

gi|460415494

Eukaryotic initiation factor 4A-2, Solanum lycopersicum

370

18

7

47.10/5.46

1.82 ± 0.06

1.72 ± 0.15

0.35^* ± 0.02

0.37^* ± 0.02

 47

gi|460399092

Eukaryotic initiation factor 4A-2, Solanum lycopersicum

304

13

4

47.14/5.54

1.22 ± 0.22

2.73^* ± 0.07

0.49^* ± 0.22

0.22^* ± 0.05

 48

gi|460391817

Elongation factor TuB, Solanum lycopersicum

125

5

2

56.29/6.69

0.62 ± 0.16

4.33^* ± 0.23

2.45^* ± 0.23

0.34^* ± 0.03

 49

gi|460399098

Elongation factor 2 isoform X1, Solanum lycopersicum

248

7

4

94.97/5.84

1.35 ± 0.24

3.39^* ± 0.23

3.06^* ± 0.11

1.22 ± 0.19

 50

gi|460396224

Eukaryotic translation initiation factor 3 subunit K, Solanum lycopersicum

134

11

2

26.55/5.28

0.46^* ± 0.03

1.12 ± 0.17

2.80^* ± 0.26

1.15 ± 0.12

 51

gi|460391351

Cell division cycle protein 48 homolog, Solanum lycopersicum

172

9

5

90.15/5.10

24.39^* ± 0.39

1.57 ± 0.13

0.38^* ± 0.04

5.90^* ± 0.81

 52

gi|460411520

Cell division cycle protein 48 homolog, Solanum lycopersicum

138

5

3

90.25/5.20

5.85^* ± 0.22

0.91 ± 0.08

1.09 ± 0.04

7.00^* ± 0.60

 53

gi|2492530

Leucine aminopeptidase 2, Solanum lycopersicum

79

8

3

60.08/8.18

4.80^* ± 0.15

2.68^* ± 0.29

0.81 ± 0.07

1.46 ± 0.07

 54

gi|350536267

Subtilisin-like protease precursor, Solanum lycopersicum

301

5

3

79.57/6.25

0.24^* ± 0.02

0.07^* ± 0.01

4.17^* ± 0.29

14.46^* ± 0.40

 55

gi|460381101

28 kDa ribonucleoprotein, Solanum lycopersicum

100

8

3

32.69/4.70

1.11 ± 0.19

1.15 ± 0.31

2.17^* ± 0.70

2.05^* ± 0.25

 56

gi|723717714

Phosphoglycerate kinase, Solanum lycopersicum

275

17

6

42.26/5.78

1.24 ± 0.46

0.47^* ± 0.02

0.42^* ± 0.02

1.11 ± 0.41

 57

gi|460404838

Adenosylhomocysteinase, Solanum lycopersicum

119

12

4

53.59/5.57

1.10 ± 0.34

0.53 ± 0.16

0.21^* ± 0.06

0.45^* ± 0.19

 58

gi|460395681

Ketol-acid reductoisomerase, Solanum lycopersicum

68

5

2

64.19/6.31

0.83 ± 0.40

0.34^* ± 0.20

0.39^* ± 0.09

0.97 ± 0.21

 59

gi|460415192

S-adenosylmethionine synthase 2, Solanum lycopersicum

207

7

2

43.51/5.41

2.09^* ± 0.26

2.04^* ± 0.07

0.64 ± 0.06

0.86 ± 0.09

 60

gi|460399143

Glycine dehydrogenase (decarboxylating), Solanum lycopersicum

192

9

6

114.02/6.69

1.90 ± 0.14

1.39 ± 0.08

4.02^* ± 0.25

5.51^* ± 0.19

 61

gi|460399143

Glycine dehydrogenase (decarboxylating), Solanum lycopersicum

153

7

5

114.02/6.69

3.80^* ± 0.19

5.08^* ± 0.31

6.81^* ± 0.38

5.09^* ± 0.21

 62

gi|460370413

Glycine dehydrogenase, Solanum lycopersicum

183

9

3

42.52/6.56

0.28^* ± 0.02

12.57^* ± 0.28

3.33^* ± 0.16

0.07^* ± 0.02

 63

gi|170458

Threonine deaminase, partial, Solanum lycopersicum

194

9

4

65.05/5.26

1.01 ± 0.01

0.82 ± 0.04

5.90^* ± 0.09

7.29^* ± 0.29

 64

gi|170458

Threonine deaminase, partial, Solanum lycopersicum

443

18

7

65.05/5.26

0.22^* ± 0.01

0.40^* ± 0.02

5.28^* ± 0.62

2.96^* ± 0.28

 65

gi|170458

Threonine deaminase, partial, Solanum lycopersicum

175

7

3

65.05/5.26

0.97 ± 0.01

0.55 ± 0.02

4.35^* ± 0.03

7.62^* ± 0.14

 66

gi|460398434

Cysteine synthase, Solanum lycopersicum

317

20

4

41.26/5.41

0.99 ± 0.02

6.39^* ± 0.21

2.11^* ± 0.22

0.33^* ± 0.04

 67

gi|460404180

Cysteine synthase, Solanum lycopersicum

274

17

5

34.34/5.93

1.89 ± 0.13

0.63 ± 0.38

0.33^* ± 0.16

1.09 ± 0.19

 68

gi|460389504

Protein disulfide-isomerase-like, Solanum lycopersicum

82

6

2

55.11/4.81

0.53 ± 0.02

0.55 ± 0.01

3.51^* ± 0.28

3.39^* ± 0.22

 69

gi|460395973

Heat shock protein 83, Solanum lycopersicum

76

1

1

90.77/5.23

0.96 ± 0.04

1.99 ± 0.03

19.73^* ± 0.24

9.53^* ± 0.23

 70

gi|460395973

Heat shock protein 83, Solanum lycopersicum

193

3

3

90.77/5.23

1.24 ± 0.23

3.10^* ± 0.37

2.07^* ± 0.26

0.82 ± 0.07

 71

gi|762844

Hsc70, Solanum lycopersicum

115

4

2

71.87/5.18

5.38^* ± 0.40

0.60 ± 0.15

1.04 ± 0.28

9.20^* ± 0.21

 72

gi|170386

Glucose-regulated protein 78, Solanum lycopersicum

211

12

3

41.32/8.51

2.45^* ± 0.40

0.73 ± 0.14

1.31 ± 0.26

4.32^* ± 0.41

 73

gi|145341034

AAA-metalloprotease FtsH, Ostreococcus lucimarinus

131

6

4

67.77/5.23

0.92 ± 0.05

0.63 ± 0.29

0.44^* ± 0.01

0.75 ± 0.32

 74

gi|1168191

14-3-3 protein 4 OS, Solanum lycopersicum

58

25

4

29.40/4.69

0.78 ± 0.33

0.67 ± 0.29

0.10^* ± 0.04

0.11^* ± 0.05

 75

gi|3041662

14-3-3 protein 3, Solanum lycopersicum

165

12

2

29.40/4.74

0.56 ± 0.23

1.33 ± 0.24

0.21^* ± 0.04

0.08^* ± 0.02

 76

gi|460405902

Plasma membrane-associated cation-binding protein 1, Solanum lycopersicum

95

6

1

21.98/5.03

1.71 ± 0.37

0.99 ± 0.19

0.20^* ± 0.04

0.34^* ± 0.04

 77

gi|590715109

Transducin family protein/WD-40 repeat family protein isoform 1, Theobroma cacao

57

2

1

87.16/6.40

0.82 ± 0.01

0.18^* ± 0.01

2.87^* ± 0.03

12.76^* ± 0.11

 78

gi|460393840

Proliferation-associated protein 2G4-like, Solanum lycopersicum

134

7

2

43.07/6.41

2.16^* ± 0.17

0.59 ± 0.15

0.27^* ± 0.09

0.97 ± 0.19

 79

gi|525314284

Hop-interacting protein THI113, Solanum lycopersicum

117

10

2

37.34/5.82

0.93 ± 0.14

0.11^* ± 0.07

0.24^* ± 0.18

1.96 ± 0.10

 80

gi|350536897

Cytosolic ascorbate peroxidase 1, Solanum lycopersicum

113

14

2

27.73/5.61

1.54 ± 0.26

0.66 ± 0.06

0.42^* ± 0.09

0.96 ± 0.09

 81

gi|350536897

Cytosolic ascorbate peroxidase 1, Solanum lycopersicum

115

7

1

27.73/5.61

7.20^* ± 0.13

7.42^* ± 0.32

6.03^* ± 0.16

5.85^* ± 0.07

 82

gi|350539113

Ascorbate peroxidase, Solanum lycopersicum

141

5

2

42.38/8.65

1.90 ± 0.20

0.75 ± 0.18

0.32^* ± 0.04

0.81 ± 0.07

 83

gi|460373807

Putative lactoylglutathione lyase, Solanum lycopersicum

126

15

5

32.95/5.95

0.82 ± 0.22

0.17^* ± 0.07

0.44^* ± 0.21

2.05^* ± 0.24

 84

gi|50400860

Monodehydroascorbate reductase, Solanum lycopersicum

255

17

5

47.12/5.77

0.85 ± 0.07

0.49^* ± 0.17

0.40^* ± 0.18

0.69 ± 0.16

 85

gi|251895

Polyphenol oxidase, Solanum lycopersicum

169

7

5

66.83/6.61

1.96 ± 0.06

2.87^* ± 0.04

15.32^* ± 0.10

10.49^* ± 0.42

 86

gi|460397526

Heme-binding protein 2, Solanum lycopersicum

183

17

3

26.12/7.59

0.84 ± 0.08

0.82 ± 0.05

4.29^* ± 0.25

4.41^* ± 0.18