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Table 3 Disease resistance annotated-genes which were DE (p < 0.05) between the two hosts before PVY inoculation

From: RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection

Gene ID

Pseudo counts PR

Pseudo counts RB

Ratio Pseudo counts PR over RB

Change of expression after PVY inoculation in PR

Change of expression after PVY inoculation in RB

Chr.

PGSC0003DMG400006296

68

0

Inf.

n.s.

n.s.

1

PGSC0003DMG400006297

24

10

2.4

n.s.

n.s.

1

PGSC0003DMG400013094

42

21

2.0

n.s.

n.s.

2

PGSC0003DMG400024337

8

0

Inf.

n.s.

n.s.

3

PGSC0003DMG400029452

116

42

2.8

n.s.

n.s.

4

PGSC0003DMG400029456

48

21

2.3

n.s.

n.s.

4

PGSC0003DMG400029457

68

25

2.7

n.s.

n.s.

4

PGSC0003DMG400029505

1018

281

3.6

n.s.

n.s.

4

PGSC0003DMG400029506

55

17

3.2

n.s.

n.s.

4

PGSC0003DMG400029460

43

13

3.3

n.s.

n.s.

4

PGSC0003DMG400013486

194

54

3.6

n.s.

n.s.

5

PGSC0003DMG400013490

1681

489

3.4

n.s.

n.s.

5

PGSC0003DMG400025615

16

0

Inf.

n.s.

n.s.

5

PGSC0003DMG400038713

15

0

Inf.

n.s.

n.s.

5

PGSC0003DMG400033131

238

127

1.9

n.s.

n.s.

6

PGSC0003DMG400024206

401

128

3.1

n.s.

n.s.

7

PGSC0003DMG400011907

16

0

Inf.

n.s.

n.s.

9

PGSC0003DMG400011906

20

0

Inf.

n.s.

n.s.

9

PGSC0003DMG400009272

9

5

1.8

n.s.

n.s.

11

PGSC0003DMG400027797

631

111

5.7

n.s.

n.s.

11

PGSC0003DMG401004578

65

17

3.8

n.s.

n.s.

12

PGSC0003DMG400029415

348

173

2.0

−0.79 (4 hpi O)

n.s.

12

−1.06 (4 hpi NTN)

PGSC0003DMG400007870

105

12

8.8

n.s.

n.s.

12

PGSC0003DMG400007872

162

24

6.8

n.s.

n.s.

12

PGSC0003DMG400034825

16

0

Inf.

n.s.

n.s.

12

PGSC0003DMG400030045

5

11

0.5

n.s.

n.s.

4

PGSC0003DMG400002217

141

383

0.4

n.s.

n.s.

4

PGSC0003DMG401011522

20

70

0.3

n.s.

n.s.

4

PGSC0003DMG400011527

35

89

0.4

n.s.

n.s.

4

PGSC0003DMG401015877

126

397

0.3

n.s.

n.s.

4

PGSC0003DMG400002961

32

81

0.4

n.s.

n.s.

4

PGSC0003DMG400003380

155

679

0.2

n.s.

n.s.

5

PGSC0003DMG400025547

14

32

0.4

n.s.

n.s.

5

PGSC0003DMG400005173

0

22

Inf.

n.s.

n.s.

6

PGSC0003DMG400033154

8

19

0.4

n.s.

n.s.

6

PGSC0003DMG400024203

0

14

Inf.

n.s.

n.s.

7

PGSC0003DMG400029586

0

51

Inf.

n.s.

+1.25 (4 hpi)

8

PGSC0003DMG400029590

32

119

0.3

n.s.

n.s.

8

PGSC0003DMG400042937

0

13

Inf.

n.s.

n.s.

8

PGSC0003DMG400002278

0

9

Inf.

n.s.

n.s.

8

PGSC0003DMG400002279

14

34

0.4

n.s.

n.s.

8

PGSC0003DMG400016599

13

136

0.1

n.s.

n.s.

9

PGSC0003DMG400016628

6

29

0.2

n.s.

n.s.

9

PGSC0003DMG401008349

40

137

0.3

n.s.

n.s.

10

PGSC0003DMG400011426

41

247

0.2

n.s.

n.s.

10

PGSC0003DMG403008349

85

264

0.3

n.s.

n.s.

10

PGSC0003DMG400019669

125

323

0.4

n.s.

n.s.

11

PGSC0003DMG400027410

0

78

Inf.

n.s.

n.s.

11

PGSC0003DMG400030239

8

25

0.3

n.s.

n.s.

11

PGSC0003DMG400030240

0

7

Inf.

n.s.

n.s.

11

PGSC0003DMG400004295

70

171

0.4

n.s.

n.s.

12

PGSC0003DMG400024273

17

104

0.2

n.s.

n.s.

12

PGSC0003DMG401029345

265

589

0.4

n.s.

n.s.

12

PGSC0003DMG400045101

0

17

Inf.

n.s.

n.s.

12

PGSC0003DMG400047046

26

85

0.3

n.s.

n.s.

12

  1. Pseudo counts were determined with NBP-Seq. Genes which were identified as pseudogenes by Lozano et al. [11] are italicized