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Table 4 Differentially expressed Fom genes significantly up-regulated in planta during infection of DZA315 or A17 at 2 and 7 dpi. DEGs are ranked by DZA315 fold change (FC) over in vitro at 2 dpi. Bold FC indicates DZA315 fold changes greater than A17

From: Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors

Protein ID

Chrom./scaffolda

Sec. pred.b

SSPc

Eff.P pred.d

AAe

Potential rolef

DZA315 FCg

A17 FCg

IV h

2dpi

7dpi

2dpi

7dpi

 

Fom_SIX13

CDC

+

SSP

-

292

SIX effector

397336

1290948

280959

1123836

-

Fom_16257

CDC

+

SSP

+

91

uncharacterised

172951

741455

150562

301124

-

Fom_16301

CDC

+

SSP

+

144

LysM

161369

912838

114105

425854

-

Fom_16235

CDC

+

SSP

+

264

uncharacterised

37641

172951

35120

131072

+

Fom_15517

CDC

-

  

567

abhydrolase/peptidase

12417

7132

7643

8780

+

Fom_16729

core

-

  

54

Protease (partial)

11585

212927

23170

114105

-

Fom_16326

CDC

+

SSP

+

111

uncharacterised

11585

106464

7132

57052

+

Fom_SIX1

CDC

+

SSP

-

279

SIX effector

11585

61147

10809

40342

+

Fom_SIX8

CDC

+

SSP

+

141

SIX effector

8780

106464

8192

70240

+

Fom_16154

CDC

+

 

-

610

GMC_oxidoreductase

4390

20171

3566

12417

+

Fom_16208

core

-

  

185

peptidase

2896

37641

2048

15287

+

Fom_12303

core

+

SSP

+

169

uncharacterised

2195

61147

2353

23170

-

Fom_16263

CDC

-

  

235

uncharacterised

2195

14263

1911

6208

+

Fom_15948

CDC

+

SSP

+

215

peroxidase

1911

16384

1097

6654

+

Fom_10610

core

+

 

-

478

oxidoreductase

1552

5793

1448

2896

+

Fom_16592

CDC

-

  

87

uncharacterised

1261

5043

630

3566

+

Fom_15730

CDC

-

  

199

GST

776

891

315

588

+

Fom_15949

CDC

-

  

373

peroxidase

776

8192

776

4096

+

Fom_09820

core

-

  

545

p450

512

239

388

239

+

Fom_09550

core

-

  

87

uncharacterised

446

3566

1097

3822

+

Fom_SIX9

CDC

+

SSP

+

122

SIX effector

239

1552

208

1024

+

Fom_15614

CDC

+

SSP

-

221

glyco_hydrolase

223

478

181

274

+

Fom_06101

core

-

  

420

uncharacterised

194

239

181

128

+

Fom_14503

core

-

  

138

SnoaL

169

119

223

45

+

Fom_07856

core

-

  

533

MFS

147

169

97

84

+

Fom_16718

core

-

  

79

protease

111

2702

208

1176

+

Fom_07866

core

-

  

123

uncharacterised

79

69

60

34

+

Fom_16085

CDC

-

  

403

2OG-FeII_Oxy

60

446

52

315

+

Fom_10284

core

-

  

112

ligase

60

239

49

338

+

Fom_02574

core

+

SSP

+

87

uncharacterised

49

32

32

24

+

Fom_04867

core

-

  

300

NAD_binding

39

23

32

9

+

Fom_07859

core

-

  

292

LigB, dioxyenase

37

17

11

11

+

Fom_01704

core

-

  

398

methionine synth.

24

26

32

23

+

Fom_13701

core

-

  

391

oxidoreductase

24

24

20

11

+

Fom_12076

core

+

 

-

324

uncharacterised

21

45

26

20

+

Fom_02353

core

+

SSP

-

295

endoglucanase

21

39

23

23

+

Fom_15788

CDC

+

SSP

+

199

uncharacterised

18

69

11

49

+

Fom_04087

core

+

SSP

+

158

uncharacterised

16

91

13

42

+

Fom_10931

core

+

 

-

330

pectinesterase

11

60

20

26

+

Fom_08395

core

+

SSP

-

291

abhydrolase

9

17

6

5

+

Fom_16385

CDC

-

  

195

glyco_hydrolase

9

39

10

30

+

Fom_07662

core

-

  

438

aminotransferase

9

34

4

16

+

Fom_08559

core

+

 

-

433

glyco_hydrolase

8

64

9

37

+

Fom_04883

core

-

  

514

p450

7

9

7

5

+

Fom_15521

CDC

-

  

660

AMP-binding

6

5

5

5

+

Fom_05481

core

+

SSP

-

292

uncharacterised

6

5

5

3

+

Fom_01040

core

-

  

124

uncharacterised

6

7

12

8

+

Fom_16221

CDC

-

  

83

glyco_hydrolase

5

37

6

23

+

Fom_16350

core

-

  

174

abhydrolase

5

2

5

4

+

Fom_10260

core

-

  

255

flavodoxin

5

10

3

5

+

Fom_09704

core

+

 

-

418

glyco_hydrolase

4

32

4

17

+

  1. apredicted core or CD chromosome (CDC) location
  2. bpredicted secreted based on SignalP
  3. cpredicted small secreted protein (SSP) based on ≤ 300 amino acids, SignalP, and ≤1 transmembrane domains
  4. dEffectorP prediction (performed if predicted to be secreted): + effector, - non-effector
  5. eBold font: protein length ≤ 300 amino acids
  6. fPotential role based on Pfam domain, best BlastP match or other characteristics
  7. gFold change in planta gene expression over in vitro conditions
  8. hexpression in vitro, –: 0-10 % RNA-Seq read coverage over all replicates, +: >10 % RNA-Seq read coverage over all replicates