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Table 1 DEGs between Wild type (WT) and StRIK-RNAi (RIK) tuber periderm

From: Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress

Functional group

Normalized reads

DE

Uniref gene Description

Best BLASTP TAIR

WT (1)

StRIK-RNAi (2)

RNA metabolism

PGSC0003DMT400063700

47

747

2 > 1

RNase H family protein

AT5G35695

PGSC0003DMT400071451

63

729

2 > 1

RRNA intron-encoded homing endonuclease

-

PGSC0003DMT400091537

280

2636

2 > 1

RRNA intron-encoded homing endonuclease

-

PGSC0003DMT400085242

214

2014

2 > 1

RRNA intron-encoded homing endonuclease

-

PGSC0003DMT400079124

0

3

2 > 1

RNA recognition motif-containing protein

AT5G19030

PGSC0003DMT400063698

0

15

2 > 1

RNase H family protein

-

PGSC0003DMT400094705

509

6089

2 > 1

RRNA intron-encoded homing endonuclease

-

Transposable elements (TE)-related genes

PGSC0003DMT400046437

20

1

1 > 2

TNP2, partial

-

PGSC0003DMT400041204

34

485

2 > 1

Retrotransposon protein

AT5G41980

PGSC0003DMT400092517

47

1

1 > 2

LINE-type retrotransposon LIb DNA, complete sequence, Insertion at the S14 site

-

PGSC0003DMT400085583

0

5

2 > 1

Transposon MuDR mudrA

-

PGSC0003DMT400039369

1188

296

1 > 2

Transposase

-

PGSC0003DMT400003803

6

92

2 > 1

Transposase

AT1G43722

Stress

PGSC0003DMT400083063

1

48

2 > 1

Ribulose bisphosphate carboxylase large chain

ATCG00490

PGSC0003DMT400026705

3

30

2 > 1

11S globulin isoform 4

AT5G44120

PGSC0003DMT400080875

2528

27100

2 > 1

Senescence-associated protein

-

PGSC0003DMT400013091

0

4

2 > 1

PR-1

AT3G19690

PGSC0003DMT400005448

0

5

2 > 1

Vacuolar H+-pyrophosphatase

AT1G15690

PGSC0003DMT400024872

0

12

2 > 1

K+ channel inward rectifying

AT5G46240

PGSC0003DMT400061541

3

60

2 > 1

Dehydration responsive element binding protein

AT5G05410

Proteolysis

PGSC0003DMT400026261

316

3520

2 > 1

Nb cell deth marker

AT1G17860

PGSC0003DMT400026262

439

6499

2 > 1

Conserved gene of unknown function

AT1G17860

PGSC0003DMT400024552

3

38

2 > 1

Gene of unknown function

AT1G50690

PGSC0003DMT400049320

0

4

2 > 1

Ulp1 protease family, C-terminal catalytic domain containing protein

-

PGSC0003DMT400040325

16

2

1 > 2

F-box family protein

AT3G07870

Signaling

PGSC0003DMT400047864

5

37

2 > 1

Signal transducer

AT1G67900

PGSC0003DMT400001990

2

8

2 >1

Calcium/calmodulin-dependent protein kinase CaMK3

AT3G50530

PGSC0003DMT400047866

16

79

2 > 1

Signal transducer

AT1G67900

PGSC0003DMT400054991

0

4

2 > 1

Calcium-dependent protein kinase 20

AT2G38910

PGSC0003DMT400047867

14

71

2 > 1

Signal transducer

AT1G67900

Metabolism

PGSC0003DMT400052839

1

18

2 > 1

Beta-amylase PCT-BMYI

AT4G17090

PGSC0003DMT400049003

686

12004

2 > 1

Cytochrome P450 like_TBP

-

PGSC0003DMT400070122

5

26

2 > 1

Glucosyltransferase

AT4G36770

PGSC0003DMT400014902

3

0

1 > 2

Cytochrome P450

AT1G12740

PGSC0003DMT400019561

0

5

2 > 1

Cytochrome P450

AT5G36110

Acyl lipid Metabolism

PGSC0003DMT400042102

1

10

2 > 1

Acetyl-coenzyme A carboxylase carboxyl transferase alpha

AT2G38040

PGSC0003DMT400079076

0

3

2 > 1

Acyl-[acyl-carrier-protein] desaturase

AT1G43800

  1. List of genes showing log2FC values ≤ -2 and ≥ 2 classified in the main functional groups. For each gene the mean of normalized reads (effective counts) found in Wild type replicates (n = 3) and StRIK-RNAi (line 9 n = 1; line 12 n = 2; line 47 n = 3) is shown. Also, it is reported the potato gene identifier, the Uniref gene identifier and the best BLASTP in TAIR (e value ≤ 10-5)
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BMC Plant Biology

ISSN: 1471-2229

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