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Table 4 Validation of RNA-Seq data using

From: Transciptome profiling at early infection of Elaeis guineensis by Ganoderma boninense provides novel insights on fungal transition from biotrophic to necrotrophic phase

Genes

Fold change of expression of

 

RNA-seq data

qPCR

in Ganoderma boninense-treated (T1 samples) compared to untreated control

in mock (T0 samples) compared to untreated control

Replicate 1

Replicate 2

Replicate 1

Replicate 2

Replicate 1

Replicate 2

3 d.p.i

7 d.p.i

11 d.p.i

3 d.p.i

7 d.p.i

11 d.p.i

3 d.p.i

7 d.p.i

11 d.p.i

3 d.p.i

7 d.p.i

11 d.p.i

3 d.p.i

7 d.p.i

11 d.p.i

3 d.p.i

7 d.p.i

11 d.p.i

EgEXP18

157.59*a

337.79*b

25.99*c

51.98*d

55.72*d

21.11*e

112.05 ± 2.68*b

105.28 ± 3.58*b

62.21 ± 2.44*c

119.44 ± 4.46*d,e

120.39 ± 4.70*e

10.36 ± 0.82d

13.31 ± 1.42a

11.08 ± 0.93a

3.40 ± 0.53a

14.97 ± 0.82d,e

6.76 ± 0.65d

2.88 ± 0.18d

EgPG

9.19*a

10.56*a

3.03b

6.50*c

4.92*c

ND

12.20 ± 1.22*a

11.68 ± 1.24*a

5.52 ± 0.79a,b

21.51 ± 2.19*d

18.76 ± 2.06*d

8.76 ± 1.27c

9.62 ± 1.53*a

2.52 ± 0.33b

2.31 ± 0.51b

8.67 ± 1.40c

2.43 ± 0.32c

2.25 ± 0.48c

EgBGIA

168.90*a

29.86*b

5.28c

78.79*d

24.25*e

ND

140.66 ± 30.61*b

29.46 ± 1.26a

3.90 ± 1.17a

147.81 ± 9.69*f

16.34 ± 3.73d,e

6.08 ± 0.66d

23.81 ± 3.56a

33.43 ± 2.21a

0.30 ± 0.03a

52.79 ± 5.05*c

43.20 ± 4.04*c,e

0.19 ± 0.05d

EgCht1

13.33*a

10.40*a

2.60*b

10.70*c

3.80*d

3.90*d

11.31 ± 0.44*e

4.84 ± 0.48*a,b

3.70 ± 0.08*b,c

27.26 ± 1.80*j

9.12 ± 0.31*g,h

4.79 ± 0.11h,i

5.62 ± 0.33*a

2.13 ± 0.09c,d

0.45 ± 0.02d

45.12 ± 1.69*f

11.00 ± 0.81*g

2.11 ± 0.16i

EgERF113

2.05*a

7.52a

13.30*b

3.65c

13.64d

45.30*e

6.30 ± 0.20*b

8.95 ± 0.50*c

21.04 ± 0.58*d

12.95 ± 0.85*f

7.35 ± 0.27*f

31.97 ± 2.26*g

0.20 ± 0.01a

0.06 ± 0.01a

0.13 ± 0.01a

1.37 ± 0.30e

0.79 ± 0.07e

0.70 ± 0.22e

EgFIT

5.50a

9.40*a

22.20*b

11.20*c

ND

76.50*d

8.40 ± 0.40*b

2.90 ± 0.12a

48.73 ± 2.12*c

4.72 ± 0.54*e

4.89 ± 0.34*e

18.32 ± 0.45*f

0.12 ± 0.02a

0.55 ± 0.03a

0.32 ± 0.05a

1.28 ± 0.13d

3.17 ± 0.13*d,e

2.55 ± 0.47d

EgMTP10

2.60a

2.50a

8.30a

5.60b

ND

35.50*c

8.18 ± 0.73a

7.81 ± 0.96a

172.68 ± 10.14*b

3.31 ± 0.56c

3.23 ± 2.71c

25.03 ± 1.56*d

ND

1.74 ± 0.10a

0.45 ± 0.02a

1.22 ± 0.08c

2.47 ± 0.07c

1.75 ± 0.22c

EgPIN8

2.30a

2.20a

3.00*a

7.80*b

5.40*b

41.80*c

75.66 ± 11.13a

7.44 ± 2.00a

1557.48 ± 33.63*b

27.48 ± 3.21d,e

57.97 ± 10.70*e

165.38 ± 14.24*f

ND

ND

ND

0.61 ± 0.05c

ND

ND

  1. EgEXP18: E. guineensis expansin-B18-like; EgPG: E. guineensis polygalacturonase-like; EgBGIA: E. guineensis glu S.griseus protease inhibitor-like; EgCht1: E. guineensis chitinase 1-like; EgERF113: E. guineensis ethylene-responsive transcription factor 113; EgMTP10: E. guineensis metal tolerance protein 10-like; EgPIN8: E. guineensis putative auxin efflux carrier component 8; EgFIT: E. guineensis FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR-like
  2. qPCREach replicate consisted of pooled root from six plants. Pairwise comparison of RNA-seq data was evaluated according to cut-off values of log2 fold change (FC) ≥ |1.0| and P-value < 0.01. Data of qPCR are expressed as fold change mean ± SEM of three individual technical replicates of T0 and T1 samples compared to untreated control. The fold expressions of each gene were normalized by three reference genes; GAPDH 2, NADH 5 and ß-actin expression levels. Significant differences between qPCR groups were determined using one-way ANOVA analysis followed by Tukey’s test. * indicate significant different compared to corresponding control at: P < 0.01 and log2 FC ≥ |1.0| for RNA-seq; and P < 0.01 for qPCR. Different superscript letters (a-j) between samples (within replicate) indicate significant different at: P < 0.01 and log2 FC ≥ |1.0| for RNA-seq; and P < 0.01 in mean values for qPCR. ND: not detected
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BMC Plant Biology

ISSN: 1471-2229

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