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Table 1 Cd-regulated differentially expressed genes (DEGs) mapped to the metabolic pathways

From: Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes

BinName

FPKM

Cd1h/ck1h

Rice gene annotation

Transcript ID

ck1h

Cd1h

log2FC

q_value

Jasmonate synthesis-degradation and signaling

 Os06g11290.1

5.18

435.09

6.39

0.0019

12-oxophytodienoate reductase, OsOPR1

 Os06g11210.1#

58.99

717.03

3.60

0.0019

OsOPR5 [Q69TI0]

 Os06g11240.1

14.15

339.14

4.58

0.0019

OPR

 Os06g11200.1

0.15

2.40

3.98

0.0188

OPR

 Os03g55800.1

29.03

146.45

2.33

0.0019

allene oxide synthase, AOS1

 Os03g12500.1

2.23

13.52

2.60

0.0019

allene oxide synthase, AOS2

 Os12g05440.1*

1.85

58.66

4.98

0.002

cytochrome P450, CYP94C2b

 Os03g08310.1*

1.88

27.26

3.86

0.002

ZIM domain containing protein, OsJAZ9

 Os03g28940.1

38.17

106.38

1.48

0.0019

ZIM domain containing protein

 Os09g02710.1

0.63

4.20

2.73

0.0035

Arabidopsis loss of the timing of Et and JA biosynthesis 1

Abscisic acid synthesis-degradation and signaling

 Os03g44380.1

0.53

5.75

3.43

0.0019

9-cis-epoxycarotenoid dioxygenase, OsNCED3

 Os07g05940.1

0.59

99.97

7.41

0.0019

OsNCED4

 Os12g42280.1

2.63

32.42

3.62

0.0019

OsNCED5

 Os12g29400.1

5.88

14.09

1.26

0.0019

ABA-responsive protein [Q2QQY9]

 Os04g44510.1

51.06

244.45

2.26

0.0019

ABA-responsive protein (GRAM domain)

 Os04g44500.1

17.60

49.88

1.50

0.0019

ABA-responsive protein (GRAM domain)

 Os10g04860.1

5.05

2.26

−1.16

0.0019

aldehyde oxidase

 Os02g52780.2

0.71

14.01

4.30

0.0019

OsbZIP23

Ethylene signaling

 Os07g48630.1

52.93

109.98

1.06

0.002

ethylene-insensitive 3

 Os02g43790.1

41.57

265.23

2.67

0.002

ethylene-responsive transcription factor, OsBIERF3

 Os03g09170.1

20.44

218.22

3.42

0.002

ERF

 Os04g46220.1

44.26

119.27

1.43

0.002

ERF

 Os08g31580.1

102.51

268.56

1.39

0.002

ERF

 Os01g54890.1

4.75

31.18

2.71

0.034

ERF2

 Os01g58420.1

49.28

134.22

1.45

0.002

OsERF3

 Os11g06770.2*

0.10

0.70

2.75

0.027

ERF110

 Os02g43970.1*

2.93

7.61

1.37

0.002

ABA-responsive DREB gene, ARAG1

 Os10g41330.2*

5.79

64.06

3.47

0.002

AP2 domain

 Os06g10780.1*

2.17

6.55

1.59

0.002

AP2 domain

 Os02g43940.1*

1.74

6.56

1.92

0.002

AP2 domain, OsDREB4–1

 Os09g28440.1

0.59

47.37

6.32

0.002

AP2 domain, OsEATB

 Os08g36920.1#

0.76

70.32

6.53

0.002

AP2 domain

 Os03g08460.1

91.75

42.47

−1.11

0.002

AP2 domain

 Os03g08490.1

215.27

81.73

−1.40

0.002

AP2 domain

 Os03g08500.1

538.17

256.44

−1.07

0.002

AP2 domain

 Os04g08740.3

68.92

31.96

−1.11

0.002

ethylene receptor, OsETR2 [Q7XX84]

Gibberellin synthesis-degradation

 Os06g37300.2

0.22

0.01

−2.36

1.1290

ent-kaurene oxidase 4, OsKO4 [Q0DBF4]

 Os03g63970.1*

18.68

0.00

−1.12

40.5099

gibberellin 20 oxidase 1

 Os05g48700.1

2.84

0.01

1.34

1.1252

gibberellin 2-beta-dioxygenase

Metal binding, chelation and storage

 Os04g57200.1

54.50

169.43

1.64

0.002

heavy metal transport/detoxification protein

 Os04g57200.2

3.10

47.85

3.95

0.002

 Os04g17100.1

2.63

32.28

3.62

0.0063

heavy metal-associated domain protein, HMAD

HMAD

 Os04g17100.2

43.72

123.38

1.50

0.0019

 Os03g05750.1

0.54

89.45

7.38

0.003

HMAD

 Os03g05750.2

9.01

212.68

4.56

0.002

 Os02g37290.1

38.65

132.69

1.78

0.002

HMAD

 Os02g37300.1

11.63

66.20

2.51

0.002

HMAD

 Os02g37330.1

3.99

98.49

4.63

0.002

HMAD

 Os04g39350.1

4.57

33.87

2.89

0.002

HMAD

 Os04g39010.1

0.94

3.69

1.97

0.022

HMAD

 Os02g37320.1

2.57

19.20

2.90

0.002

HMAD

 Os02g37320.2

9.45

84.16

3.15

0.002

 Os01g48710.1

116.94

46.15

−1.34

0.002

HMAD

 Os03g64340.1*

5.31

12.44

1.23

0.0050

HMAD

Divalent cations transporters

 Os08g10630.1

19.33

6.55

−1.56

0.0019

ZRT/IRT-like protein, OsZIP4 [Q6ZJ91]

 Os05g10940.1

40.47

19.81

−1.03

0.0019

OsZIP7 [Q6L8F7]

 Os05g39560.1

5.37

1.36

−1.98

0.0113

OsZIP5 [Q6L8G0]

 Os05g39560.2

40.35

9.21

−2.13

0.002

 Os06g37010.1

5.56

2.13

−1.39

0.0050

OsZIP10 [Q5Z653]

 Os05g39540.2*

97.22

25.45

−1.93

0.0019

OsZIP9 [Q0DHE3]

 Os03g46470.1*

14.68

2.46

−2.58

0.0076

Iron-regulated transporter 1, OsIRT1

ABC transporters and pleiotropic drug resistance proteins

 Os01g42380.1#

1.35

5.99

2.15

0.0019

ABCG36/OsPDR9 , pleiotropic drug resistance protein

 Os01g42410.1

3.66

21.96

2.59

0.0050

ABCG37/OsPDR8 [Q8GU89]

 Os02g11760.1

0.34

2.90

3.10

0.0019

ABCG39/OsPDR7 [Q8GU88]

 Os01g42370.1

0.28

0.91

1.68

0.0019

ABCG35/OsPDR11 [Q8GU92]

 Os08g29570.1

0.32

8.42

4.72

0.0101

ABCG44/OsPDR17 [Q6YW62]

 Os08g29570.2

4.95

18.57

1.91

0.002

 Os01g61940.1*

10.43

25.90

1.31

0.0019

ABC transporter family protein

MATE family of citrate/H+ antiport transporters

 Os08g43654.1*

1.05

2.52

1.26

0.026

MATE efflux family protein

 Os12g03260.1*

1.50

4.33

1.53

0.047

MATE

 Os04g48290.1

3.72

8.19

1.14

0.002

MATE

 Os02g45380.1

1.23

8.37

2.76

0.002

MATE

other transporters

 Os12g25200.1

123.93

50.25

−1.30

0.002

chloride transporter

 Os02g36414.1

162.32

70.28

−1.21

0.002

transporter family protein

 Os04g37970.1

118.36

43.01

−1.46

0.002

transporter family protein

 Os07g24230.1

1.26

0.38

−1.71

0.014

integral membrane transporter family protein

 Os01g14520.1

131.86

45.76

−1.53

0.002

dicarboxylate /malic acid transport protein

 Os09g31130.1

1.58

7.13

2.17

0.035

citrate transporter

 Os10g30790.1

26.30

94.24

1.84

0.046

inorganic phosphate transporter, OsPT8

 Os10g30790.3*

25.00

80.55

1.69

0.016

Mitochondrial electron transport

 Os07g37730.1

0.15

9.07

5.96

0.0035

NADH-ubiquinone oxidoreductase

 Os04g51150.1

14.41

35.47

1.30

0.0019

AOX1A, alternative oxidase

 Os04g51160.1

0.66

46.99

6.15

0.0019

AOX1B

 Os10g39870.1

10.79

29.33

1.44

0.0019

Arabidopsis Transmembrane protein G1P-related 1

 Os05g09550.1

1.37

4.81

1.81

0.0482

Der1-like family domain containing protein

 Os02g37000.1*

6.37

16.29

1.35

0.0019

mitochondrial prohibitin complex protein 1

Heat-shock transcription factor (HSF) family

 Os09g35790.1*

0.76

6.99

3.20

0.0168

OsHsfB2c [Q652B0]

 Os09g35790.2*

9.03

26.10

1.53

0.0019

 Os02g32590.1

1.21

7.07

2.55

0.0019

OsHsfA3 [Q6H6Q7]

 Os02g32590.2

0.38

2.76

2.88

0.0218

 Os04g48030.1

3.05

14.05

2.20

0.0178

OsHsfB2a [Q7XRX3]

 Os10g28340.1

0.62

12.76

4.36

0.0019

OsHsfA2c

 Os10g28340.2

3.72

15.96

2.10

0.0135

 Os03g12370.3

0.40

4.95

3.65

0.0101

OsHsfA9 [Q10PR4]

 Os08g43334.2

2.45

44.04

4.17

0.0019

OsHsfB2b [Q6Z9C8]

 Os02g13800.1

15.01

50.05

1.74

0.0019

OsHsfC2a [Q6EUG4]

NAC domain transcription factor family

  

 Os01g50360.1*

2.52

1.09

−1.21

0.026

NAC domain containing protein

 Os11g03300.2

16.07

38.93

1.28

0.002

OsNAC10

 Os01g60020.1

5.77

25.25

2.13

0.002

OsNAC4

 Os07g12340.1

12.81

455.79

5.15

0.002

OsNAC3 [Q7EZT1]

 Os03g60080.1#

88.35

942.97

3.42

0.002

SNAC1

WRKY domain transcription factor family

 Os02g08440.1#

2.03

125.38

5.95

0.0019

WRKY71

 Os02g08440.4

24.26

179.27

2.89

0.0019

 Os05g27730.1

101.45

430.59

2.09

0.0019

OsWRKY53

 Os01g61080.1

6.51

92.36

3.83

0.0019

OsWRKY24

 Os01g09100.1

29.32

195.59

2.74

0.0019

OsWRKY10

 Os05g50610.2

0.89

2.44

1.45

0.0317

WRKY8

 Os08g13840.2

130.82

404.49

1.63

0.0019

WRKY25

 Os05g09020.1

1.47

13.65

3.21

0.0019

WRKY67

 Os05g09020.2

9.62

51.47

2.42

0.0019

 Os11g29870.1

5.02

15.26

1.60

0.0019

WRKY72

 Os09g25060.1

3.11

24.14

2.95

0.0019

OsWRKY76

 Os01g60600.1*

0.42

1.68

1.99

0.0323

WRKY108

  1. The Cuffdiff utility was used to evaluate the transcript differential expression between ck1h and Cd1h samples. The DEGs uniquely identified in our RNAseq samples are marked with stars. Rice genes with experimentally verified functions are presented in bold fonts. Rice gene annotation was also referred from UniProt (square brackets contain the accession number). The DEGs marked with pound signs were also upregulated by medium and low Cd stress in rice seedling roots in 3 previous reports [21, 27, 48]. The DEGs marked with sigma were also upregulated uniformly by the lowest Cd treatment [48] as well as in one of the two high-throughput transcriptome study [21, 27]. Those marked with triangle were regulated uniformly by Cd treatment in the two high-throughput studies, and those labeled M were detected only in the microarray analysis [21]