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Table 1 Putative DNA methylation pathway genes in Pineapple

From: Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple

   

Pineapple (Ananas comosus) expression level (FPKM)

  

Name

Length (a.a)a

Locus

4 am

10 am

4 pm

10 pm

  

(Arabidopsis)

Green

White

Green

White

Green

White

Green

White

MET1

 

VIM1,2,3,4,5,6

645

Aco016212.1

7.46

5.59

3.27

8.46

4.72

7.90

7.54

6.88

 

MET1,2a,2b,3

1534

Aco005236.1

1.31

6.52

1.96

4.58

2.42

3.87

1.93

5.87

CMT3

 

SUVH4

624

Aco004654.1

9.77

19.22

7.51

18.30

9.94

17.35

10.49

18.84

 

CMT2

1295

Aco015994.1

2.87

15.82

3.24

18.74

7.69

18.30

4.58

18.97

 

CMT3

839

Aco013381.1

0.19

19.10

0.00

11.51

0.29

22.40

0.09

21.01

RdDM

Pol IV recruit

CLSY1/CLSY2

1256

Aco011099.1

0.98

4.92

1.84

4.19

4.69

6.64

3.16

6.52

SHH1/SHH2

258

Aco017233.1

27.03

21.65

30.40

31.64

23.48

22.87

31.70

22.40

Pol IV

NRPD1

1453

Aco015559.1

1.16

3.66

4.37

8.40

10.37

7.46

3.21

6.56

Pol IV+V

NRPD2/NRPE2

1172

Aco009438.1

14.13

36.95

17.12

42.20

22.25

41.79

19.55

44.53

Pol IV+V

NRPD4/NRPE4

205

Aco018391.1

40.66

93.33

53.21

59.94

55.36

87.71

64.26

78.54

Pol V

NRPE1

1976

Aco023234.1

9.14

13.25

10.37

14.25

14.42

13.37

16.44

13.77

Pol V

NRPE5

222

Aco000628.1

9.73

10.40

6.58

17.27

10.27

13.87

9.90

13.93

Pol V

NRPE9B

114

Aco027798.1

0.00

0.22

0.00

0.00

0.00

0.00

0.00

0.00

Pol V recruit

DRD1

888

Aco017413.1

6.13

13.41

6.31

14.46

5.84

13.52

7.04

14.76

DMS3

420

Aco010843.1

14.16

34.50

32.62

47.87

25.58

41.69

22.55

42.65

RDM1

163

Aco004257.1

10.29

4.50

7.48

2.37

9.67

3.65

7.14

3.46

SUVH2/9

650

Aco026941.1

5.11

11.78

8.82

15.09

7.62

12.09

7.19

12.68

 

RDR2

1133

Aco015280.1

3.58

5.88

2.37

6.57

6.99

7.47

6.29

7.62

 

DCL1

1910

Aco016650.1

8.67

20.76

15.73

31.37

20.01

18.71

13.42

22.14

 

DCL2

1388

Aco016157.1

10.64

10.61

5.64

38.63

3.61

24.86

6.48

22.66

 

DCL3

1580

Aco009891.1

4.10

18.07

8.23

18.51

13.62

17.98

8.24

18.58

 

DCL4

1702

Aco008189.1

7.31

5.42

5.36

9.13

7.24

7.44

7.01

7.26

 

HEN1

942

Aco008418.1

1.21

2.49

2.54

3.03

2.46

2.48

2.32

3.50

 

AGO4

924

Aco017860.1

46.97

108.59

28.67

76.68

60.74

107.18

48.73

115.22

 

KTF1

1493

Aco005272.1

20.73

32.16

15.42

33.56

19.91

34.61

23.67

39.20

 

IDN2

647

Aco002916.1

10.84

25.56

7.05

19.13

11.89

21.67

11.84

26.22

 

SUVR2

740

Aco006945.1

4.65

17.09

5.42

17.02

13.64

20.20

9.10

20.00

 

DMS4

346

Aco012515.1

5.56

10.02

6.94

9.22

11.65

11.35

9.82

11.16

 

UBP26

1067

Aco013188.1

5.62

8.95

10.84

9.96

10.93

9.95

9.63

9.20

 

DRM2

626

Aco007653.1

7.66

12.17

7.38

13.61

4.34

10.75

6.97

12.09

 

LDL1

844

Aco002795.1

9.81

5.76

7.29

11.43

10.36

6.00

12.07

6.54

 

LDL2

746

Aco009449.1

5.12

6.00

4.22

6.48

3.19

5.43

4.89

5.99

 

JMJ14

954

Aco010573.1

9.71

36.65

18.16

28.14

14.35

29.02

13.24

38.39

Others

 

HDA6

471

Aco016535.1

34.31

15.17

12.77

26.36

13.70

20.04

24.47

21.08

 

RDR6

1196

Aco016551.1

2.61

2.88

1.65

6.96

2.61

4.84

4.30

4.50

 

MOM1

2001

Aco008982.1

14.63

19.69

18.57

29.89

12.73

20.91

12.70

22.35

 

MORC6

663

Aco020316.1

0.03

0.13

0.00

0.00

0.08

0.21

0.29

0.10

 

DDM1

764

Aco027111.1

49.64

41.94

41.52

34.79

44.96

39.71

58.30

40.03

 

DME

1987

Aco018501.1

9.56

40.31

7.75

31.70

15.71

38.49

10.70

40.59

 

ROS1

1393

Aco018808.1

0.17

2.21

0.06

0.57

0.34

2.25

0.33

2.34

 

DML2

1332

Aco002923.1

2.49

8.54

5.19

11.25

3.70

9.58

2.84

9.71

  1. a indicates length of the longest protein of this gene family