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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