Table 1.
Putative DNA methylation pathway genes 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 | ||
a indicates length of the longest protein of this gene family