| 5 hmC | 5-hydroxymethylcytosine |
| 5 mC | 5-methylcytosine |
| ATR-FTIR | Attenuated Total Reflectance Fourier Transform Infrared |
| CG_DMV | demethylation of the CG contexts |
| CHG_DMV | demethylation of the CHG contexts |
| dcAdoMet | decarboxylated form of SAM |
| DMV | demethylation |
| IDM | increased DNA methylation complex |
| IF | indirect effect |
| metAFLP | methylation-sensitive Amplified Fragment Length Polymorphism |
| MMR | mismatch repair |
| NER | nucleotide excision repair |
| RdDM | RNA-directed DNA methylation |
| ROS1 | REPRESSOR OF SILENCING 1 |
| SAM | S-adenosyl-L-methionine, |
| SV | sequence variation |
| TCA | tricarboxylic acid cycle |
| TE | total effect |
| VAF | variance accounted for |
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