Table 2.
Number of differentially methylated regions (DMRs) between T1, T8 and T8P samples. DRMs (i.e., regions presenting significantly different methylation levels between one sample and the other two samples (FDR < 0.01)) were determined using a three-sample Kruskal-Wallis test. Methylation levels were analysed by sliding window analysis using swDMR. DMRs were determined for all cytosines and for three methylation contexts. DMRs were grouped according to their changing patterns into recovery (T1 = T8P) and non-recovery (T1< > T8P). Two subgroups were found for recovery (T1 = T8P < T8 (Type 0) and T1 = T8P > T8 (Type 2)) and non-recovery (T1 > T8 = T8P (Type 1a) and T1 = T8 < T8P (Type 1b)). Percentage of the total DMRs for each pattern type/sequence context is shown in parenthesis.
| Total | Recovery (%) | Total Recovery (%) |
No Recovery | |||
|---|---|---|---|---|---|---|
| Type 0 | Type 2 | In Vitro Induced (Type 1a) |
Plant Induced (Type 1b) |
|||
| mC | 2822 | 757 (26.82) | 860 (30.47) | 1617 (57.30) | 452 (16.02) | 753 (26.68) |
| CG | 70 | 17 (24.29) | 15 (21.43) | 32 (45.71) | 14 (20.00) | 24 (34.29) |
| CHG | 82 | 14 (17.07) | 30 (36.59) | 44 (53.66) | 15 (18.29) | 23 (28.05) |
| CHH | 1248 | 303 (24.28) | 490 (39.26) | 793 (63.54) | 137 (10.98)) | 318 (25.48) |
| Total | 4222 | 1395 (33.04) | 1091 (25.84) | 2486 (58.88) | 618 (14.64) | 1118 (26.48) |