Table 1.
Botrytis cinerea genes with known function presenting a sequence variant and/or overlapping with in vitro culture-induced DMRs. Columns that Gene Variant and Gene/DMR overlap indicate the number (#) and percentage (%) of genes in each functional group with a genetic variant or overlapping with a differentially methylated region, respectively. Column DMR type indicates how methylation levels changed when comparing all three samples (T1, T8 and T8P). 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)). Virul. s.l. indicates virulence genes in abroad sense and includes genes associated with: appressorium formation, virulence in a strict sense (virulence s.s.) and CAZyme genes.
| Gene Function | Total | Gene Variant | Gene/DMR Overlap | DMR Type | Reference | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| #G/D | %G/D | #G/D | %G/D | Recovery | Non- Recovery |
||||||
| 0 | 2 | 1a | 1b | ||||||||
| Housekeeping | 5 | - | - | - | - | - | - | - | - | [25] | |
| Apoptosis | 10 | 2 | 20 | 4 | 40.0 | 3 | 1 | - | - | [25] | |
| Conidiation | 16 | - | - | 6 | 37.5 | 1 | 2 | - | 3 | [25] | |
| Mating and fruit body development | 32 | 6 | 18.8 | 6 | 18.7 | 1 | 4 | 1 | 1 | [25] | |
| Secondary metabolism | 51 | 4 | 7.8 | 14 | 27.5 | 9 | 3 | 2 | 3 | [25] | |
| Signalling pathways | 176 | 6 | 3.4 | 54 | 30.7 | 12 | 17 | 7 | 20 | [25] | |
| Sclerotium formation | 249 | 7 | 2.8 | 67 | 26.9 | 26 | 31 | 10 | 13 | [25] | |
| Virul. s.l. | Appressorium | 12 | 2 | 16.7 | 3 | 25.0 | 1 | - | - | 3 | [25] |
| Virulence s.s. | 17 | 1 | 5.9 | 4 | 23.5 | 1 | 1 | 1 | 2 | [26] | |
| CAZyme genes | 1155 | 50 | 4.3 | 320 | 27.7 | 112 | 132 | 45 | 99 | [27] | |
| Total | 1577 | 68 | 4.3 | 478 | 30.3 | 166 | 191 | 66 | 144 | ||