WGBS of European beech cambium
DNA was extracted from cambium tissue using Qiagen's DNeasy Plant Pro Kit (catalog no. 69204, Qiagen) following the manufacturer's protocol with the addition of 100 l of the solution PS per sample due to high amounts of phenolic compounds in beech species. We used NEBNext Ultra II DNA Library Prep Kit (catalog no. E7103, New England BioLabs) for sequencing library preparation and EZ-96 DNA Methylation-Gold MagPrep (catalog no. D5042, ZYMO) for bisulfite treatment. The protocol involved: i) end repair and 3' adenylation of sonicated DNA fragments by Covaris R230 (Covaris), ii) NEBNext adaptor ligation, iii) cleanup of libraries with AMPure XP Beads (catalog no. A63881, Beckman Coulter), iv) bisulfite treatment, v) PCR enrichment and index ligation using KAPA HiFi Uracil+ Kit (catalog no. KK2802, Agilent) and NEBNext Multiplex Oligos for Enzymatic Methyl-seq (catalog no. E7140L, New England BioLabs) for bisulfite libraries (12 cycles), vi) final cleanup with AMPure XP Beads. Finally, they were sequenced on a NovaSeq X Plus platform (Illumina) in a paired-end 150bp format.