title: Whole Genome Bisulfite Sequencing of Q. petraea buds
design: Whole genome bisulfite sequencing was performed using the Ovation Ultralow Methyl-seq kit (Tecan Genomics/ Nugen, San Carlos, CA, USA, http://www.nugen.com/products/ovation-ultralow-methyl-seq-library-systems) as indicated in  Daviaud et al. (2018). The workflow of the library preparation protocol follows the classical library preparation protocol, in which methylated adaptors are ligated to the fragmented DNA prior to bisulfite conversion. Briefly, 200 ng of genomic DNA was fragmented to approximately 200 base pairs (bp) using a Covaris ultrasonicator (Woburn, Massachusetts, USA). The purified and methylated adaptors compatible with sequencing on an Illumina HiSeq instrument were the ligated. The resulting DNA library was purified and bisulfite converted. A qPCR assay was performed to determine the optimal number of PCR amplification cycles (between 10 to 15 cycles) required to obtain a high diversity library with minimal duplicate reads prior to the actual library amplification. The twelve samples to be sequenced were combined at equimolar concentrations in a single pool and the sequencing was performed in paired ends (2 x 150 pb) on four lanes of an Illumina HiSeq4000 flow-cell to a minimal theoretical coverage of 30 X for each sample.