RRBS libraries were prepared according to [31 (link)] modified by [31 (link),32 (link)]. Briefly, RRBS libraries were prepared using an RRBS-adapted protocol for which all the steps were automated on a robot (NGS STARlet, Hamilton, Bonaduz, Switzerland) as previously described [33 (link)]. After MspI cleavage of gDNA (200 ng), end-repair and ligation to 55 bp Illumina adapters for subsequent PCR amplification and paired-end sequencing, size selection was performed using SPRIselect magnetic beads (Beckman Coulter Life Sciences, Villepinte, France). Fragments ranging from 150 to 400 bp (genomic fragments of 40–290 bp with adapters) were selected and submitted to two consecutive bisulphite conversions with the EpiTect bisulphite kit (Qiagen, Les Ulis, France) following the manufacturer’s instructions. The libraries were produced by amplification with Pfu Turbo Cx hotstart DNA polymerase (Agilent Technologies, Les Ulis, France) using 14 PCR cycles and purified using AMPure XP beads (Beckman Coulter Life Sciences, Villepinte, France). All libraries were sequenced on an Illumina HiSeq4000 sequencer to produce 75 bp paired-end reads (Integragen SA, Evry, France).