E_SE_28
Whole-genome bisulfite sequencing was performed by the CNRGH laboratory (J. Tost, Evry, France) in accordance with the published procedure (http://www.nugen.com/products/ovation-ultralow-methyl-seq-library-systems) adapted from 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. Sequence capture following ROCHE recommendation was done. A Roche NimbleGen SeqCap EZ Design (https://sequencing.roche.com/content/dam/rochesequence/worldwide/resources/brochure-seqcap-ez-prime-choice-probes-SEQ100193.pdf) of custom 200 Mb was realized by NimbleGen service using the 3 following supporting reference sequences and conditions (see Fig. 1B and Supplementary Material 1 for details): i) 866 Pinus pinaster gene models from Seoane-Zonjic et al. (2016) with the condition of covering the whole gene sequences , ii) 206,574 Pinus pinaster Unigenes derived from Caas et al. (2017) with the conditions of covering the whole Unigene sequences ifsize is under 1,578 bp and 789 pb in 5 and 3 for a total of 1,578 bp per unigene if sizeis  over or equal to 1,578 pb and iii) 51,749 Promoters from Pita v2.0 genome (https://treegenesdb.org/FTP/Genomes/Pita/v2.0/; Zimin et al., 2017) with the condition of covering until 1,205 bp upstream to the transcription starting site (TSS).