2.2 Tissue sampling
For each condition, the four left gill arches were sampled in 5 fish/salinity for epigenetic analysis and stored at -80°C. In the same fish, the four right gill arches were sampled for transcriptomic analysis. They were immersed into RNAlater (Qiagen, Mississauga, ON, Canada) overnight at 4 °C and stored at −80 °C for further analyses. The experiments were conducted according to the guidelines of the European Union (directive 86/609) and of the French law (decree 87/848) regulating animal experimentation. The experimental design has been approved by the French legal requirement concerning welfare of experimental animals (APAFIS permit no. 9045-201701068219555).

2.3 Genomic DNA extraction

Genomic DNA (gDNA) was isolated from a pool of the four sampled gill arches of each juvenile using a Maxwell Blood®16 DNA purification kit (Promega) with the following modifications: before adding proteinase K, gill arches were homogenized with 300 μl of lysis buffer and crushed for 30 seconds at room temperature with a laboratory mill and stainless steel beads (Mixer Mill MM 400, Retsch, Germany) and then briefly centrifuged for 10 seconds. Then the manufacturer’s instructions were followed for further gDNA extraction. Purity and concentration of gDNA was estimated using the Qubit ™ dsDNA BR Assay Kit and the Qubit ™ Fluorimeter (Thermo Scientific, Waltham, MA, USA).

2.4 Whole-genome bisulfite sequencing (WGBS)

Bisulfite-conversion, library construction and sequencing (Paired-end reads - 150 bp) were performed by Génome Québec (Montréal, Canada) on an Illumina HiSeq X (Illumina, San Diego, CA, USA). Quality of the metrics are indicated in Table 1S. Reads quality analysis and alignments were performed on the local Galaxy platform (http://bioinfo.univ-perp.fr). The quality of the reads was checked using FastQC (version 0.11.8, Andrews 2010), and MultiQC (version 1.9, Ewels et al., 2016) was used to aggregate fastQC results into a single report. Phred scores were higher than 25 for more than 90% of the reads’ length for all the sequences. FastQ reads were trimmed by Trim Galore (version 0.6.3, Krueger 2012) based on Phred score below 20 and the adaptors sequences were removed from reads. Trimmed reads were mapped with Bismark (version 0.22.1, Krueger et Andrews 2011) and aligned to the reference genome of European sea bass (Tine et al. 2014) providing global methylation percentages per genomic context (CpG, ChG and CHH). Methylation was called using Bismark Meth. Extractor tool which generated BED files.