Whole genome bisulphite sequencing of Symbiodinium microadriaticum: 29D
For both bisulphite DNA libraries, NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, Ipswich, MA) were used with manufacturers instructions. Methylated TruSeq Illumina adapters (Illumina, San Diego, CA) were used, followed by bisulphite conversion with the EpiTect Bisulfite kit (Qiagen, Hilden, Germany) with cycling conditions of 95 C for 5 min, 60 C for 25 min, 95 C for 5 min, 60 C for 85 min, 95 C for 5 min, 60 C for 175 min, then 3 cycles of 95 C for 5 min, 60 C for 180 min, and held at 20 C for  5 hours. Libraries were subsequently enriched with KAPA HiFi HotStart Uracil+ ReadyMix (2X) (KAPA Biosystems, Wilmington, MA), and quality checked on a Bioanalyzer DNA 1K chip (Agilent, Santa Clara, CA) and quantified using Qubit 2.0 (Thermo Scientific), prior to pooling in approximate equimolar ratios for sequencing.