Capsella Grandiflora BS-seq
Total DNA for C. grandiflora leaves was isolated using the DNeasy Plant Kit (Qiagen). Approximately two micrograms of genomic DNA were sonicated to ~100 bp using the Covaris S2 System and purified using Qiagen DNeasy mini-elute columns (Qiagen). The sequencing library was constructed using the NEBNext DNA Sample Prep Reagent Set 1 (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions but using methylated adapters instead of the standard genomic DNA adapters. Ligation products were purified with AMPure XP beads (Beckman, Brea, CA), and eluted DNA was bisulfite treated using the MethylCode Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s guidelines, followed by PCR amplification using Pfu Cx Turbo (Agilent, Santa Clara). Libraries were sequenced using the Illumina HiSeq 2500 as per manufacturer’s instructions. Image analysis and base calling were performed with the Illumina pipeline version RTA 2.8.0.