BS-seq of Quercus lobata: leaf
Total genomic DNA at a concentration of 500 ng in 60uL was sonicated using an S2 Focused-ultrasonicator (Covaris, Woburn, MA, USA) for 60 seconds to obtain fragments in the 200-300 bp range (Duty cycle: 10%, intensity: 5, cycles/burst: 200, Mode: Frequency sweeping). Kapa DNA hyper kit (Kapa Biosystems, Inc., MA, USA) was used to repair the ends of the DNA fragments and to ligate the DNA fragments with Illumina TruSeq DNA LT Nano adapters. Subsequently, the adapter ligated DNA was treated with the Epitect bisulfite kit (Qiagen, Hilden, Germany). Finally, bisulfite treated DNA was PCR amplified once with MyTaq DNA polymerase (Bioline, MA, USA) at 15 cycles. WGBS libraries were pooled and sequenced on an Illumina HiSeq 4000 machine.