Illumina Bisulfite-Seq of Bombyx mori paired-end library
DNA was fragmented by sonication with a Sonicator (Sonics & Materials) to a mean size of approximately 250 bp, followed by blunt ending, 3'-end addition of dA, and adapter ligation, in which Illumina methylated adapters were used according to the manufacturer's instructions (Illumina). The bisulfite conversion of silkworm DNA was carried out using a modified NH4SO4-based protocol28 and amplified by 12 cycles of PCR. Ultra-high-throughput pair-end sequencing was carried out using the Illumina Genetic Analyzer (GA2) according to manufacturer instructions. Raw GA sequencing data were processed by Illumina base-calling pipeline (SolexaPipeline-1.0).