Distinct patterns of DNA methylation between diploid uni-parental and bi-parental honey bee embryos
Library construction, bisulfite conversion and sequencing were performed at the Beijing Genomics Institute, China. DNA was fragmented into 100-300 bp fragments by sonication (S-2; Covaris). The fragmentation parameters were:duty cycle 10%; intensity: 5; cycles/burst: 200; cycles: 16; total fragmentation time: 960 s. Fragmentation was confirmed using a 2100 Bioanalyzer (Agilent). Fragments were end repaired (Illumina) as recommended by the manufacturer. Repaired fragments were ligated with methylated sequencing adaptors using a paired end adaptor oligo kit and oligo mix (Illumina). Ligated fragments were selected by gel electrophoresis and fragments of 360 bp size extracted using a QIAquick gel extraction kit (Qiagen). Size-selected fragments were bisulfite treated using an EZ-DNA methylation kit (Zymo Research) and enriched using a MethylMiner methylated DNA enrichment kit (Invitrogen). Libraries were amplified using T4 polymerase (Enzymatics) and sequenced on an Illumina HiSeq platform.