MNase-Seq, ChIP-Seq and data analysis

The isolated fragments in MNase digestion and precipitated DNA in ChIP were used for library construction using the Illumina TruSeq Sample Prep Kit following the manufacturer's recommendations. For each sample, a total of 3 ng DNA and Input control DNA were used for library construction. MNase-Seq and ChIP-Seq were performed with the Illumina HiSeq 3000 system (paired-end 150-bp reads). After clipping adapters and trimming low-quality reads, the clean sequencing reads were mapped to the G. barbadense genome using Bowtie2 (version 2.2.4) (40). After potential PCR duplicates were removed, MACS software (version 2.1.0) was used to call histone modification peaks with the default parameters (FDR < 0.05) (41). The genes (including upstream 2 kb and gene body regions) overlapping with identified peaks were considered to have epigenetic modifications.