DNA methylation during seed development in small-seeded chickpea

In this study, we performed bisulphite of two stages of seed development in a small-seeded chickpea cultivar (Himchana 1) using Illumina platform. Paired-end reads were generated from 5 libraries. Data obtained in FASTQ files were pre-processed to remove adapters and low-quality reads. We identified methylation level at each cytosine residue covered in sequencing and differentially methylated regions (DMRs) between stages of seed development. Genomic DNA was extracted from all the samples were fragmented to a mean size of 200-500 bp via sonication followed by sodium bisulphite conversion (DNA Methylation-GoldTM Kit, Zymo Research). TrueSeq-methylated adaptors were ligated and sequenced using Illumina HiSeq platform. Adapters and low-quality reads were removed using NGS QC Toolkit (v2.3). High-quality filtered reads were mapped on kabuli reference genome using Bismark (v0.14.3). Methylation level in each cytosine residue(s) and differentially methylated regions (DMRs) were detected using Methylkit (v0.5.6).