DNA methylation during seed development in large-seeded chickpea

In this study, we performed bisulphite of five stages of seed development in a large-seeded chickpea cultivar (JGK 3) using Illumina platform. Paired-end reads were generated from 11 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. Overall design: 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).