Epigenetic regulation during salinity stress response in chickpea (WGBS)

Bisulphite sequencing of salinity sensitive and salinity tolerant chickpea genotypes during salinity stress response using Illumina platform has been performed. At least 195 million reads in bisulphite sequencing were generated in each sample. Methylated cytosines in each sample were identified for their genomic location and sequence context. Overall design: Genomic DNA was extracted from all the samples using Qiagen DNeasy kit and treated with sodium bisulphite (Zymo research) to induce cytosine to uracil conversion. Bisulphite sequencing was performed on Illumina platform to generate 90bp long reads in paired-end mode. Adapter contamination and low-quality reads were removed using NGS QC Toolkit (v2.3.3). High-quality filtered reads were mapped on Kabuli reference genome using Bismark (v0.14.3). Methylation levels in each cytosine residues and differentially methylated regions under stress conditions and between the two different genotypes were determined using Methylkit (v1.5.3).