show Abstracthide AbstractIn this study, global transcriptome profiling was performed for different organs of ICC 4958 (leaves, roots, flowers and young pod) and leaves of wild chickpea, PI 489777. More than 50 million high-quality reads were obtained from each sample using Illumina platform. A consensus reference-guided assembly was generated for the transcriptome data from all samples and gene expression was analysed. Overall design: Total RNA was extracted from all samples and cDNA libraries were prepared. Sequencing was performed on Illumina HiSeq platform to generate 51 bp single-end (leaf, flower and young pod), 46 bp single-end (root) or 100 bp paired-end (leaf of wild chickpea) reads. Pre-processing was performed using NGS QC Toolkit to remove adapters and low-quality reads. Filtered high-quality reads were mapped on the chickpea genome using TopHat2 pipeline (v2.0.0). To analyze gene expression, reference-guided assembly was generated using Cufflinks (v2.0) and differential expression of genes was determined by Cuffdiff.