Expression atlas of chickpea during development

In this study, we aim to present a global view of transcriptome dynamics in different tissues/organs/developmental stage in chickpea. We generated about ~31-95 million reads from each of 94 libraries representing 32 different tissues/organs using Illumina platform. We generated a hybrid assembly of these data along with PacBio data to produce full-length transcriptome assembly. We mapped the reads to the transcriptome assembly for estimation of the abundance of coding and long non-coding transcripts in different tissue samples. The transcriptome dynamics was studied by differential and tissue-specific expression analyses, and co-expression network and transcriptional regulatory network analyses. Overall design: We collected different tissues/organs from vegetative and reproductive stages of development. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to the chickpea transcriptome assembly using Bowtie and fragments per exon kilobase per million (FPKM) was calculated using RSEM for each gene in all the samples to measure their gene expression.