Chickpea (Cicer arietinum L.) is one of the most important legume crops for human nutrition all over the world. However, several factors limit the efforts for its improvement. Understanding the gene expression profiles of genes in different tissues/organs during plant development can provide important insights into function and regulation of the genes. To gain insights into the transcriptional regulatory programs underlying different tissues/organs during chickpea development, we generated a comprehensive expression atlas of protein-coding and long non-coding RNAs in chickpea. Although short read sequencing using Illumina is widely used for RNA-seq and is excellent technology for quantification of gene expression, it is quite challenging to assembly accurate full-length assembly of transcripts and their isoforms of all the genes. Thus, we constructed the transcriptome of chickpea using long read technology of Pacific Biosciences Iso-seq and complemented it with RNA-seq from Illumina sequencing. We described dynamic transcriptional profiles, tissue-specific expression and co-expressed modules of protein-coding genes and lncRNAs along with their functional relevance. The comprehensive transcriptional map reported here provide a comprehensive resource for functional analysis of selected protein-coding genes and lncRNAs.

A full-length transcriptome assembly was generated using long-read PacBio (11,068,364 subreads) and high-depth Illumina sequencing data (~6.5 billion reads from 94 libraries). In total, 38,818 unique transcripts/gene loci were predicted in chickpea, which represented full-length transcriptome assembly (FLTA) of chickpea. The FLTA was used for prediction of lncRNAs using PlncPRO followed by PFam domain analysis. A total of 5,293 unique transcripts were identified as lncRNAs and thee remmaining 33,525 transcripts as mRNAs. Further, we performed comprehensive functional annotation, expression profilling, tissue-specificity and co-expression network analyses of these sets of lncRNAs and mRNAs in different tissues/organs/developmental stages of chickpea. All these data are public and available for download via the links given below. We anticipate that the data will provide a valuable resource for functional genomics of important traits in chickpea.

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Reseachers who find this database useful in their research, please cite our recent publication:
Jain M, Bansal J, Rajkumar MS, Garg R. (2022) An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea. Communications Biology 5, 1106. doi: 10.1038/s42003-022-04083-4 https://www.nature.com/articles/s42003-022-04083-4
Jawaharlal Nehru University, New Delhi, India
This work is supported by the Department of Biotechnology, Government of India, New Delhi