Abstract
Non-coding RNAs constitute a major portion of the transcriptome in most of eukaryotes. Long non-coding transcripts originating from the DNA segment present between the protein coding genes are termed as long intergenic non-coding RNAs (lincRNAs). Several evidences suggest the role of lincRNAs in regulation of various biological processes. In this study, we identified a total of 2248 lincRNAs in chickpea using RNA-seq data from eight successive stages of flower development and three vegetative tissues via an optimized pipeline. Different characteristic features of lincRNAs were studied and compared with those of predicted mRNAs in chickpea. Further, we utilized a method using network propagation algorithm to reveal the putative function of lincRNAs in plants. In total, at least 79% of the identified chickpea lincRNAs were assigned with a putative function. A comprehensive expression profiling revealed differential expression patterns and tissue specificity of lincRNAs in different stages of flower development in chickpea. In addition, potential lincRNAs-miRNA interactions were explored for the predicted lincRNAs in chickpea. These findings will pave the way for understanding the role of lincRNAs in the regulatory mechanism underlying flower development in chickpea and other legumes.
Highlights
Recent study of transcriptional landscape in human revealed that most of the genome sequence can transcribe into RNAs and have some biological role[1]
LincRNAs represent a class of non-coding transcripts with minimum length of 200 nt originating from intergenic region
The transcripts with length ≤200 bp and putative open reading frame (ORF) length of >300 bp were removed as transcripts having ORF length >300 bp might encode for a functional protein
Summary
Recent study of transcriptional landscape in human revealed that most of the genome sequence can transcribe into RNAs and have some biological role[1]. A few studies have provided evidence for the role of lncRNAs in stress response, male sterility and phosphate homeostasis in plants[13,15,16]. Due to recent demonstration of their important biological roles in various aspects of development, lncRNAs have become the focus of plant biology research. Small non-coding RNA component (miRNAs) in various tissues/organs have been characterized in chickpea[24,25]. We identified lincRNAs from 11 different tissue samples using RNA-seq data in chickpea. Our study provides the first systematic study of lincRNAs in chickpea and lay the foundation for further studies to elucidate their precise functions
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