title: Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development.
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.
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India.
authors.forename: Niraj
authors.initials: N
authors.lastname: Khemka
authors.affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India.
authors.forename: Vikash Kumar
authors.initials: VK
authors.lastname: Singh
authors.affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India.
authors.forename: Rohini
authors.initials: R
authors.lastname: Garg
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India.|National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India.
authors.forename: Mukesh
authors.initials: M
authors.lastname: Jain
mesh_terms: D029863:Cicer / Q000235:genetics*; D019295:Computational Biology; D035264:Flowers / Q000235:genetics*; D020869:Gene Expression Profiling; D018745:Genome, Plant / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000302:isolation & purification; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding