Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development

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 reg...

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Bibliographic Details
Published in:Scientific reports 2016-09, Vol.6 (1), p.33297-33297, Article 33297
Main Authors: Khemka, Niraj, Singh, Vikash Kumar, Garg, Rohini, Jain, Mukesh
Format: Article
Language:English
Subjects:
38/90
38/91
631/449/1659
631/449/2653/1359
631/449/2661/2146
Cell cycle
Cicer - genetics
Computational Biology
Deoxyribonucleic acid
Developmental stages
DNA
Flowers
Flowers & plants
Flowers - genetics
Gene expression
Gene Expression Profiling
Genes
Genome, Plant - genetics
Genomes
Humanities and Social Sciences
Legumes
miRNA
multidisciplinary
Propagation
Proteins
Ribonucleic acid
RNA
RNA, Long Noncoding - genetics
RNA, Long Noncoding - isolation & purification
Science
Sequence Analysis, RNA
Transcriptome - genetics
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Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/srep33297