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

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Title Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development
 
Creator Khemka, Niraj
Singh, Vikash Kumar
Garg, Rohini
Jain, Mukesh
 
Subject Drought
Plant morphogenesis
Plant molecular biology
 
Description Accepted date: 22 August 2016
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.
This work was financially supported by the Department of Biotechnology, Government of India, New Delhi, under the Challenge Programme on Chickpea Functional Genomics (BT/AGR/CG-PhaseII/01/2014) and the Department of Science & Technology, Government of India, under the Promotion of University Research and Scientific Excellence (PURSE) grant (Phase II) scheme.
 
Date 2016-09-19T10:12:32Z
2016-09-19T10:12:32Z
2016
 
Type Article
 
Identifier Scientific Reports, 6: 33297
2045-2322
http://59.163.192.83:8080/jspui/handle/123456789/684
http://www.nature.com/articles/srep33297
10.1038/srep33297
 
Language en_US
 
Publisher Nature Publishing Group