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Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing

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Title Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing
 
Creator Jain, Mukesh
Chevala, VVS Narayana
Garg, Rohini
 
Subject Chickpea (Cicer arietinum)
deep sequencing
differential expression
microRNA
miRNA targets
tissue specificity
 
Description Accepted date: 11 July 2014
MicroRNAs (miRNAs) are essential components of complex gene regulatory networks that orchestrate plant development. Although several genomic resources have been developed for the legume crop chickpea, miRNAs have not been discovered until now. For genome-wide discovery of miRNAs in chickpea (Cicer arietinum), we sequenced the small RNA content from seven major tissues/organs employing Illumina technology. About 154 million reads were generated, which represented more than 20 million distinct small RNA sequences. We identified a total of 440 conserved miRNAs in chickpea based on sequence similarity with known miRNAs in other plants. In addition, 178 novel miRNAs were identified using a miRDeep pipeline with plant-specific scoring. Some of the conserved and novel miRNAs with significant sequence similarity were grouped into families. The chickpea miRNAs targeted a wide range of mRNAs involved in diverse cellular processes, including transcriptional regulation (transcription factors), protein modification and turnover, signal transduction, and metabolism. Our analysis revealed several miRNAs with differential spatial expression. Many of the chickpea miRNAs were expressed in a tissue-specific manner. The conserved and differential expression of members of the same miRNA family in different tissues was also observed. Some of the same family members were predicted to target different chickpea mRNAs, which suggested the specificity and complexity of miRNA-mediated developmental regulation. This study, for the first time, reveals a comprehensive set of conserved and novel miRNAs along with their expression patterns and putative targets in chickpea, and provides a framework for understanding regulation of developmental processes in legumes.
This work was financially supported by the core grant from
NIPGR and the Department of Biotechnology, Government
of India, under the Next Generation Challenge Programme
on Chickpea Genomics (grant number BT/PR12919/
AGR/02/676/2009 from 2009–2014). RG acknowledges the
INSPIRE Faculty Award from the Department of Science
and Technology, Government of India.
 
Date 2015-12-16T07:12:34Z
2015-12-16T07:12:34Z
2014
 
Type Article
 
Identifier J. Exp. Bot., 65(20): 5945-5958
1460-2431
http://172.16.0.77:8080/jspui/handle/123456789/415
http://jxb.oxfordjournals.org/content/65/20/5945
10.1093/jxb/eru333
 
Language en_US
 
Publisher Oxford University Press