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Identification, characterization and expression profiling of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in foxtail millet

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Title Identification, characterization and expression profiling of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in foxtail millet
 
Creator Yadav, Chandra Bhan
Muthamilarasan, Mehanathan
Pandey, Garima
Prasad, Manoj
 
Subject Foxtail millet (Setaria italica)
Dicer like (DCL)
Argonautes (AGO)
RNA-dependent RNA polymerases (RDR)
Genome-wide analysis
Expression profiling
Phylogenetic analysis
Homology modelling
 
Description Post-transcriptional control of gene expression is achieved through RNA interference where the activities of Dicer-like (DCL), Argonautes (AGO) and RNA-dependent RNA polymerases (RDRs) are significant. Hence, considering the importance of DCL, AGO and RDRs, a comprehensive genome-wide analysis was performed in foxtail millet. The study identified 8 DCL, 19 AGO and 11 RDR genes. Phylogenetic and domain analysis provided interesting information on the evolutionary and structural aspects of these proteins. The orthologs of Setaria italica DCL (SiDCL), AGO (SiAGO) and RDRs (SiRDRs) were identified in sorghum, maize and rice, and the evolutionary relationships among the orthologous gene pairs were investigated. Promoter analysis of SiDCL, SiAGO and SiRDR genes revealed the presence of unique and common cis-acting elements at the upstream of respective gene sequences, which serves as binding sites for several developmental and stress-related transcription factors. In silico expression profiling using RNA-sequence data showed tissue-specific expression patterns of these genes in foxtail millet. Candidate genes representing each sub-family were chosen for expression analysis through quantitative real-time PCR (qRT-PCR) under salinity, dehydration and hormonal treatments. It revealed the differential expression pattern of candidate genes at different time points of stresses. This is the first report on genome-wide analysis of SiDCL, SiAGO and SiRDR gene families in foxtail millet, which provides basic genomic information and insights into the putative roles of these genes in abiotic stresses. The present study will serve as a base for further functional characterization of these gene families in foxtail millet and related grass species.
The authors’ work in this area is supported by the
core grant of National Institute of Plant Genome Research (NIPGR),
Govt. of India, New Delhi. Mr Mehanathan Muthamilarasan and Ms.
Garima Pandey acknowledge the award of Research Fellowship from
University Grants Commission, New Delhi, India. Timely assistance of
Mr. Yusuf Khan, NIPGR, is appreciated. The authors also thank the
anonymous reviewers for their constructive comments.
 
Date 2016-01-27T06:05:20Z
2016-01-27T06:05:20Z
2015
 
Type Article
 
Identifier Plant Mol. Biol. Rep., 33(1): 43-55
1572-9818
http://172.16.0.77:8080/jspui/handle/123456789/595
http://link.springer.com/article/10.1007%2Fs11105-014-0736-y
10.1007/s11105-014-0736-y
 
Language en_US
 
Publisher Springer