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Identification, Characterization and Expression Profiling of Dicer-Like, Argonaute and RNA-Dependent RNA Polymerase Gene Families in Foxtail Millet

Abstract

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.

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Acknowledgments

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.

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Correspondence to Manoj Prasad.

Electronic Supplementary Materials

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Supplementary Fig. S1
figure8

Number of DCL, AGO and RDR genes present in the sequenced plant species. The total number of DCL, AGO and RDR genes found in each genome is indicated on the right. The data was retrieved from Phytozome. The number of genes in Setaria italica excludes alternate transcripts. (GIF 287 kb)

Supplementary Fig. S2
figure9

Details of different functional domains identified in SiDCL, SiAGO and SiRDR proteins using PIECE tool. (GIF 318 kb)

Supplementary Fig. S3
figure10

Intron-exon positioning of all the 8 SiDCL, 19 Si AGO and 11 SiRDR genes. (GIF 443 kb)

Supplementary Fig. S11
figure11

Sequence-based clustering of SiDCL, AtDCL, SlDCL and OsDCL proteins. (GIF 145 kb)

Supplementary Fig. S12
figure12

Sequence-based clustering of SiAGO, AtAGO, SlAGO and OsAGO proteins. (GIF 162 kb)

Supplementary Fig. S13
figure13

Sequence-based clustering of SiRDR, AtRDR, SlRDR and OsRDR proteins. (GIF 162 kb)

Supplementary Fig. S14
figure14

Predicated structures of SiDCL proteins. The structures with >90 % confidence level were shown. (GIF 212 kb)

Supplementary Fig. S15
figure15

Predicated structures of SiAGO proteins. The structures with >90 % confidence level were shown. (GIF 434 kb)

Supplementary Fig. S16
figure16

Predicated structures of SiRDR proteins. The structures with >90 % confidence level were shown. (GIF 294 kb)

Supplementary Table S1

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Supplementary Table S2

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High resolution image (TIFF 396 kb)

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Supplementary Fig. S4

Multiple sequence alignment of SiDCL protein sequence. (PPT 374 kb)

Supplementary Fig. S5

Multiple sequence alignment of SiAGO protein sequence. (PPT 581 kb)

Supplementary Fig. S6

Multiple sequence alignment of SiRDR protein sequence. (PPT 351 kb)

Supplementary Fig. S7

Multiple sequence alignment of PAZ and DICER-DIMER domains of SiDCL, AtDCL and OsDCL protein sequence. (PPT 319 kb)

Supplementary Fig. S8

Multiple sequence alignment of PAZ domain of SiAGO, AtAGO and OsAGO protein sequence. (PPT 353 kb)

Supplementary Fig. S9

Multiple sequence alignment of PIWI domain of SiAGO, AtAGO and OsAGO protein sequence. (PPT 643 kb)

Supplementary Fig. S10

Multiple sequence alignment of RdRP domain of SiRDR, AtRDR and OsRDR protein sequence. (PPT 453 kb)

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High resolution image (TIFF 288 kb)

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Yadav, C.B., Muthamilarasan, M., Pandey, G. et al. Identification, Characterization and Expression Profiling of Dicer-Like, Argonaute and RNA-Dependent RNA Polymerase Gene Families in Foxtail Millet. Plant Mol Biol Rep 33, 43–55 (2015). https://doi.org/10.1007/s11105-014-0736-y

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Keywords

  • Foxtail millet (Setaria italica)
  • Dicer like (DCL)
  • Argonautes (AGO)
  • RNA-dependent RNA polymerases (RDR)
  • Genome-wide analysis
  • Expression profiling
  • Phylogenetic analysis
  • Homology modelling