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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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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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  1. National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110 067, India

    Chandra Bhan Yadav, Mehanathan Muthamilarasan, Garima Pandey & Manoj Prasad

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  1. Chandra Bhan Yadav
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  2. Mehanathan Muthamilarasan
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  3. Garima Pandey
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  4. Manoj Prasad
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Correspondence to Manoj Prasad.

Electronic Supplementary Materials

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Supplementary Table S1

(DOC 36 kb)

Supplementary Table S2

(XLS 39 kb)

Supplementary Fig. S1

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)

High resolution image (TIFF 396 kb)

Supplementary Fig. S2

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

High resolution image (TIFF 352 kb)

Supplementary Fig. S3

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

High resolution image (TIFF 986 kb)

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)

Supplementary Fig. S11

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

High resolution image (TIFF 102 kb)

Supplementary Fig. S12

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

High resolution image (TIFF 103 kb)

Supplementary Fig. S13

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

High resolution image (TIFF 116 kb)

Supplementary Table S3

(XLS 31 kb)

Supplementary Table S4

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Supplementary Table S5

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Supplementary Table S6

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Supplementary Table S7

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Supplementary Table S8

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Supplementary Table S9

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Supplementary Table S10

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Supplementary Table S11

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Supplementary Table S12

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Supplementary Table S13

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Supplementary Table S14

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Supplementary Table S15

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Supplementary Fig. S14

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

High resolution image (TIFF 288 kb)

Supplementary Fig. S15

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

High resolution image (TIFF 682 kb)

Supplementary Fig. S16

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

High resolution image (TIFF 433 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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