Open Access Highly Accessed Research article

High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice

Blanca E Barrera-Figueroa12, Lei Gao1, Zhigang Wu1, Xuefeng Zhou3, Jianhua Zhu4, Hailing Jin5, Renyi Liu1* and Jian-Kang Zhu6

Author Affiliations

1 Department of Botany and Plant Sciences and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA

2 Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec, Oaxaca, 38601, Mexico

3 Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA

4 Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA

5 Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA

6 Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA

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BMC Plant Biology 2012, 12:132  doi:10.1186/1471-2229-12-132

Published: 3 August 2012

Additional files

Additional file 1:

Summary of small RNA sequencing data. Detailed information of preprocessing of small RNA reads from four libraries in rice inflorescences.

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Additional file 2:

miRNAs that were identified in rice inflorescences. Detailed information of the predicted rice miRNAs and their targets.

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Additional file 3:

Predicted secondary structures of the precursors of new miRNA candidates. Free energy and miRNA ID are on the bottom of each structure. Nucleotides that constitute mature RNAs are drawn in blue.

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Additional file 4:

Small RNA reads from four libraries that were mapped to the precursors of new candidate miRNAs. On each map, the first line contains the miRNA ID. The second line contains the miRNA precursor sequence, with mature miRNA region in red. The third line contains the notation of secondary structure with parentheses denoting base-pairing and dots denoting mismatches or bulges. The number on the right is the free energy. Every line starting from line 4 contains the sequence, mapping position, and count of a mapped unique small RNA read.

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Additional file 5:

Detailed information of known miRNAs that were identified in rice inflorescences. For each miRNA gene that match a known miRNA gene in the miRBase, precursor sequence is listed first, followed by alignment of mature miRNA sequence identified in this study, and then alignment of mature miRNA sequence that is listed in the miRBase (if it is different). Length of miRNA and normalized expression values in four small RNA libraries are listed on the right side of each mature miRNA.

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Additional file 6:

Validation of predicted miRNAs with published small RNA data from DCL1, DCL3, RDR2 RNAi lines and small RNAs in Argonaut protein pulldown.

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Additional file 7:

Confirmation of some of the predicted targets using two published degradome data in rice.

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Additional file 8:

Candidate miRNAs that are derived from transposons or repeats. Candidate miRNAs that were predicted using anchor sRNAs that match annotated transposons or repeats, or have high copy number (>20) in the genome.

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Additional file 9:

Detailed information of 80 candidate miRNAs that were derived from transposable elements or repeats and were validated with expression data from DCL1, DCL3, and RDR2 RNAi lines.

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Additional file 10:

MITEs are rich sources for generating miRNAs. Relative abundance of different classes of TEs in the genome is compared to the proportion of miRNAs that were derived from different classes of TEs. MITEs are apparently enriched in TEs from which miRNAs were derived.

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Additional file 11:

List of oligos that were used as probes to detect the expression of miRNAs in Northern blot assays. Probes are complimentary to the predicted mature miRNA sequences.

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