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Open Access Highly Accessed Research article

Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems

Martín Calviño, Rémy Bruggmann and Joachim Messing*

Author Affiliations

Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854-8020, USA

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BMC Genomics 2011, 12:356  doi:10.1186/1471-2164-12-356

Published: 8 July 2011

Additional files

Additional File 1:

Table S1 - 25 nt hotspots in the sorghum genome.

Format: XLS Size: 33KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Frequency counts of small RNA reads for known microRNA families. Table S2 displays a quantitative analysis of microRNAs.

Format: XLS Size: 25KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Predicted targets of miR169, miR172, and miR395. Table S3 provides a list of predicted target genes of miR169, miR172, and miR395.

Format: XLS Size: 44KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Targets of predicted for miR169, miR172 and miR395 microRNAs. Figure S1 displays an alignment between miR169, miR172 and miR395 microRNAs and their target sequences.

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Open Data

Additional file 5:

Mapping of miR172-guided cleavage sites in predicted target genes. Figure S2 displays an alignment of miR172 with its target sequences and cleavage sites. The locations of the miRNA-cleavage sites are indicated with downward arrows and the frequency of the cleavages are indicated as the number of clones for each RACE product with respect to the total clones sequenced.

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Additional file 6:

Pipeline for the de novo miRNA detection. Figure S3 presents a diagram of computational steps involved in de novo miRNA detection. All reads from SOLiD sequencing were mapped in colorspace to the sorghum genome using SHRiMP. Perfect matching reads were clustered with Vmatch then filtered against the sorghum repeat sequences and compared with know sorghum miRNAs to classify them. The remaining sequences were taken for de novo miRNA prediction using miRDeep.

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Open Data

Additional file 7:

Hairpin structures of the newly discovered miRNAs. Figure S4 presents a collection of hairpin structures from newly discovered miRNAs. Sequences are depicted together with the frequency distribution of the small RNA reads aligned to the hairpin. The 2D hairpin structure produced by the miRDeep software is also shown.

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Open Data

Additional file 8:

Predicted targets for the newly discovered miRNAs in sorghum. Figure S5 presents a list of alignments between new discovered miRNAs and their predicted targets in sorghum.

Format: TXT Size: 33KB Download file

Open Data

Additional file 9:

Frequency counts of small RNA reads for new MIR genes. Table S4 displays a quantitative analysis of new MIR genes.

Format: XLS Size: 16KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data