Open Access Highly Accessed Research article

Genome-wide profiling of Populus small RNAs

Daniel Klevebring1, Nathaniel R Street2, Noah Fahlgren3, Kristin D Kasschau3, James C Carrington3, Joakim Lundeberg1 and Stefan Jansson2*

Author Affiliations

1 School of Biotechnology, Division of Gene Technology, AlbaNova University Center, Royal Institute of Technology, 106 91 Stockholm, Sweden

2 Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden

3 Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA

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BMC Genomics 2009, 10:620  doi:10.1186/1471-2164-10-620

Published: 20 December 2009

Additional files

Additional file 1:

Significant loci of short RNAs. Loci identified across all short RNA size classes using the siLoCo tool from the UEA sRNA toolkit.

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Open Data

Additional file 2:

Significant loci of short 21 nt short RNAs. Loci identified for 21 nt short RNAs using the siLoCo tool from the UEA sRNA toolkit.

Format: CSV Size: 80KB Download file

Open Data

Additional file 3:

Significant loci of short 24 nt short RNAs. Loci identified for 24 nt short RNAs using the siLoCo tool from the UEA sRNA toolkit.

Format: CSV Size: 115KB Download file

Open Data

Additional file 4:

Genes with > 100 Over-lapping siRNAs. short RNA distribution within genes having > 100 over-lapping sequences. The frequency within the gene is shown on the plus strand (above) and the minus strand (below) the gene structure. Exons are shown as solid bars and introns as connecting lines. The size class (18-24 nt) frequency distribution is also shown.

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Additional file 5:

Phylogenetic tree of predicted ARF gene family members. Phylogenetic tree of predicted members of the ARF gene family. Family members were identified using an HMM model search for the presence of the ARF domain within the Jamboree gene model set. Phylogenetic tree was used using [57].

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Additional file 6:

Predicted phased loci. Phased loci with a p values <0.001 using the UEA sRNA toolkit.

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Open Data

Additional file 7:

Hairpin structure of miR475. Diagrammatic representation of the predicted stem-loop hairpin structure of miR475. The read count of sequences along the sequence is indicated using coloured shading.

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Additional file 8:

Hairpin structure of miR476. Diagrammatic representation of the predicted stem-loop hairpin structure of miR475. The read count of sequences along the sequence is indicated using coloured shading.

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Open Data

Additional file 9:

Chromosome distribution plots. short RNA, gene and repeat density plots for all chromosomes. Coloured bars, above the axis for plus strand and below the axis for minus strand, show expression counts in 0.1 Mb windows for 18 (grey), 19 (yellow), 20 (purple), 21 (cyan), 22 (dark blue), 23 (green) and 24 (red) nucleotide sequences. Below each plot the frequency distribution in 0.1 Mb windows for gene (top) and repeat density (bottom) is shown. Repeat density was calculated using RepeatMasker data from the PopGenIE web resource [29].

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Additional file 10:

Chromosome distribution plot for 1st 1 Mb of chromosome 19. short RNA, gene and repeat density plot for the 1st 1 Mb of chromosome 19 (LG_XIX). Coloured bars, above the axis for plus strand and below the axis for minus strand, show expression counts in 0.1 Mb windows for 18 (grey), 19 (yellow), 20 (purple), 21 (cyan), 22 (dark blue), 23 (green) and 24 (red) nucleotide sequences. Below each plot the frequency distribution in 0.1 Mb windows for gene (top) and repeat density (bottom) is shown. Repeat density was calculated using RepeatMasker data from the PopGenIE web resource [29].

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Open Data

Additional file 11:

Chromosome distribution plot of scaffold_117. short RNA, gene and repeat density plots of scaffold_117. Coloured bars, above the axis for plus strand and below the axis for minus strand, show expression counts in 0.1 Mb windows for 18 (grey), 19 (yellow), 20 (purple), 21 (cyan), 22 (dark blue), 23 (green) and 24 (red) nucleotide sequences. Below each plot the frequency distribution in 0.1 Mb windows for gene (top) and repeat density (bottom) is shown. Repeat density was calculated using RepeatMasker data from the PopGenIE web resource [29].

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Additional file 12:

Matches to mature miRNA sequences in miRBase. Counts of sequences matches mature miRNAs for all plant species within miRBase (release 13.0).

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Additional file 13:

Predicted miRNA loci. All loci predicted as miRNA using the miRCat tool from the UEA sRNA toolkit.

Format: CSV Size: 88KB Download file

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Additional file 14:

Predicted miRNA loci with no match the miRBase. All loci predicted as miRNA using the miRCat tool from the UEA sRNA toolkit that do not match existing miRBase entries and are therefore candidate non-conserved miRNAs.

Format: CSV Size: 23KB Download file

Open Data

Additional file 15:

Predicted miRNA hairpin structures. Predicted stem-loop hairpin structures for all miRNA loci represented in Additional File 11. The location of the miRNA and miRNA*sequence is indicated in green and purple respectively.

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Additional file 16:

Frequency of starting base pairs for different classes of predicted miRNAs. The frequency of predicted miRNAs starting with an A, U, C or G for miRNA loci matching existing miRBase entries, not-matching and with predicted targets and not-matching with no predicted targets.

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