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Open Access Research article

MicroRNAs and their putative targets in Brassica napus seed maturation

Daiqing Huang, Chushin Koh, J Allan Feurtado, Edward WT Tsang and Adrian J Cutler*

Author Affiliations

Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon S7N 0W9, Canada

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BMC Genomics 2013, 14:140  doi:10.1186/1471-2164-14-140

Published: 28 February 2013

Additional files

Additional file 1: Table S1:

Conserved miRNAs in Brassica napus with sequences identical to miRNAs in miRBase (Release 18).

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Additional file 2: Table S2:

Additional conserved miRNAs in Brassica napus with sequences homologous to miRNAs in miRBase (Release 18).

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Additional file 3: Table S3:

Expression profiles of conserved miRNAs (threshold read count of 300).

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Additional file 4: Table S4:

MIRNA loci identified in the Brassica napus A genome (Brapa_sequence_v1.1).

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Additional file 5: Figure S1:

Secondary structures of MIRNA precursor loci and patterns of matching sequencing reads in the Brassica napus A genome (Brassica rapa). For each precursor, small RNA sequencing raw reads (with a minimum number of at least 5 identical reads) from all libraries (10 SOLiD and 17 Illumina, which together total 12 M unique reads) were combined. Annotated miRNA and miRNA* sequences were downloaded from the miRBase database (Release 18). Only reads with perfect matches to the genomic sequence are shown. Green represents the forward (5’ to 3’) reads, red represents reverse reads. The number of reads of each sequence (read count) was integrated into the sequence name as _x [read count for each unique sequence]. The most likely (most abundant) mature miRNA sequence from each MIRNA locus was underlined in red.

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Additional file 6: Figure S2:

Putative novel Brassica napus MIRNAs based on the Brassica A genome (Brassica rapa). The read mapping patterns are displayed and the putative novel miRNA mature sequences underlined in red. Only reads with perfect matches are shown. Green represents the forward reads, red color represents reverse reads. The read count for each specific sequence was integrated into the sequence name as _x [read count of each unique sequence]. The secondary structures of each locus with their folding energy are shown below the genomic sequence.

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Additional file 7: Table S5:

Conserved miRNAs and expression of their target genes.

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Additional file 8: Figure S5:

BiNGO graph of enriched GO terms associated with miRNA targets (based on Arabidopsis homologs). The size of node indicates the number of genes in a GO category. The yellow and orange nodes represent terms with significant enrichment, with darker orange representing a higher degree of significance, as shown by the legend. White nodes are terms with no significant enrichment, but are included because they have a significant child term. Branches of GO with no significant terms are not shown.

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Additional file 9: Table S6:

Putative novel miRNAs and their precursors in the B. napus A genome (B. rapa v1.1).

Format: XLSX Size: 35KB Download file

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Additional file 10: Table S7:

Expression of novel putative miRNAs and their targets.

Format: XLSX Size: 72KB Download file

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Additional file 11: Table S8:

Comparison of data reported in this paper to that reported by Zhao et al. [15].

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Additional file 12: Figure S3:

Integration of putative miRNAs identified from Zhao et al. [15] into mapping results reported in this paper. The mapping patterns of sequence reads to 10 putative miRNA loci are displayed. Three sequences from Zhao et al. were also predicted as novel miRNAs in this study. They are miR2203, miR2204, miR2207, corresponding to our miR5802, miR5806, miR5803. miR2202 is identical to our miR5802*. Because the Zhao et al. designations miR2202-miR2225 were assigned to other species in miRBase (Release 18), we retained our assigned numbers (miR5801-miR5810) for these novel putative miRNAs. Mapping patterns suggest that Zhao et al. miRNAs 2205, 2206 and 2225 are actually siRNAs.

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Additional file 13: Table S9:

Comparison of miRNAs identified in Xu et al. [16] with current study.

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Additional file 14: Table S10:

Expression of known miRNAs in Zhou et al. [15] and current study.

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Additional file 15: Table S11:

Comparison of predicted targets with Category I miRNA target genes in Zhou et al. [15].

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Additional file 16: Figure S4:

Gene expression profiles during seed development and maturation. Each line represents one gene. A. Expression profiles of 90K Brassica EST contigs (Baseline transformed to median), miR156 targets -- SPLs are highlighted in orange. B. Expression profiles of 90K Brassica EST contigs (no transformation), SPLs are highlighted in orange. C. Expression profiles of 22K Arabidopsis genes (baseline transformed to median) during seed development (Schmid et al., 2005), SPLs are highlighted in orange.

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Additional file 17: Table S12:

miRNA Taqman Assays for qPCR validation.

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