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Open Access Research article

Genome-wide analysis of small RNAs reveals eight fiber elongation-related and 257 novel microRNAs in elongating cotton fiber cells

Wei Xue, Zhengming Wang, Mingjian Du, Yidi Liu and Jin-Yuan Liu*

Author Affiliations

Laboratory of Molecular Biology, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China

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BMC Genomics 2013, 14:629  doi:10.1186/1471-2164-14-629

Published: 17 September 2013

Additional files

Additional file 1: Table S1:

The 79 known cotton miRNA families expressed in cotton fibers.

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Additional file 2: Table S2:

The 213 known cotton miRNA precursors derived from ESTs (CGI11), genome survey sequences (GSS) and G. raimondii genome sequences.

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Additional file 3: Figure S1:

The 139 novel stem-loop structures of known miRNA precursors in elongating cotton fibers. In most cases, the red highlighting indicates the miRNA sequence and the blue highlighting indicates the miRNA* sequence. For example, in ‘17-MIR159-[hbr-MIR159a MI0022053]’, the ‘17’ came from the “index” column in the Additional file 2; “MIR159” came from the “name” column in the Additional file 2; and [hbr-MIR159a MI0022053] was the homolog of the precursor in miRBase. tcc: Theobroma cacao; ctr: Citrus trifoliate; hbr: Hevea brasiliensis; vvi: Vitis vinifera; ptc: Populus trichocarpa; mdm: Malus domestica.

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Additional file 4: Table S3:

The 257 novel miRNAs in cotton fibers.

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Additional file 5: Figure S2:

The 314 Vienna RNA secondary structures of 257 novel miRNAs. The Vienna structures showed that the reliable candidate miRNA reads (at least five reads) accounted for more than 75% of the corresponding sets of reads according to rule (1) described in the “newly identified miRNAs in elongating cotton fibers” section.

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Additional file 6: Figure S3:

The 310 stem-loop structures of novel miRNA precursors in cotton fibers. The stem-loop structure shows the miRNA* sequence, mismatches between the miRNA and the other arm of the hairpin, and the size and frequency of asymmetric bulges. There were 314 novel miRNA gene loci, as shown in Additional file 5. The two miRNA gene loci each for novel_mir_2455, GhmiRnJ, novel_mir_4037 and novel_mir_860 had the same precursor sequences, so there were 310 distinct stem-loop structures.

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Additional file 7: Figure S4:

Genomic overview of 174 known and 311 novel GhmiRNA gene loci on the 13 G. raimondii chromosomes. There were 314 novel miRNA gene loci, as shown in Additional file 5. The three miRNA gene loci of GhmiRnA and GhmiRnB were not anchored on any of the 13 chromosomes of the G. raimondii genome, so 311 novel miRNA gene loci were mapped on the 13 G. raimondii chromosomes.

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Additional file 8: Figure S5:

Quantitative RT-PCR analysis of GhmiR156, GhmiR167 and GhmiR168. The data represent the mean values ± SD of three replicates. U6 was used as a reference gene. Types A, B and C are shown in red, yellow, and blue, respectively, in Figure 2A.

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Additional file 9: Figure S6:

Size distribution of cotton ta-siRNA generated from the DW503626 gene.

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Additional file 10: Table S4:

Target prediction for novel cotton fiber elongation-related miRNAs.

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Additional file 11: Table S5:

Target prediction for known cotton fiber elongation-related miRNAs.

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Additional file 12: Figure S7:

GhSPL9, a target of GhmiR156/157, may positively regulate anthocyanin synthesis in cotton fiber. (A) Quantitative RT-PCR analysis of GhDFR, GhANS, and GhF3H at different fiber developmental stages. Error bars indicate the ± SD of three replicates. (B) The anthocyanin content in the cotton fiber at different development stages. Error bars represent the SD.

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Additional file 13: Figure S8:

Quantitative RT-PCR analysis of LRR-RLK in the elongating fibers of G. hirsutum and G. arboretum.

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Additional file 14: Table S6:

Normalized abundances of miRNAs and tasiRNA in fibers and seeds at 15 dpa.

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Additional file 15: Figure S9:

RNA integrity of samples from 5, 10, 15 and 20 dpa fibers and 15 dpa seeds. Right: Electropherograms of the samples, as generated by the Agilent 2100 Bioanalyzer. The x-axis indicates the size of the nucleic acid, and the y-axis indicates the fluorescence. The red and black arrowheads indicate the 28S and 18S ribosomal RNA peaks, respectively. The RIN and 28S to 18S ratio are also shown in the image. RIN: RNA integrity number; FU: Fluorescence units.

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Additional file 16: Table S7:

The primers used in this study.

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