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Open Access Highly Accessed Research article

Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type

Qiang Xu12*, Yuanlong Liu2, Andan Zhu2, Xiaomeng Wu2, Junli Ye2, Keqin Yu2, Wenwu Guo12 and Xiuxin Deng12*

Author Affiliations

1 Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China

2 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China

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BMC Genomics 2010, 11:246  doi:10.1186/1471-2164-11-246

Published: 17 April 2010

Additional files

Additional file 1:

WT-derived sRNAs from coding RNA. This file contains the information of WT-derived sRNAs which were mapped on protein-coding EST genes from sweet orange (Citrus sinensis).

Format: XLS Size: 2.9MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

MT-derived sRNAs from coding RNA. This file contains the information of MT-derived sRNAs which were mapped on protein-coding EST genes from sweet orange (Citrus sinensis).

Format: XLS Size: 3.8MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

WT-derived sRNAs from non-coding RNA. The file lists WT-derived sRNAs which were mapped on non-protein coding RNAs (tRNA, snRNA, snoRNA and rRNA).

Format: XLS Size: 472KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

MT-derived sRNAs from non-coding RNA. The file lists MT-derived sRNAs which were mapped on non-protein coding RNAs (tRNA, snRNA, snoRNA and rRNA).

Format: XLS Size: 703KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Known citrus miRNAs. Known citrus miRNAs and their expression in WT and MT sweet oranges.

Format: XLS Size: 52KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Fold-back structures for known miRNA from sweet orange (Citrus sinensis). Precursor sequences for known miRNAs from sweet orange were shown in black letters with miRNA and miRNA* (The sequence complementary to miRNA in the fold-back structure) sequences highlighted in yellow and pink, respectively. Precursor secondary structures and dG value were produced using the mfold software http://mfold.bioinfo.rpi.edu/ webcite.

Format: PDF Size: 917KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

Target prediction of citrus known miRNAs. This file contains the predicted target genes for known miRNA genes in sweet orange.

Format: XLS Size: 234KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Fold-back structures for novel miRNAs from sweet orange (Citrus sinensis). Precursor sequences for novel miRNA from sweet orange were shown in black letters with miRNA and miRNA* (The sequence complementary to miRNA in the fold-back structure) sequences highlighted in yellow and pink, respectively. Precursor secondary structures and dG value were produced using the mfold software http://mfold.bioinfo.rpi.edu/ webcite.

Format: PDF Size: 269KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 9:

Target prediction of citrus novel miRNAs. This file contains the predicted target genes for novel miRNA genes in sweet orange.

Format: XLS Size: 307KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 10:

miRNA target genes are hotspots for generation small RNAs. This file contains the information of citrus sRNA loci located in miRNA-target genes in both sense and antisense way.

Format: XLS Size: 109KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 11:

The computational annotation of target genes of differential miRNA genes. This file shows the annotation information of citrus miRNA-target genes; the annotation was performed using arbidopsis homologous gene and Uniprot database.

Format: XLS Size: 179KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 12:

The primer sequence information. This file lists the primers used for miRNA expression detection by stem-loop qRT-PCR.

Format: PDF Size: 38KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data