Open Access Highly Accessed Research article

Genome wide identification of chilling responsive microRNAs in Prunus persica

Abdelali Barakat1*, Aditya Sriram12, Joseph Park3, Tetyana Zhebentyayeva1, Dorrie Main4 and Albert Abbott1

Author Affiliations

1 Department of Biochemistry and Genetics, Clemson University, Clemson, SC, 29631, USA

2 Department of Computer Sciences, Clemson University, Clemson, SC, 29631, USA

3 Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA

4 Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, 99164-6414, USA

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BMC Genomics 2012, 13:481  doi:10.1186/1471-2164-13-481

Published: 15 September 2012

Additional files

Additional file 1:

Table S1. Conserved miRNAs identified in peach. The length (len) of each miRNA, the chromosome location (Chr), the start (start) and the end (stop) position on the chromosome of each miRNA and miRNA*sequences, the miRNA orientation (Dir), whether or not a miRNA* was observed are indicated, miRNA and miRNA* sequences, and sequence coordinates on the genome.

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Additional file 2:

Table S2. Conserved microRNA (miRNA) distribution in plant lineages. miRNA data are a compilation from miRBase 17 and this study. Divergence dates for land plant clades is from Leebens-Mack et al. (2005).

Format: XLSX Size: 12KB Download file

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Additional file 3:

Table S3. Non-conserved miRNAs identified in peach. The length (len) of each miRNA, the chromosome location (Chr), the start (start) and the end (stop) position on the chromosome of each miRNA and miRNA*sequences, the miRNA orientation (Dir), whether or not a miRNA was observed are indicated, and miRNA and miRNA* sequences.

Format: XLSX Size: 31KB Download file

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Additional file 4:

Table S4. Expression of conserved miRNAs in leaf and bud samples. Number of reads in leaf (L18 to L23) and bud (B18 to B23) dataset corresponding the different length variants (18 to 23 nt) of conserved miRNAs identified in peach. The number of reads of miRNA variants and the total count are indicated.

Format: XLSX Size: 54KB Download file

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Additional file 5:

Table S5. Expression of non-conserved miRNAs in leaf and bud samples. Number of reads in leaf (L18 to L23) and bud (B18 to B23) dataset corresponding the different length variants (18 to 23 nt) of non-conserved miRNAs identified in peach. The number of reads of miRNA variants and the total count are indicated.

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Additional file 6:

Table S6. List of conserved and non-conserved miRNAs up-regulated or down-regulated in winter buds and leaves.

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Additional file 7:

Table S7. List of targets of peach conserved miRNAs with the best scores. The name, the target score, peach CDS name, the Arabidopsis homolog to peach CDS and its annotation are indicated.

Format: XLSX Size: 163KB Download file

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Additional file 8:

Table S8. List of all peach genes targeted by conserved miRNAs with a score less than 4. The name, the target score, peach CDS name, the Arabidopsis homolog to peach CDS and its annotation are indicated.

Format: XLSX Size: 25KB Download file

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Additional file 9:

Table S9. List of targets of peach non-conserved miRNAs with the best scores. The name, the target score, peach CDS name, the Arabidopsis homolog to peach CDS and its annotation are indicated.

Format: XLSX Size: 63KB Download file

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Additional file 10:

Table S10. List of all peach genes targeted by non-conserved miRNAs with a score less than 4. The name, the target score, peach CDS name, the Arabidopsis homolog to peach CDS and its annotation are indicated.

Format: XLSX Size: 22KB Download file

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