Open Access Research article

Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation

Ruben Parra1, Miguel A Paredes1, Isabel M Sanchez-Calle2 and Maria C Gomez-Jimenez1*

Author Affiliations

1 Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz 06006, Spain

2 Department of Plant Physiology, University of Granada, Campus de Cartuja s/n, Granada 18071, Spain

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BMC Genomics 2013, 14:866  doi:10.1186/1471-2164-14-866

Published: 9 December 2013

Additional files

Additional file 1:

Results for the 454 sequencing runs.

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Additional file 2:

Summary of parameters used for the sequencing and assembly in the study of the olive transcriptomes: fruit (blue bars) and AZ (green bars) at 217 DPA. (A) Read-length distribution. A total of 443,811 good-quality sequence reads were obtained from the 2 samples. (B) Contig-length distribution. A total of 19,062 contigs were assembled from 199,075 redundant reads obtained after clustering and assemblage. The average contig length was around 500 bases. (C) Contig-read total distribution from fruit and AZ 454 sequencing data. (D) Isotig-length distribution.

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Additional file 3:

List of 7,756 transcripts with Unigene ID in our experiment.

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Additional file 4:

List of 4,391 differentially expressed genes in our experiment (P < 0.01, group I).

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Additional file 5:

Genes overexpressed in the fruit pericarp in our experiment (P < 0.01, group I: Cluster A).

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Additional file 6:

Genes overexpressed in the fruit AZ in our experiment (P < 0.01, group I: Cluster B).

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Additional file 7:

Subcluster A1, A2, B1 and B2.

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Additional file 8:

Proportion of annotated isotigs in each of the samples, and the proportion of annotated isotigs that present functional annotations of Gene Ontology (GO) or that are found annotated with the enzyme commission (EC) number.

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Additional file 9:

Pathways identified through KEGG mapping.

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Additional file 10:

Graphic representation of the starch and sucrose metabolism pathway by KEGG. Boxes colored in red represent the EC number of the enzymes encoded by differentially expressed genes generated by this study (fruit at 217 DPA vs. AZ at 217 DPA) that are homologous to genes involved in the starch and sucrose metabolism pathway.

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Additional file 11:

Graphic representation of the amino sugar and nucleotide sugar metabolism pathway by KEGG. Boxes colored in red represent the EC number of the enzymes encoded by differentially expressed genes generated by this study (fruit at 217 DPA vs. AZ at 217 DPA) that are homologous to genes involved in the amino sugar and nucleotide sugar metabolism pathway.

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Additional file 12:

Graphic representation of the cysteine and methionine metabolism pathway by KEGG. Boxes colored in red represent the EC number of the enzymes encoded by differentially expressed genes generated by this study (fruit at 217 DPA vs. AZ at 217 DPA) that are homologous to genes involved in the cysteine and methionine metabolism pathway.

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Additional file 13:

Graphic representation of the methane metabolism pathway by KEGG. Boxes colored in red represent the EC number of the enzymes encoded by differentially expressed genes generated by this study (fruit at 217 DPA vs. AZ at 217 DPA) that are homologous to genes involved in the methane metabolism pathway.

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Additional file 14:

Graphic representation of the glycolysis/gluconeogenesis pathway by KEGG. Boxes colored in red represent the EC number of the enzymes encoded by differentially expressed genes generated by this study (fruit at 217 DPA vs. AZ at 217 DPA) that are homologous to genes involved in the glycolysis/gluconeogenesis pathway.

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Additional file 15:

Graphic representation of the glycine, serine and threonine metabolism pathway by KEGG. Boxes colored in red represent the EC number of the enzymes encoded by differentially expressed genes generated by this study (fruit at 217 DPA vs. AZ at 217 DPA) that are homologous to genes involved in the glycine, serine and threonine metabolism pathway.

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Additional file 16:

Graphic representation of the arginine and proline metabolism pathway by KEGG. Boxes colored in red represent the EC number of the enzymes encoded by differentially expressed genes generated by this study (fruit at 217 DPA vs. AZ at 217 DPA) that are homologous to genes involved in the arginine and proline metabolism pathway.

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Additional file 17:

Fruit-or AZ-enriched transcription factors at the last stage of olive fruit ripening. Sequences were selected after establishing a P < 0.01. The table shows the total read count in RPKMx1000 for each gene after normalization across the 2 samples: (a) fruit at 217 DPA, (b) AZ at 217 DPA.

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