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The plasticity of the grapevine berry transcriptome

Silvia Dal Santo1, Giovanni Battista Tornielli1, Sara Zenoni1, Marianna Fasoli1, Lorenzo Farina2, Andrea Anesi1, Flavia Guzzo1, Massimo Delledonne1 and Mario Pezzotti1*

Author Affiliations

1 Department of Biotechnology, University of Verona, Strada Le Grazie 15 - Ca' Vignal, 37134 Verona, Italy

2 Department of Computer, Control, and Management Engineering Antonio Ruberti, Sapienza University of Rome, Via Ariosto 25, 00185 Rome, Italy

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Genome Biology 2013, 14:r54  doi:10.1186/gb-2013-14-6-r54

Published: 7 June 2013

Additional files

Additional File 1:

Table S1. Description of Corvina clone 48 grape collection sites, listing geographical parameters, farming, and agricultural practices. a.s.l: above sea level.

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Additional File 2:

Table S2. Description of sample names sorted by year of harvesting. Names are composed by vineyard abbreviations, followed by the indication of the harvesting year (06, 07, or 08), by the indication of the developmental stage (1, 2, or 3) and by the description of the biological replicate (A, B, or C). When the biological replicate is not indicated, names are referred to the average of the three replicates.

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Additional File 3:

Table S3. Maturation parameters of samples used for microarray analysis sorted by year of harvesting. Values represent mean ± standard deviation of three biological replicates. Total acidity is expressed in g/L of tartaric acid. For metabolic parameters, values are expressed as mean peak area ± standard deviation of three biological replicates.

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Additional File 4:

Dataset S1. Four clusters of genes differentially modulated among the 2006, 2007, and 2008 seasons at veraison. Expression was measured as the average log2 intensity of each biological triplicate. Each value has been normalized on the median value of each row/gene.

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Additional File 5:

Figure S1. Cluster dendrogram of (a) the second developmental stage and (b) the third developmental stage datasets using the average expression value of the three biological replicates. The Pearson's correlation values were converted into distance coefficients to define the height of the dendrograms. Blue, green, and red indicate samples harvested in 2006, in 2008, and in 2007, respectively.

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Additional File 6:

Dataset S2. Genes that are differentially expressed between average climate seasons (2006 to 2008) and an exceptionally warm spring (2007) in second and third ripening time point samples. Transcripts modulated also at veraison (Dataset S1) are highlighted in the column 'Cluster Figure 2B'. Expression was measured as the average log2 intensity of each biological triplicate. Each value has been normalized on the median value of each row/gene.

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Additional File 7:

Figure S2. Differential accumulation of metabolites between the 2006/2008 and 2007 vintages. Values were calculated as mean peak area ± standard deviation of three biological replicates and are expressed as fold-change of vintages 2006 to 2008 compared to 2007.

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Additional File 8:

Figure S3. Plastic and vintage-specific transcripts. Kruskal-Wallis non-parametric variance analysis was carried out three times (P <0.05, four groups) on each vintage-specific dataset to obtain differentially-modulated genes among the four vineyards studied in each year. The Venn diagram was constructed using Venn [84] and redrawn.

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Additional File 9:

Figure S4. k-means clustering of fluorescence log2 intensities. Increasing values of k were used until only one cluster displayed bimodal distribution (k = 10) with a low expression level mean value.

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Additional File 10:

Dataset S3. Set of 13,752 transcripts with a unimodal expression profile in the 2008-harvested samples. Expression was measured as the average log2 intensity in all developmental stages and in all biological triplicates.

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Additional File 11:

Dataset S4. Functional categories and expression values of 1478 plastic transcripts in 2008. The Kruskal-Wallis Statistic (H) and P value are indicated for each transcript. Expression was measured as the average intensity of each biological triplicate.

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Additional File 12:

Figure S5. Enriched GO terms for the 1,478 plastic genes listed in Dataset S4. The network graphs show BiNGO visualizations of the overrepresented GO terms. Categories in GoSlimPlants [79] were used to simplify this analysis. Non-colored nodes are not over-represented, but they may be the parents of overrepresented terms. Node size is positively correlated with the number of genes belonging to the category. Colored nodes represent GO terms that are significantly over-represented (P value <0.1), with the shade indicating significance as shown in the color bar.

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Additional File 13:

Figure S6. Validation of O2PLS-DA model. The three-latent-component O2PLS-DA model in Figure 3E was partially cross-validated and a permutation test (100 permutations) was used to highlight putative overfitting.

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Additional File 14:

Dataset S5. Functional categories of specific transcripts from each of four O2PLS-DA clusters. Pq(corr) values are indicated for each direction.

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Additional File 15:

Figure S7. Hierarchical clustering analysis of environment-specific differentially expressed genes in (a) vineyards using parral or Guyot replacement cane trelling systems and (b) vineyards located in one of the three macro-areas we investigated. Pearson's correlation distance was used as the metric. The heat map of transcriptional profiles was generated with TMeV 4.8 using the average expression value of the three biological replicates per each developmental stage.

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Additional File 16:

Dataset S6. Differentially-expressed genes in the 'Trelling System' category. Expression was measured as the average log2 intensity of each biological triplicate. Each value has been normalized on the median value of each row/gene.

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Additional File 17:

Dataset S7. Differentially-expressed genes in the 'Geographical Area' category. Expression was measured as the average log2 intensity of each biological triplicate. Each value has been normalized on the median value of each row/gene.

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Additional File 18:

Dataset S8. Plastic transcripts from the grape berry transcriptome at harvesting in 2008.

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Additional File 19:

Figure S8. Differentially modulated genes at harvesting. (a) Cluster dendrogram of the third developmental stage dataset using the average expression value of the three biological replicates. Pearson's correlation values were converted into distance coefficients to define the height of the dendrogram. Different colors indicate the disparity in the degree of ripening as analyzed in (c). (b) Differentially-expressed genes between the two groups of vineyards highlighted in (a). A t-test (α = 0.05) was performed between the two groups of vineyards, and a k-means analysis was computed using Pearson's distance to generate the line plots. (c) Functional category distribution of the differentially-modulated genes between the two groups of vineyards during harvesting. Transcripts were grouped into the 18 most represented functional categories, based on Plant GO Slim classification of biological processes. Sample VM083, GIV083, CC083, PM083, AM083, and FA083 category distribution is depicted in purple, while sample CS083, PSP083, BA083, BM083, and MN083 category distribution is depicted in light green. (d) Total acidity, expressed in g/L of tartaric acid and °Brix/total acidity of samples from the third developmental stage. Values represent mean ± standard deviation of three biological replicates. Different colors indicate the disparity in the degree of ripening as shown in (a) and in (c).

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Additional File 20:

Dataset S9. Markers for grape berry development. Markers also showing significance in other vintages are labeled accordingly.

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Additional File 21:

Figure S9. Non-plastic genes. Stage-specific datasets were analyzed by SAM multiclass analysis and one-way ANOVA (11 groups). Transcripts not shown to be significant in either analysis (that is, not differentially modulated) were tested for stage-specificity. The Venn diagram was calculated using Venn [84] and redrawn.

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Additional File 22:

Dataset S10. Non-plastic and constitutive transcripts. Expression was measured as the average log2 intensity of each biological triplicate.

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Additional File 23:

Figure S10. Expression profile of five non-plastic constitutive genes in the whole grapevine expression atlas [33].

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