Open Access Research article

General and species-specific transcriptional responses to downy mildew infection in a susceptible (Vitis vinifera) and a resistant (V. riparia) grapevine species

Marianna Polesani1, Luisa Bortesi1, Alberto Ferrarini1, Anita Zamboni1, Marianna Fasoli1, Claudia Zadra2, Arianna Lovato1, Mario Pezzotti1, Massimo Delledonne1 and Annalisa Polverari1*

Author Affiliations

1 Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy

2 Department of Agricultural and Environmental Science, University of Perugia, B.go XX Giugno 72, 06121 Perugia, Italy

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BMC Genomics 2010, 11:117  doi:10.1186/1471-2164-11-117

Published: 18 February 2010

Additional files

Additional file 1:

Differences in basal gene expression levels between the two species at 12 h after mock-inoculation with distilled water. The file contains a list of transcripts showing statistically significant differential expression, with a False Discovery Rate (FDR) ≤5%. The fold change of V. vinifera vs. V. riparia expression levels (Fold Change Vv/Vr) is reported, along with the q-value (%) indicating the FDR. A separate list reports the subset of defense-related genes, functionally categorized as 'resistance', 'stress', 'cell wall' and 'secondary metabolism' considered in Additional file 3.

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Additional file 2:

Differences in basal gene expression levels between the two species at 24 h after mock-inoculation with distilled water. The file contains a list of transcripts showing statistically significant differential expression, with a False Discovery Rate (FDR) ≤5%. The fold change of V. vinifera vs. V. riparia expression levels (Fold Change Vv/Vr) is reported, along with the q-value (%) indicating the FDR. A separate list reports the subset of defense-related genes, functionally categorized as 'resistance', 'stress', 'cell wall' and 'secondary metabolism' considered in Additional file 3.

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Additional file 3:

Comparison between defense-related genes in V. vinifera and V. riparia at 12 and 24 h after mock-inoculation with distilled water. Defense-related genes considered for the comparison are those functionally categorized as 'resistance', 'stress', 'cell wall' and 'secondary metabolism' and are shown in the 'defense-related' lists in Additional files 1 and 2. The tables on the left show the total numbers of genes whose basal expression is higher in V. riparia (overexpressed in Vr) or V. vinifera (overexpressed in Vv) within each category. The tables on the right report mean logarithmic fluorescence values of transcripts within each category (mean Vr and mean Vv), the ratio of the means calculated for each genotype and the resulting fold change. Microarray fluorescence data from the two time-points were normalized and analyzed separately to avoid detecting basal differences based on the response to illumination.

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Additional file 4:

Subset of transcripts showing a difference in basal expression level between V. vinifera and V. riparia at both the 12 and 24 h time points after mock-inoculation with distilled water. The file contains a list of transcripts showing statistically significant differential expression, with a False Discovery Rate (FDR) ≤5%. The fold change of V. vinifera vs. V. riparia expression levels (Fold Change Vv/Vr) is reported, along with the q-value (%) indicating the FDR. A separate list reports the subset of defense-related genes, functionally categorized as 'resistance', 'stress', 'cell wall' and 'secondary metabolism' considered in Additional file 5.

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Additional file 5:

Comparison between defense-related genes in the subset of transcripts differentially expressed in the two species both at 12 and 24 h after mock-inoculation with distilled water. Defense-related genes considered for the comparison are those functionally categorized as 'resistance', 'stress', 'cell wall' and 'secondary metabolism' and are shown in the 'defense-related' list in Additional file 4. The tables on the left show the total numbers of genes whose basal expression is higher in V. riparia (overexpressed in Vr) or V. vinifera (overexpressed in Vv) within each category. The tables on the right report mean logarithmic fluorescence values of transcripts within each category (mean Vr and mean Vv), the ratio of the means calculated for each genotype and the resulting fold change.

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Additional file 6:

Differential gene expression in V. riparia and V. vinifera following infection with P. viticola. The file lists transcripts showing a statistically significant differential expression (fold change ≥2, FDR ≤5%) in P. viticola infected samples of V. riparia (Vr) and V. vinifera (Vv), in comparison to their respective mock-inoculated controls, at 12 and 24 hpi. Species-specific and 'common' transcriptional changes associated with infection are also reported in separate lists for easier access.

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Additional file 7:

Representative V. riparia and V. vinifera transcripts modulated after infection with P. viticola. A selection of representative transcripts modulated in both species ('common') or specifically in V. riparia (Vr) or V. vinifera (Vv) after infection with P. viticola. Target descriptions are provided, corresponding to gene annotations in the source databases, along with the corresponding functional category and the microarray fold change (FC) value for each time point.

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Additional file 8:

Real-Time RT-PCR analysis of selected genes. The figure reports the comparison of transcriptional changes of selected genes as determined by microarray (white bars) and Real-Time RT-PCR analysis (black bars). The black bars indicate the average fold change obtained for the three independent biological replicates, and the error bars indicate the standard deviations. Individual fold change values and standard errors for each Real-Time experiment are available in Additional file 9.

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Additional file 9:

Details of the Real-Time RT-PCR analysis. The file contains: the sequence ID of each gene analyzed by Real-Time RT-PCR; the corresponding primer pairs used for the amplification (FOR = forward primer, REV = reverse primer); an indication of the region amplified by each primer pair (3' UTR = 3'untranslated region; CDS = coding sequence; CDS-probe = region of the coding sequence covered by the microarray probe; CDS-3' UTR = region between the coding sequence and the 3'untranslated region); the time point after treatment at which the leaves were sampled; the Real-Time RT-PCR results, reported as fold change (FC) relative to the untreated control sample and with the standard error (SE), for each species (Vv = V. vinifera Vr = V. riparia) and divided in biological replicates (1, 2 and 3); the mean values of the FC for the three replicates for each genotype. The corresponding microarray results for the same transcripts are also reported as fold change at the end of the list.

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