Search

Additional file 3. Dynamic visualisation of immune signalling network response in potato cv. NahG-D\'esir\'ee infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for NahG-Désirée plants.

Additional file 2. Dynamic visualisation of immune signalling network response in potato cv. Désirée infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for Désirée plants.

Additional file 1. Dynamic visualisation of Arabidopsis thaliana response to Pseudomonas syringae. AtCKN network, cluster 40, GSE56094 experimental data, Pseudomonas syringae pv. tomato DC3000 vs Mock subset. Relative expression between Pseudomonas syringae and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red-induction, blue-repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression following 0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 14, 16 and 17.5 hpi are shown.

Additional file 3. Dynamic visualisation of immune signalling network response in potato cv. NahG-D\'esir\'ee infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for NahG-Désirée plants.

Additional file 2. Dynamic visualisation of immune signalling network response in potato cv. Désirée infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for Désirée plants.

Additional file 1. Dynamic visualisation of Arabidopsis thaliana response to Pseudomonas syringae. AtCKN network, cluster 40, GSE56094 experimental data, Pseudomonas syringae pv. tomato DC3000 vs Mock subset. Relative expression between Pseudomonas syringae and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red-induction, blue-repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression following 0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 14, 16 and 17.5 hpi are shown.

Symptom development and callose accumulation after PVY NTN inoculation. (A) Phenotypes of the PVYNTN-inoculated (right panel) and mock-inoculated plants (left panel). Symptoms on PVYNTN-inoculated leaves are shown at 7 and 11 dpi, and compared to control mock inoculated leaves for cv. Désirée (upper) and NahG-Désirée (bottom). (B) Callose deposition stained with aniline blue. Leaves of NT Désirée and transgenic NahG-Desiree were either PVY or mock-inoculated. In NT Désirée plants (NT- PVYNTN and NT-mock) and mock inoculated NahG-Désirée (NahG-mock) there was no callose accumulating. Callose deposition was observed only at the sites of necrotic lesions in PVYNTN-inoculated NahG-Désirée leaves. Two samples of callose accumulation at the site of necrotic lesion are demonstrated (NahG-PVYNTN). (Blue for aniline blue, red for background fluorescence, gray for transmission field, most bottom panel for superposition) (PDF 511 kb)

Statistical analysis of PVY accumulation and photosynthetic parameters. The significance of increase (+++: p

Validation of microarray results by RT-qPCR. Microarray results were validated by analyzing eight biologically relevant genes involved in photosynthesis (chlorophyll a-b binding protein: CAB and RuBisCO activase: RA), defense response (β-1,3-glucanase of three classes: Glu-I, Glu-II, Glu-III and pathogenesis-related protein1b: PR-1b), and sugar metabolism (granule bound starch synthase I: GBSSI and CwINV: cell wall invertase) by quantitative real-time PCR. Expression values were log2 transformed, and a fold-change difference (log2FC) was calculated for PVYNTN versus mock in cv. Désirée and NahG-Désirée at 1, 3, 4, 5 and 7 dpi are shown in the table. Statistically significant values (p

Transcriptional dynamic changes (log 2 FC) of genes involved in primary metabolism visualized with MapMan. Gene expression for cv. Désirée (A) and NahG-Désirée (B) plants infected with PVYNTN are visualized at 1 dpi, 3 dpi, 4 dpi, 5 dpi and 7 dpi. Only statistically significant DE genes (FDR p