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Additional file 2. Principal component analysis (PCA) of the RNA-seq data showing samples distribution of DESeq2 analysis before (a) and (b) after removal of Plant_Control_2 sample. See Additional file 3 for raw data.

Additional file 10. Significant Gene Ontology (GO) categories of (a) biological process (BP), (b) molecular function (MF), (c) cellular components (CC) among the deregulated genes identified by the NOISeq analysis in the aphid M. persicae following feeding on artificial medium containing TuYV purified particles or artificial medium only. The percentage of deregulated genes from the total number of genes included in each GO category is indicated on the horizontal axis (% DE); counts: number of genes differentially expressed in the GO term. GO term boxed in blue represents categories potentially implicated in virus uptake and intracellular transport.

Additional file 5. Principal component analysis (PCA) of the RNA-Seq data showing samples distribution (NOISeq analysis) before (a) and (b) after batch correction. See Additional file 6 for raw data.

Additional file 9. Significant Gene Ontology (GO) categories of (a) biological process (BP), (b) molecular function (MF), (c) cellular components (CC) among the deregulated genes identified by the DESeq2 analysis in the aphid M. persicae following feeding on artificial medium containing TuYV purified particles or artificial medium only. The percentage of deregulated genes from the total number of genes included in each GO category is indicated on the horizontal axis (% DE); counts: number of genes differentially expressed in the GO term. GO term boxed in blue represents categories potentially implicated in virus uptake and intracellular transport.

Additional file 11. Common deregulated genes in aphids between plant and artificial medium feeding conditions with the DESeq2 program.

Additional file 7. Significant Gene Ontology (GO) categories of (a) molecular function (MF), (b) cellular components (CC) among the deregulated genes identified by the NOISeq analysis in the aphid M. persicae following feeding on TuYV-infected or non-infected plants. The percentage of deregulated genes from the total number of genes included in each GO category is indicated on the horizontal axis (% DE); counts: number of genes differentially expressed in the GO term. GO term boxed in blue represents categories potentially implicated in virus uptake and intracellular transport and GO term boxed in red categories potentially involved in aphid behavior and signal perception.

Additional file 12. Locomotor activity of viruliferous and non-viruliferous M. persicae fed on plants or on artificial medium. (a) maximum zone reached and (b) duration (in seconds) spent in each zone. Box plot show median (line), 25-75% percentiles (box) and 10-90% percentiles (whisker). Letters indicate significant differences between aphid status with the GLM followed by multiple comparisons; p-value

Additional file 4. Significant Gene Ontology (GO) categories of (a) biological process (BP), (b) molecular function (MF), (c) cellular components (CC) among the deregulated genes identified by the DESeq2 analysis in the aphid M. persicae following feeding on TuYV-infected or non-infected plants. The percentage of deregulated genes from the total number of genes included in each GO category is indicated on the horizontal axis (% DE); counts: number of genes differentially expressed in the GO term. GO term boxed in blue represents categories potentially implicated in virus uptake and intracellular transport and GO term boxed in red categories potentially involved in aphid behavior and signal perception.

Additional file 1. Comparison of the expression of 6 genes by RNA-Seq and RT-qPCR analyses.

Additional file 8. Protein content of the purified extract prepared from TuYV-infected M. perfoliata and used to feed aphids artificially before RNASeq analysis. (a) Polyacrylamide gel electrophoresis of the TuYV purified extract (3 µg) stained with Coomassie blue; (b) Western blot analysis of the same purified extract. The blot was incubated with a mixture of antisera specific for the CP and RT*. CP: major coat protein (CP); RT*: minor coat protein (RT*). The band corresponding to a major plant protein (P90) in the TuYV purified preparation is indicated. The molecular mass markers are indicated in kDa.

Additional file 5. Genes regulated between consecutive stages of berry development at both transcriptional and splicing level. Gene IDs correspond to the VCost.v3 genome annotation.

Additional file 3. Functional classification of the genes affected by differential AS in stage and variety comparisons. The classification was performed using the PANTHER GO-slim tool ( www.pantherdb.org/ ). GO terms are split in the three usual categories a Biological Process (BP). b Molecular Function (MF). c Cellular Component (CC). The percent of genes belonging to each category is given on the x-axis.

Additional file 1. Total number of AS events and DAS events in comparisons between consecutive stages or varieties. Retained events were supported by a minimum number of 15 reads of the rarest isoform under at least one condition, and a minimum inclusion level (IL) of 10%.

Additional file 4. Differential isoform ratios between Gw and Ri, for fifteen AS events regulated between véraison and mid-ripening in only one variety.

Additional file 7. Review History.

Additional file 1: Figures S1 to S9, Tables S1 to S12, Text S1.

DC_104: Designing Co-Constructed Extended Live Event Coverage Experiences