## 2 Results
### Targeted and Untargeted Molecular Responses: Comparison of DYE-Treated versus Untreated Berries
Most of the genes identified as DEGs at TP2 were not conserved as DEGs at H (data not shown). Gene ontology enrichment analysis was carried out to highlight the pathways mainly affected by the DYE treatment by using three different approaches, namely G:Profiler, Mapman, and KEGG. Among the categories identified by G:Profiler within the upregulated genes at H, terms related to protein stability (\"unfolded protein binding\", \"chap-erone binding\", and \"protein folding\"), transcriptional regulation (e.g., \"regulation of transcription\" and \"DNA-binding transcription factor activity\"), stress hormone action (\"ethylene-activated signaling pathway\"), and abiotic stress (\"response to heat\" and \"response to hypoxia\") were abundantly represented. Among the downregulated genes at H, the categories \"ADP and ATP binging\", \"protein binding\", \"cellular glucan metabolic process\", and \"xyloglucan-xylo-glucosyl transferase\", and \"defence response\" were enriched (Figure 7A,B). Figure 6: Overview of RNA-seq results of samples collected at TP2 and H in 2020. (**A**) symbolizes the differentially expressed genes (DEGs) between treated and control samples, observed at each time point (TP2 or H) separately. The two colors represent downregulated (blue) and upregulated (red) genes. (**B**) categorizes the DEGs to differentiate between highly differentially expressed (red and dark blue) (\(-2>\log 2\text{FC}>2\)) and slightly differentially expressed (yellow and light blue) (\(0.6<\log 2\text{FC}<1\) and \(-1<\log 2\text{FC}<-0.6\), respectively) genes identified amongst the significant differential expressions. Figure 7: Enrichment analysis obtained with G:Profiler (**A**,**B**) and Mapman (**C**) softwares. (**A**) shows upregulated and downregulated pathways for TP2 (left panel) and H (right panel). (**B**) represents the number of DEGs involved in each pathway at TP2 (left panel) and H (right panel). (**C**) reports in a heatmap the pathways identified by Mapman as up- (red squares) or down-regulated (blue squares) at TP2 or at H.  
channels and primary active transport ABC superfamily\", \"response to pathogens and effector triggered immunity\", and \"transferases\" were downregulated at this time point. Conversely, \"Phytohormone action: jasmonic acid\", \"RNA biosynthesis: transcriptional regulation AP2/ERF transcription factor superfamily\", \"protein homeostasis: protein quality control and ubiquitin-proteasome system\", \"protein homeostasis: serine type peptidase activities\", \"External response to temperature: cold response and ICE-CBF cold acclimation transcriptional cascade\", were upregulated at H. The enriched categories \"Secondary metabolism of terpenoids: terpene biosynthesis\" and \"protein homeostasis proteolysis: aspartic-type peptidase activity\" were downregulated both at TP2 and at H.  
KEGG analyses highlighted several biochemical pathways underpinning the previously identified enrichments (data not shown). As far as glutathione and sulphur metabolisms were concerned, an upregulation of glutathione peroxidase (EC 1.111.9), responsible for the conversion of reduced GSH into its oxidized version GSSG, and a downregulation of adenylyl-sulphate reductase (EC 1.8.4.9), leading to cysteine production, were observed. Regarding the regulation of genes potentially involved in plant-pathogen interaction, the transcription of CDPKs (calcium-dependent protein kinase), CaM/CML (calcium sensors involved in the regulation of plant development and stress responses), HSP90 (heat shock protein 90), and RBOHs (respiratory burst oxidase, responsible for ROS generation) was upregulated. Within the same pathway, the upstream components CNGSs (cyclic nucleotide gated channels) and RPM1 (NBS-LRR protein) were downregulated. Furthermore, a gene encoding WRKY229 and involved in the MAPK signaling pathway, linked to H\({}_{2}\)O\({}_{2}\) production and leading to programmed cell death, was upregulated.