## 2 Results
### Targeted and Untargeted Molecular Responses: Comparison of DYE-Treated versus Untreated Berries
The treatment clearly impacted plant hormonal signaling by downregulating the transcription of two genes encoding a protein homologous to AUX1 (auxin influx transporter) and CRE1 (cytokinin receptor 1), respectively [20; 21], while a gene encoding a putative ABA receptor (PYR/PYL) was upregulated. Carotenoid biosynthesis and metabolism, connected with ABA biosynthesis, were affected through the downregulation of a gene encoding zeaxanthin epoxidase and the upregulation of a gene encoding an epoxica carotenoid dioxygenase, the latter enzyme being the limiting step responsible for producing xanthoxin and, consequently, abscisic acid (ABA). The transcription of a gene encoding jasmonate o-methyltransferase was upregulated, meaning that the conversion of jasmonate into methyl- jasmonate may be favored. Several genes encoding ABC transporters were differentially regulated: ABCB (participating in the mediation of polar auxin transport and multidrug resistance), ABCC (associated with detoxification), and ABCG (PDRS) subfamily members were down-regulated, while an ABCG subfamily member (responsible for secondary metabolite transport) was up-regulated (Table S5). Besides the previously mentioned pathways, KEGG analysis also highlighted transcriptional changes related to amino acids. Genes encoding acetlactate synthase and L-proline dehydrogenase, which are involved in the pathway of biosynthesis of L-valine, L-leucine, and L-isoleucine and in the conversion of proline into arginine, respectively, were downregulated. Moreover, the biosynthetic pathway of mugineic acid (an iron chelating compound) from methionine was altered after the DYE application through the upregulation of nicotinamide synthase. The gene encoding hydroxypyruvate reductase, belonging to the serine biosynthetic pathway and responsible for the transformation of hydroxypyruvate into glycerate, was upregulated. Finally, in the nucleotide metabolism, the transformation of uridine (a by-product of L-glutamine) into uracil was upregulated (Table S5). Untargeted Analysis of Molecular Responses to DYE Application: Combined Effects of Time and Treatment  
The effect of the treatment on the overall time-course expression of genes during the ripening of the berry was analyzed by comparing the dynamics of the transcriptional profiles from TP2 to H in treated and control samples using the likelihood ratio test (LRT) in DESeq2. LRT allowed the identification of all genes that showed a change of expression across the different timepoints as a function of the effect of treatment with DYE on their expression trends during berry ripening. After statistical analysis (Figure 8), it was possible to cluster the genes into four groups according to their transcriptional expression behavior. In the three groups 1, 2, and 4, genes that, in untreated berries, displayed an intrinsically slightly decreasing (groups 1 and 4) or clearly decreasing (group 2) expression trend along with the ripening of the fruit were included. Conversely, group 3 included genes that displayed an upregulation from TP2 towards ripening (H) (Figure 8A,B). The treatment with DYE interfered with these naturally occurring gene expression trends by smoothing or even reversing them. Genes belonging to groups 1 and 2 were in fact up-regulated by the treatment at both time points in comparison to untreated berries, and their decreasing expression trend towards H was prevented for group 2 while it was reverted for group 1, the latter displaying a progressively increasing expression trend at H in the DYE-treated berries (Figure 8A,B). For groups 3 and 4, which included genes that displayed an up or downregulation from TP2 to H, respectively, the treatment resulted in an overall downregulation of the transcriptional expression level of the genes in comparison to their untreated control counterparts.