## 2 Results
### Targeted and Untargeted Molecular Responses: Comparison of DYE-Treated versus Untreated Berries
\begin{table}
\begin{tabular}{c c c c c c} \hline
**Grapevine Gene** & **Arabidopsis** & **Function in** & **Group** & **Reference** & **Putative Role** \\
**Homologue** & **Arabidopsis** & **Group** & **Reference** & **Putative Role** \\ \hline \multicolumn{6}{c}{Response to chitin and regulatory burst involved in defence response} \\ \hline _Vitvi08g02053_ & _AT_2G35930_ & Plant U-box 23 & 1 & [PERSON] et al., 2008 [22] & Ubiquitin ligase homologous to U-Box E3 playing a role in response to drought stress. \\ \hline _Vitvi08g02051_ & _AT_2G35930_ & Plant U-box 23 & 1 & [PERSON] et al., 2008 [22] & Ubiquitin ligase homologous to U-Box E3 playing a role in response to drought stress. \\ \hline _Vitvi12g00139_ & _AT_1G29340_ & Plant U-box 17 & 4 & [PERSON] et al., 2006 [24] & ubiquitin-proteasome system in defences against pathogens. \\ \hline _Vitvi15g01003_ & _AT_5G24110_ & \begin{tabular}{c} WRKY Transcription \\ Factor Group III \\ \end{tabular} & 1 & [PERSON] et al., 2013 [25] & AtWRKY30, putative role in the activation of defence responses. \\ \hline _Vitvi07g03110_ & _AT_5G65530_ & \
\begin{tabular}{c} Protein kinase \\ superfamily protein \\ \end{tabular} & 1 & [PERSON] et al., 2015 [33] & RLCK VI, regulating basal resistance to powdery milder. \\ \hline \multicolumn{6}{c}{ROS Homeostasis} \\ \hline _Vitvi02g00332_ & _AT_1G63460_ &
\begin{tabular}{c} Glutathione \\ peroxidase 8 \\ \end{tabular} & 1 & [PERSON] et al., 2012 [27] & Involvement in the suppression of oxidative damage. \\ \hline \end{tabular}
\end{table} 
Table 1: Genes differently expressed in the analysis of the combined effects of time per treatment with DYE. The columns in the table report the gene ID in _Vitís vinifera_, the closest corresponding Arabidopsis homologue and its biochemical function identified in Arabidopsis, the group into which they clustered (groups of Figure 8), and their putative biological role as identified by the literature. \begin{table}
\begin{tabular}{c c c c c c} \hline \hline  
\begin{table}
\begin{tabular}{c c c c c c} \hline \hline
**Grapevine Gene** & **Arabidopsis** & **Function in** & & & & \\  
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**Grapevine Gene** & **Arabidopsis** & **Function in** & & & & \\  
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Interestingly, the DEGs upregulated by DYE treatment (included in groups 1 and 2) also comprised several genes encoding key enzymes of the main biosynthetic steps of jasmonic acid (JA) and ethylene, which act synergistically in response to abiotic and biotic stress, and, to some extent, of ABA and IAA. As far as JA biosynthesis is concerned, two genes encoding lipoxygenase (LOX) (_Vitvi13g01780_ and _Vitvi09g00085_, group 1), involved in the early biosynthetic steps of the hormone through metabolism of free fatty acids [43; 44], were up-regulated in concert with genes encoding two GDSL-like lipases (_Vitvi09g00038_ and _Vitvi10g00669_, group 1) [48], a DAD1-like lipase (Vitvi07g00039, group 1) [49], and a phospholipase (_Vitvi15g00298_, group 1) [50]. These may likely control the upstream degradation of lipid molecules to provide free fatty acid substrates for subsequent LOX action. JA-responsive genes were also upregulated by the treatment, including genes encoding a jasmonic acid carboxyl methyltransferase (_Vitvi04g02169_, group 1), catalyzing the methylation of JA [46; 47], and one gene encoding sulfotransferase 2A (_Vitvi13g00864_, group 1), involved in the sulfonation of hydroxy-JA [51]. Among the downregulated genes (groups 3 and 4) putatively involved in JA responses, a second gene encoding a sulfotransferase 2A (_Vitvi13g01379_, group 3) and a JA-responsive gene encoding proline dehydrogenase (PDH2) (_Vitvi14g01283_, group 4) [52], together with genes encoding a MAPK kinase (_Vitvi12g02545_, group 4), which negatively regulate wound responses [53], and a leucine rich repeat receptor kinase (_Vitvi11g01479_, group 4), which represses ethylene and JA signaling pathways [54], were identified.