## 2 Results
### Effects of ABA and NAA on Berry Development and Ripening
#### 2.1.3 Strong Transcriptional Changes of Ripening Switch Genes  
A previous study has identified 190 grapevine berry switch genes, which trigger the onset of the ripening process [16]. All those genes were observed to express at low levels during the immature phase and show a significant increase at veraison. They were mainly involved in transcription activation, cell wall metabolism and the development process. In the present study, the expression pattern of the switch genes was investigated to detect the roles of these genes in varied ripening process induced by ABA and NAA treatments. After removing the switch genes with low expression (RPKM < 1) among our samples, the remaining 184 switch genes were performed K-means clustering analysis, and two clusters were generated (Figure S1). The expression of 107 genes in cluster 1 kept increasing from E-L 34 to E-L 38 stage in all samples and these genes expressed at a higher level in NAA-treated berries at E-L 36 stage. In the contrast, the transcript abundance of 77  
Figure 3: Expression of genes involved in ABA and auxin signaling pathway. Green and cyan boxes represent significantly downregulated and upregulated genes, respectively, in treated berries compared to the control.  
genes in cluster 2 increased at the early stage then decreased, and these genes showed lower expression level under NAA treatment. Among the switch genes of cluster 1 and 2, the 147 significant differentially expressed switch genes (DESGs) between treatments and control were shown in Figure 4, and the biological process annotation of these DESGs was listed in Table S1. According to their distinct responses to the treatments, the DESGs in the above-mentioned cluster 1 and cluster 2 were roughly divided into 3 (a-c) and 2 (d-e) groups, respectively. Interestingly, we found most genes in the group a and d were up-regulated by ABA at E-L 34 or E-L 35 stage, while down-regulated by NAA at the early stages. These genes encompassed TFs of VviMYBA2 (VIT_202s0033g00390) and zinc finger family genes (VIT_206s0061g00760 and VIT_212s0028g03860) in group a, as well as VviMYBA1 (VIT_202s0033g00410) and VviMYBA3 (VIT_202s0033g00450) in group d. Additionally, a total of 50 genes in group b were only up-regulated in NAA-treated berries particularly at E-L 36 stage. The most overrepresented biological process in this group is \"Secondary Metabolic Process\", including the genes of cytochrome P450 family, glutathione S-transferase and carotenoid cleavage dioxygenase 4b (CCD4b). The genes in the group of c and e showed lower levels of expression at specific stages under NAA treatment, and they are mainly related to the transcription factor activity and cell wall metabolism. The TFs of VviWRKY75 (VIT_217s0000g01280), VviWRKY23 (VIT_207s0005g01710), VviNAC33 (VIT_219s0027g00230), VviNAC60 (VIT_208s0007g07670), three zinc finger proteins (VIT_20 5s0020g04730, VIT_208s0040g01950 and VIT_218s0001g01060) and two lateral organ boundaries proteins (VIT_206s0004g07790 and VIT_20s0091g00670), were found in these genes. It also included several genes encoding cellulase (VIT_201s0137g00430), endo-1,4-beta-glucanase (VIT_200s2526g00010, VIT_200s0340g00050 and VIT_200s0340g0060) and xyloglucan endotransglucosidase/hydrolase (VIT_206s0061g00550 and VIT_205s0062g00610) that are involved in fruit softening [25, 26]. Moreover, among these NAA-inhibited genes, three genes are involved in carbohydrate metabolism (glycolysis and sucrose biosynthesis), including phosphopyruvate hydratase (VIT_216s0022g01770), sucrose synthase (VIT_207s0005g00750), sucrose-phosphate synthase (VIT_218s0075g00350).