## 3 Results and Discussion
### Transcriptome Analysis of Grapes Receiving Different Cluster-Thinning Treatments
The green dots represent downregulated differentially expressed genes, the red dots upregulated differentially expressed genes, and the black dots non-differentially expressed genes. Figure 4: Differential expression volcano map of L vs. H, L vs. M, and M vs. H at the E-L 36 stage, respectively **(a–c)**. Venn diagram depicting the shared and unique differentially expressed genes (DEGs) identified by RNA-Seq analysis between grapes at the E-L 36 stage (**d**). Each point in the differential expression volcano map represents a gene, and the abscissa represents the logarithm of the multiple of the differential expression of a gene in the two samples. The ordinate represents the negative logarithm of statistically significant changes in gene expression. The green dots represent downregulated differentially expressed genes, the red dots upregulated differentially expressed genes, and the black dots non-differentially expressed genes. Figure 5: Differential expression volcano map of L vs. H, L vs. M, and M vs. H at the E-L 38 stage, respectively (**a–c**). Venn diagram depicting the shared and unique differentially expressed genes (DEGs) identified by RNA-Seq analysis between grapes at the E-L 38 stage (**d**). Each point in the differential expression volcano map represents a gene, and the abscissa represents the logarithm of the multiple of the differential expression of a gene in the two samples. The ordinate represents the negative logarithm of statistically significant changes in gene expression. The green dots represent downregulated differentially expressed genes, the red dots upregulated differentially expressed genes, and the black dots non-differentially expressed genes. To further understand the transcriptome data, a GO functional enrichment based on DEGs was performed (Figure 6). Using the GO database, the functions of DEGs were classified into three main categories: biological processes, cellular components, and molecular functions. At E-L 35, the cellular components, molecular functions, and biological process contained 14, 11, and 17 groups, respectively (Figure 6a); at E-L 36, these categories contained 14, 11, and 18 groups, respectively, (Figure 6b), and at E-L 38, they contained 15, 13, and 18 groups, respectively (Figure 6c). The DEGs from the comparisons of L vs. H, L vs. M, and M vs. H were significantly enriched in the biological process terms \"metabolic process\", \"cellular process\", and \"single-organism process\"; the cellular component terms \"cell\", \"cell part\", \"membrane\", and \"membrane part\"; and the molecular function terms \"binding\" and \"catalytic activity\". The DEGs having relatively higher expression levels in the three main functional categories were relatively stable during development. At E-L 35, 552 (58.97%) DEGs among the three treatments were related to metabolic processes in the biological process category (Figure 6a). This number decreased to 483 (58.76%) and then decreased again to 401 (51.08%) at E-L 36 and E-L 38, respectively. Cluster thinning influenced the number of DEGs related to metabolic processes in berries. The KEGG enrichment analysis of DEGs was performed by KEGG database mapping, and the results are shown in Figure 7 and Table S4. At E-L 35, 193 DEGs were enriched in 82 KEGG pathways in L vs. H, L vs. M, and M vs. H. Among them, \"phenylpropanol biosynthesis\", \"plant hormone signal transduction\", and \"protein processing in endoplasmic reticulum\" contained the most genes (Figure 7a; Table S4). In total, 200 DEGs were enriched in 86 KEGG pathways in L vs. H, L vs. M, and M vs. H at E-L 36 including \"plant-pathogen interaction\", \"phenylpropanoloid biosynthesis\", \"protein processing in endoplasmic reticulum\", and \"flavonoid biosynthesis\", which had the largest number of genes (Figure 7b; Table S4). _VIT_00s0385g00010_ and _VIT_19s0015g01010_ participated in the monoterenoid biosynthesis pathway and the terpenon backbone biosynthetic pathway, respectively. In total, 238 DEGs were enriched in 87 KEGG pathways among treatments at harvest (E-L 38).