# Transcriptional Regulatory Networks Oscillate Seasonal Plasticity of Fruit Metabolism in Melon
## 3 Results
### Conjoint Analysis of Metabolome and Transcriptome  
In the studies of metabolome and transcriptome, we identified the key role of the phenylpropanol pathway in the metabolic process and identified related gene clusters. The transcriptional expression patterns are strongly associated with the differences in metabolites (Figure 1f). To dig out the detailed relationship between changes in the different metabolites and those of gene expression, and further explore the molecular mechanisms that cause differences in fruit quality, we performed conjoint analysis of metabolome and transcriptome, then established a predicted phenylpropanol biosynthesis pathway. We analyzed the correlation between 19 DEGs and 8 DAMs, as well as their expression patterns and differential changes in the phenylpropanol pathway (Figure 4), mainly focusing on common phenylpropanol substances and their related genes such as monolignol, flavonoids (flavonoids, flavonoids, anthocyanins), and phenolic acids. Correlation heatmaps and correlation networks can provide a more intuitive understanding of the relationship between DAMs and DEGs (Figures 4d and S7a-c). Figure 4: _Cont_. The biosynthesis of phenylpropanoid pathway (GPP) and subsequent specific branch pathways. Beginning with phenylalanine and tyrosine, two aromatic amino acids synthesized by the shikimic acid pathway, there was no significant difference between spring and autumn (Figure 4a). The derived coenzyme A substances act as an intermediate and begin to enter specific branch pathways of various phenylpropanoid compounds. Mainly downstream branches following the GPP are the monolignol pathway, the phenolic acid pathway, the coumarin pathway, and the flavonoid pathway. In general, a total of 27 metabolites were detected, of which 8 metabolites showed differential accumulation in the fruits of two seasons, including two aldehydes (p-coumaraldehide and sinapaldehide), three hydroxycinnamic acids belonging to phenolic acids (p-coumaroyl quinic acid, trans-2-hydroxycinnamic acid), one alcohol (coniferol alcohol), one flavonoid glycoside (naringin), and one proanthocyanin((-)-epicatechin). Among them, there was a significant difference in the content of (-)-epicatechin between the two seasons (\(p<0.05\)) (Figure 4a,b). Interestingly, they were all more abundant in spring. Correspondingly, we found significant differences in the expression patterns of 19 genes distributed in various branches of the phenylpropanoid pathway (Figure 4a-c). The up-regulation of enzymes specific for lignin biosynthesis cinnamyl-CoA reductase (CCR)(_MELO3C009963.2_, _MELO3C012243.2_, _MELO3C023465.2_) and anthocyanin-related genes flavanone 3-hydroxylase (F3H)(_MELO3C005801.2_, _MELO3C024857.2_) and antho  
Figure 4: The DEGs and DAMs on the phenylpropanoid pathway in fruits 40 days after pollination under spring and autumn growing conditions: (**a**) The phenylpropanoid biosynthesis pathway and the downstream branch flavonoid biosynthesis pathway. (**b**) Heatmap of the differential metabolites on phenylpropanoid pathway. (**c**) Heatmap of the differential transcripts on phenylpropanoid pathway. (**d**) Heatmap of correlated differential metabolites and transcripts on phenylpropanoid pathway. cyanidin synthase (ANS)(_MELO3C023957.2_) could largely explain the high accumulation of p-coumaraldehyde, sinapaldehyde and (-)-epicatechin in the spring fruits. However, the coding genes of other proteins involved in the phenylpropanol pathway were mixed-regulated, indicating that the synthesis of metabolites was the result of multiple systems participating and coordinating together. As highlighted by the background shadings, the same enzymes act at different steps in the pathway, this speaks to the modularity, versatility, and recurring themes in the pathway (Figure 4a).