## 2 Results
### Analysis of Gene Correlation Network  
Both volatiles and genes showed dynamic changes in developing organs of finger citron. Weighted gene co-expression network analysis (WGCNA) was performed to get a better understanding of the relationships between them and their place in the complex signaling networks regulating terpenoid metabolism. A total of 45 gene modules from the dynamic hierarchical tree cut were obtained after a series of matrix transformation procedures and network construction (Figure 5). The largest module was Module Turquoise, containing 1954 genes, and the smallest, 30 genes each, was observed for Module Ivory and Module Floralwhite. Figure 5: Clustering dendrogram of expressed genes. Gene modules were identified by dynamic hierarchical tree cut and shown in different colors. Height cut = 0.25, minimal module size = 30. To evaluate the biological importance of the modules, the Pearson correlation between Module eigengenes and external sample traits (in this case, volatile concentrations) [44] were calculated and visualized in Figure 6. The most abundant two components (limonene and \(\gamma\)-terpinene) with the six characteristic components identified in Figure 3C were selected as interesting traits. The terpene synthase gene numbers in each module are shown on the left. In Figure 6, the 58 _TPSs_ were assigned to 22 modules according to their transcript profiles. Finger citron _TPSs_ occurred in more than twenty modules. This result is predictable because Figure 4 already implied a diversity of _TPS_ expression patterns. The modules with the highest number of _TPS_ genes were Module Red (11) Module Green (7) and Module Blue (5). In addition to the only sesquiterpene, \(\beta\)-bisabolene, the remaining volatiles showed similar correlation coefficients with a certain module. For example, the correlation coefficients between Module Red and seven monoterpenoids fell in a narrow interval (\(-0.62\) to \(-0.52\)) and these monoterpenoids have similar accumulation patterns in finger citron tissues (Figure 2). Module Red, Module Green and Module Blue were large modules, comprising 661, 707, and 1406 nodes, respectively. Connections of genes were hard to distinguish in the co-expression networks constructed on all nodes (Figure S7). So, to get a better view of genes strongly correlated to _TPS_ genes, subnetworks were extracted from these three modules using TPSs as seed nodes. Subnetworks constructed from Module Red and Module Blue were visualized as Figures 7 and 8, respectively. Although Module Blue is the largest of the three analyzed modules, no TF was identified in its subnetwork (Figure S8). In these subnetworks, two categories of genes which are the main focus of this work: _TPS_ genes (red nodes) and transcription factors (blue nodes). Edges in figures indicate the interactions between the node gene and surrounding TFs in a module. The subnetwork of Module Red contains four _TPSs_: Cm105420, Cm186730, Cm207000, and Cm269930 (Figure 7). Cm186730 was located on the right of the network, while the other three genes gathered in the center. A total of five TFs were observed in this subnetwork. As a member of NAC family, Cm303080 was connected to two _TPSs_, Cm207000 and Cm105420 (Figure 7). These two _TPS_ genes were also connected to MYB family member Cm258540. The _TPS_ gene Cm105420, transcript levels were also suggested to be related to transcription factor C2H2 family member Cm279030  
Figure 6: Correlation coefficients between terpene synthase (TPS), module and volatile compound. TPS numbers assigned to each module are list on the left. Correlation coefficients between volatiles and Module eigengenes are presented on the right with a color scale (\(-1\) to \(1\)). Darker blue color represents higher correlation. Coefficients with \(p<0.05\) are colored in yellow. and G2-like family member Cm127980. For _TPS_ gene Cm269930, transcription factor CPP family Cm308600 was connected (Figure 7, Table S4). No transcription factors were observed to be connected to TPS Cm186730.