## 3 Results
### WGCNA of DEGs in Lotus Tissues  
In further analyses, we screened highly expressed genes from transcriptome data and 10 key flavonoids from differential metabolites of six lotus tissues for WGCNA analysis  
Figure 6: Heatmap of key genes and metabolites expression in flavonoid biosynthesis pathway of 6 lotus tissues. to explore the gene expression profile and search for flavonoid-synthesis-related gene modules and co-expressed genes. Among the 17 co-expressed modules identified, we considered the modules that satisfied the conditions of R > 0.8 and \(p\)-value < 0.01 as highly related to the corresponding flavonoids. The module-trait heatmap (Figure 7A) showed that the highly expressed genes in Plu were majorly distributed in the blue module, which was highly correlated with (+)-catechin and (+)-gallocatechin. The highly expressed genes in Sta were mainly distributed in the black module and highly correlated with kaempfer. Most of the highly expressed genes in Pet were in the turquoise module and were highly correlated with pinobanksin and naringenin chalcone. In the Rec tissue, genes were predominantly located in the magenta module and were strongly correlated with luteoforol. The red module, which was highly expressed in both Rec and Flo, showed a significant correlation with phlorizin and luteoforol. Meanwhile, the light cyan and yellow modules mainly comprised genes that were highly expressed in Flo and strongly correlated with delphinidin. Among these modules strongly correlated with flavonoid metabolites, the black module, turquoise module, magenta module, light cyan module, and yellow module contained one, two, six, one, and three structural genes related to the flavonoid biosynthesis pathway, respectively. These five modules were screened as key modules and used to identify the genes in the modules (Table 2, Table S3). The black module contains LOC104608517 (_FLS_) which primarily affects the synthesis of kaempfer. LOC104603248 (_HCT_), and LOC104588272 (\(C3^{\prime}H\)) in the turquoise module modulate the synthesis of pinobanksin and naringenin chalcone. The important genes in the magenta module for luteoforol synthesis include LOC104601277 (_PAL_), LOC104589393 (_PAL_), LOC104602160 (_CHS_), LOC104602224 (_CHS_), LOC104605233 (_F3H_), and LOC104585744 (_ANR_). The light cyan module has LOC10461136 (_CCoAOMT_), which is important for delphinidin synthesis. The important genes in the yellow module for delphinidin synthesis include LOC104595050 (_PAL_), LOC104601739 (_CCoAOMT_), and LOC104606654 (_CCoAOMT_). Among the five key modules listed in Table 2, the structural genes related to flavonoid synthesis, along with their co-expressed genes that exhibit reciprocal relationships within these modules, were visualized in heatmaps (Figure 7B-N). Consequently, the genes included in the different modules had specific expression trends in different tissues of the lotus. These genes have an important effect on the accumulation of flavonoids in different tissues. To further identify the transcription factors involved in flavonoid synthesis, we analyzed those that were closely associated with the structural genes in the key modules. Subsequently, we constructed an interoperability network diagram using the structural genes (Figure 7O, Table S4), including 38 nodes and 167 edges. The circles represent the transcription factors and squares indicate the structural genes. These 67 transcription factors were from 26 transcription factor families including 10 WRKY, 8 HLH, 7 ERF, 4 HD-ZIP and TALE, 3 ARF, C2H2, and NAC, and other transcription factor families. The MCC algorithm was used to screen the top 10 nodes with centrality (Table 3). Among the transcription factors analyzed, bHLH demonstrated the highest degree of connectivity, interacting with seven structural genes. ERF was connected to six structural genes, while NF-YC was associated with five.