## 2 Results
### DEGs Involved in Terpenoid biosynthesis  
To unveil the regulatory mechanism of terpenoid accumulation patterns in different plant parts of sacred lotus, we analyzed the expression profiles of genes involved in terpenoid biosynthesis. In total, 105 DEGs related to terpenoid biosynthesis were identified in sacred lotus and their expression patterns are shown in Figure 5. In total, 55 DEGs were annotated to the terpenoid backbone synthesis pathway (ko00900), of which 13 and 11 DEGs participated in the MVA and MEP pathways, respectively. Furthermore, DEGs encoding key enzymes in the MVA pathways exhibited a higher expression level in YL compared with S and ML. Interestingly, _AACT2_ and _HMGS2_ exhibited the highest mRNA level in S, while _HMGR3_ was the highest expressed in ML (Figure 5 and Table S4). Similar to the MVA pathway, the expression levels of DEGs involved in MEP in leaves was still higher than seeds, and the expression levels of DEGs in ML were significantly higher than YL (Figure 5 and Table S4). Moreover, six unigenes encoding IPTS were identified, including geranyl diphosphate synthase (GPPS), farnesyl diphosphate synthase (FPPS), and geranylderivanyl diphosphate synthase (GGPPS). The expression level of _FPPS_ in YL was higher than that in S and ML and also had higher transcript levels in the three differently colored flowers, which was consistent with the expression pattern of DEGs in the MVA pathway. The expression level of _GPPS_ in S was lower than in other parts, but there was no obvious difference in leaves and flowers. The different expression patterns in the three _GGPPS_ transcripts are worth noting. The _GGPPS2_ transcript exhibited the highest  
Figure 3: Clusters of DEGs. Twelve clusters were classified based on gene expression pattern: Sub Class1–Sub Class12. The horizontal coordinate represents the sample and the vertical coordinate represents the centralized and normalized expressions. expression level in mature leaves, with the highest mRNA level of _GGPPS3_ in WF, RF, and YF. Moreover, the expression level of _GGPPS1_ was relatively lower than that of _GGPPS2_ and _GGPPS3_ (Figure 5 and Table S4). Figure 4: Annotation information of DEGs. (**A**) GO enrichment histogram of DEGs. The abscissa indicates the ratio of genes annotated to the entry to the total number of genes and the ordinate indicates the name of the GO entry. All DEGs were divided into three GO entries: biological process, cellular component, and molecular function. (**B**) KEGG classification column chart. DEGs were divided into five branches according to the KEGG metabolic pathway: Cellular Processes, Environmental Information Processing, Genetic Information Processing, Metabolism, and Organismal Systems. Figure 5: DEGs in terpenoid biosynthesis of sacred lotus. Typical terpenoid biosynthetic pathway with homology heat map of gene transcription level in transcriptome data with substrates and products. The arrows connect the substrate to their corresponding product. The expression pattern of each unigene is displayed in a six-column grid; from left to right are seed, young leaf, mature leaf, red flower, white flower, and yellow flower. Transcript-level data is represented by PFKM.