## 3 Results
### Terpenoid Backbone Biosynthesis Pathway  
Differences in gene expression were assessed using the transcriptomes of \(H\). _coralloides_ strains DK '77', MK-1, and MK-2, and the primordium (FB-A), stipe (FB-B), and spines (FB-C). KEGG enrichment of differentially expressed genes (DEGs) in MK-1 and MK-2 identified 275 DEGs, including 58 up-regulated and 217 down-regulated DEGs (Figure S3A,B). A comparison of DK with FB-A identified 494 DEGs, including 230 up-regulated and 264 down-regulated DEGs (Figure S3C,D), whereas a comparison of DK and FB-B identified 471 DEGs, including 196 up-regulated and 275 down-regulated DEGs (Figure S3E,F). A comparison of DK and FB-C identified 534 DEGs, including 203 up-regulated and 331 down-regulated DEGs (Figure S3G,H). Most DEGs were enriched in metabolic pathways, indicating that changes in terpenoids may be related to these metabolic pathways (Figure S4). The DEGs most closely associated with terpenoids were analyzed by determining the top 20 KEGG pathways in each pairwise comparison (Figure 5). In each comparison, the up-regulated genes (_Her005768_, _Her008335_, and _Her011461_) were associated with the terpenoid backbone biosynthesis pathway (ko00900). _Her005768_ was found to encode 4-diphosphocytidyl-2-C-methyl-D-erythnitrol kinase (iSPE), whereas _Her008335_ and _Her011461_ were found to encode farnesyl diphosphate synthase (FDPS)/geranylgeranyl pyrophosphate synthase1 (GGPPS) (Table S6); FDPS and GGPPS are key enzymes in the biosynthesis of geranylgeranyl pyrophosphate (GGPP), a common precursor in diterpene synthesis. iSPE, FDPS, and GGPPS have been reported to be important rate-limiting enzymes in the biosynthesis of terpenoids [37]. For example, the expression of genes regulating iSPE, FDPS, and GGPPS in Wolfioria cocos was up-regulated in the mycelial stage, a finding consistent with alterations in triterpen production and suggesting that genes regulating iSPE, FDPS, and GGPPS are involved in the biosynthesis of triterpen in the mycelial stage [38]. Similarly, FDPS, GGPPS, and iSPE likely played a positive role in terpenoid synthesis in the present study. Compared with MK-2, the levels of expression of genes encoding FDPS, GGPPS, and iSPE were 2.00-, 2.41-, and 3.81-fold higher, respectively, in MK-1. Similarly, the levels of expression of the genes encoding FDPS, GGPPS, and iSPE were 3.56-, 4.4-, and 2.77-fold higher, respectively, in DK than in FB-A; 2.83-, 3.32-, and 4.92-fold higher, respectively, in DK than in FB-B; and 4.03-, 3.92-, and 5.86-fold higher, respectively, in DK than in FB-C (Table 5). Figure 5: KEGG enrichment analysis of differentially expressed genes (DEGs) in _H. coralloides_. (**A,B**) DEGs up-regulated (**left**) and down-regulated (**right**) in comparisons of MK-1 and MK-2. (**C,D**) DEGs up-regulated (**left**) and down-regulated (**right**) in comparisons of DK and FB-A. (**E,F**) DEGs up-regulated (**left**) and down-regulated (**right**) in comparisons of DK and FB-B. (**G,H**) DEGs up-regulated (**left**) and down-regulated (**right**) in comparisons of DK and FB-C. The red boxes indicate terpenoid-related synthetic pathways. Comparisons of DK with FB-A, FB-B, and FB-C comparison groups identified two, three, and three up-regulated genes, respectively, that were significantly enriched in ubiquinone and terpenoid-quinone biosynthesis (ko00130) (Figure 5, Table S6 and Table 5).