## 3 Results
### Sesquiterpene Biosynthesis Pathway  
Sesquiterpenes are important secondary metabolites of basidiomycetes, of various structural types and physiological and ecological functions. Sesquiterpene synthases (STSs) are key enzymes in the formation of the sesquiterpene backbone. STSs of different species vary in structures and catalytic mechanisms, resulting in the structural diversity of sesquiterpenes. Although many studies have described sesquiterpene compounds in basidiomycetes, few studies have described STSs in these organisms. To identify genes encoding STSs in _H. coralloides_, a homology search was _H. coralloides_ performed using STS genes (Cop1-6) from the model basidiomycetes species _Copriminus cinerea_[43]. This search identified nine _H. coralloides_ genes possibly encoding STSs (_Her003832, Her1003788, Her005338, Her002337, Her005433, Her006723, Her006724, Her010605_, and Her010608_), located on five chromosomes (Chr02, Chr04, Chr05, Chr06, and Chr12). Preliminary phylogenetic analysis showed that these genes belonged to four clades (clades I-IV), suggesting that the STSs encoded by genes in each group may produce related sesquiterpenes via conserved cyclization pathways. The nine genes encoding STSs in _H. coralloides_ belonged to three clades (clades I, II, and IV), representing three functional groups. Two of these genes, in clade I, encoded alpha-muurolene synthase (_Her002337, Her005433_), three genes in clade II encoded linoleate 10R-lipoxygenaseoxygenase (_Her1003788, Her003832, and Her005338_), and four genes in clade IV encoded trichodiene synthase (_Her006723, Her006724, Her010650_, and _Her010608_) (Figure 7, Data S1) [44; 45]. Most of the nine genes encoding STSs were down-regulated in the four comparison groups. The four genes encoding trichodiene synthase (_Her006723, Her006724, Her010650_, and _Her010608_) were significantly down-regulated in all groups, with the levels of expression of _Her006724, Her010605_, and _Her010608_ being 9.25-, 5.82-, and 3.48-fold lower, respectively, in DK than in FB-B, and 14.22-, 4.23-, and 2.60-fold lower, respectively, in DK than in FB-C.  
antiSMASH software identified eight gene clusters involved in terpenoid biosynthesis. These clusters were located on five chromosomes (Chr02, Chr04, Chr05, Chr06, and Chr07), with each cluster spanning 20 kb of the _H. coralloide_ genome (Figure 8 and Table S7). The Chr02 gene cluster included a gene (_Her002337_) encoding alpha-muurolene synthase; the Chr04-1 cluster included a gene (_Her003788_) encoding linoleate 10R-lipoxygenaseoxygenase; and the Chr04-2 gene cluster included a gene (_Her003832_) encoding linoleate 10R-lipoxygenaseoxygenase. In addition, the Chr05-1 gene cluster contained a gene (_Her005338_) encoding linoleate 10R-lipoxygenaseoxygenase; the Chr05-2 cluster contained a gene (_Her005433_) encoding alpha-muurolene synthase; the Chr06 cluster contained genes (_Her006723, Her006724_) encoding trichodiene synthase; and the Chr07-1 cluster included a gene (_Her006804_) encoding squalene synthase. Thus, most of the predicted genes were involved in sesquiterpene synthesis, and there were no genes involved in the terpenoid backbone biosynthesis pathway and diterpenoid biosynthesis pathway. Results obtained using antiSMASH software differed from those of homology searching for terpenoid synthesis gene clusters. Although antiSMASH could be used to identify specific PKS and NRPS gene clusters in ascomycetes or bacteria, this method was not suitable for identifying terpenoid gene clusters in basidiomycota. Therefore, genes related to the terpenoid backbone, diterpenoid, and sesquiterpene biosynthesis pathways were identified by homology searching, as well as by the use of antiSMASH software. Figure 8: Identification of terpenoid gene clusters by antiSMASH software. The map includes functional annotations (red) and gene names (blue). Details for the annotation of each gene cluster are shown in Table S7. Figure 7: Unrooted neighbor-joining phylogram of sesquiterpene synthases (STSs) of \(H\).