3.2 Phylogenetic analyses and evolution of gene families

To explore the phylogenetic relationship of S. tetraptera , we first performed the phylogenetic analyses with the other 11 species (Table S11). A total of 345,243 genes from the 12 species were assigned into 28,703 gene families (Figure S7,Table S12). For S. tetraptera , 25,573 genes could be clustered into 12,826 identified gene families (Table S14). A total of 485 groups of single-copy gene families were identified and used to construct the phylogenetic topology for all species. The phylogenetic positions of all species agreed well with previous studies (Figure 2a) (Chase et al., 2016; Y. Yang et al., 2020). A sister relationship betweenS. tetraptera and G. sempervirens was indicated by our results (Figure 2a). Their divergence time was dated to around 61.50 Ma (Figure 2a).
In addition, 3,555 gene families were found to expand in S. tetraptera . GO enrichment analysis revealed that these expanded gene families were significantly enriched (P<0.01, Q<0.05) in secondary metabolic processes, mainly involved in terpenoid and flavonoid biosynthesis (Figure 2b, Figure S8-9, Table S13-S16). This may contribute to the high content of Sinoswertiamatin, sweroside, gentiopicroside, and loganin in S. tetraptera , which may be relevant to the species’ use in traditional Chinese medicine (Organization, 2002; Rao et al., 2010).