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).