3.3 Whole-genome duplication (WGD)

We obtained synonymous substitution per site (Ks ) distributions for each species based on the identified syntenic paralogues. Three rounds of WGD events were detected in S. tetraptera, different from the other previously reported Gentianales species (C. canephora, G. sempervirens , and C. gigantea ), which all had only one WGD event (Figure 2c, Figure S10, Table S17-18). For all WGD events in S. tetraptera , the most ancient one (around 121-136 Ma) was shared by all species used in our study (three Gentianales species and V. vinifera ), indicating the joint γ event shared by all core eudicots, as inferred in previous reports. The other two recent WGD events were species-specific in S. tetraptera and dated to 41-46 Ma and 67-75 Ma, respectively, the latter of which occurred shortly after the divergence between S. tetraptera and G. sempervirens (61.50Ma) (Figure 2c).
To further illustrate the WGD events in S. tetraptera , we undertook a collinearity analysis between V. vinifera andS. tetraptera . Based on the dot plots of paralogues, the observed syntenic depth ratios of 12:3 in the S. tetraptera - V. vinifera comparison indicated the occurrence of the joint γ event and two unique recent WGD events inS. tetraptera (Figure 2d). The same results were also revealed from the comparisons of S. tetraptera - C. canephora ,S. tetraptera - G. jasminoides , S. tetraptera -G. sempervirens , and S. tetraptera - C. gigantea , respectively (Figures S11-17). In addition, we identified a total of 2,269 genes that strictly originated from the most recent WGD event. We therefore examined their differentiated expressions between the two types of flowers, and found that more than 10% of these genes did exhibit contrasting expressions. They were functionally enriched in heterochronic development and growth, which may contribute to the development of the innovative dimorphic flowers in S. tetraptera(Figure 2b, Figure S18 and S19, Table S19-22).