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).