Whole genome duplication in S. romarinus.
According to both genomic covariance and paralogous homologous gene analysis, evidence supports the occurrence of ancient genome-wide duplication (WGD) events in S. rosmarinus . In particular, the identification of 125,489 homologous gene pairs in S. rosmarinus(Table S20) and the observation of two peaks in the distribution of substitutions per synonymous site (Ks ), with Ks values of approximately 0.19 (WGD-2) and 0.94 (WGD-1) (Figure 2b, Figure S12) provides strong evidence for WGD events. However, there is a whole-genome triplication occurred with Ks peaks at 1.92 (WGT-γ) (Figure S12), which is not obvious with Ks ditribution for long time ago. Additionally, homology analysis showed that WGD-2 occurred after the divergence of S. rosmarinus , S. miltiorrhiza and S. splendens , as evidenced by the identificaiton of 17,521 orthologous gene pairs between S. rosmarinus and S. miltiorrhiza , and 16,664 orthologous gene pairs between S. rosmarinus and S. splendens , with Ks values peaking at approximately 0.20 and 0.28, respectively (Figure 2a, Table S20). Furthermore, paralogous gene analysis identified 67,287, and 26,794 paralogous gene paris in S. miltiorrhiza and S. splendens respectively, with Ksvalues distributions that peaked at approximately 0.98 and 1.24, respectively (Figure 2b, Table S20). Based on the phylogenetic analysis, WGD-1 occurred prior to the divergence of S. rosmarinusS. miltiorrhiza and S. splendens and was estimated to have occurred between 70.87 and 101.37 Mya, which is consistent with the findings of the Scutellaria baicalensis genome study (Z. Xu et al., 2020). Whole-genome triplication (WGT-γ) had been reported shared in core eudicots, WGT-γoccurred at about 144.87-207.32 Mya according to the Ks distribution, close to the previous report(Murat, Armero, Pont, Klopp, & Salse, 2017).
The Ks distribution value of S. rosmarinus , which was found to be 0.18, indicated the occurrence of a whole genome duplication event (WGD-2) after the speciation of S. rosmarinus , approximately 8.80 Mya (Table S20). The genome syntenic analysis revealed that S. rosmarinus had four copies of syntenic blocks corresponding toVitis vinifera blocks (Figure S10 b). This suggests that the entire genome of S. rosmarinus was duplicated twice during evolution, corresponding to WGD-1 and WGD-2 respectively. In addition, two copies of syntenic blocks from S. rosmarinus correspondingS. miltiorrhiza blocks were also found, indicating that the most recent genome-wide duplication of the S. rosmarinus genome occurred after the divergence of S. rosmarinus and S. miltiorrhiza (Figure S8). Therefore, WGD-1 was shared by S. rosmarinus , S. miltiorrhiza and S. splendens , while WGD-2 was unique to S. rosmarinus .