Ancient WGD event prediction
To identify the ancient replication events of S. rosmarinus , WGD
analysis was performed with the predicted proteins file from its genome.
We used wgd (v1.0.1) (https://github.com/arzwa/wgd) (Zwaenepoel &
Van de Peer, 2019) and MCScanX (Wang et al., 2012) to detect genome-wide
replication events in the species by calculating the synonymous
substitution rate (Ks ). On the basis of the most representative
transcripts identified using the script of CAFÉ 5
(‘cafetutorial_longest_iso.py’)
(https://github.com/hahnlab/CAFE) (Mendes et al., 2020), sequence
alignments and analysis of all gene clustering were performed by wgd. We
then calculated the Ks distribution and plotted this using R
(v4.0.1) (https://www.r-project.org/). And we calculated and
compared the Ks distribution on the internal collinearity of gene pairs
of S. rosmarinus and the Ks distribution based on the orthologous
gene pairs between S. rosmarinus and S. miltiorrhiza andS. splendens . According to the normal distribution peaks in the
distribution, putative whole-genome duplication events could be
identified within species.