The phylogenetic position of S. rosmarinus.
We performed a comparative analysis of our assembly with 23 other
genomes from twelve Lamiales (Olea europaea , Boea
hygrometrica , Antirrhinum majus , Sesamum indicum ,Handroanthus impetiginosus , Striga asiatica ,Erythranthe guttata , Tectona grandis , Scutellaria
baicalensis , Ocimum tenuiflorum , Salvia miltiorrhiza ,S. splendens ), eight other eudicots (Vitis vinifera ,Glycine max , Populus trichocarpa , Arabidopsis
thaliana , Beta vulgaris , Daucus carota , Solanum
lycopersicum ), two monocots (Zea mays , Oryza sativa ), andAmborella trichopoda , which represents a species at the base of
the angiosperm as a sister group to all other flowering plants (Table
S10). We identified 38,709 gene families (consisting of 813,356 genes)
by analyzing gene family clustering. Of these, 1,658 were specific toS. rosmarinus , while 5,256 were shared by all species, including
456 single-copy gene families (Figure S5, Table S18).
Compared to congenra S. miltiorrhiza and S. splendens ,S. rosmarinus displayed 5,695 expanded genes and 931 contracted
genes, consistent with the previous findings (Bornowski et al., 2020).
The majority of the expanded gene families in S. rosmarinus were
associated with secondary metabolites, with a significant enrichment in
”Biosynthesis of other secondary metabolites”, involving 123 genes
(Figure S11, Table S19). KEGG analysis also revealed erichment in
pathways related to terpenoid metabolites, such as “Terpenoid backbone
biosynthesis” and “Diterpene biosynthesis” (Table S19). Secondary
metabolism-related genes, particularly those related to terpene
metabolism, underwent significant expansion in S. rosmarinus ,
which likely contributed to the abundance of terpenoids in S.
rosmarinus plants.
We retrieved 465 single-copy orthologous genes from 24 species,
multi-aligned them, and produced a super-alignment matrix, which was
used to construct a dated phylogeny. The topology and time frame in the
tree were consistent with previously reported phylogenomic analysis in
angiosperms. The divergence of and within Lamiaceae (S.
rosmarinus , S. miltiorrhiza , S. splendens ,Scutellaria baicalensis , Ocimum tenuiflorum andTectona grandis ) were estimated to be around 59.16 Mya and 52.10
Mya, respectively. The origin time of Salvia rosmarinus was
estimated to be around 21.47 million years ago (Mya), with a separation
into a S. miltiorrhiza and S. splendens clade (Figure 2a).