Phylogenomic analysis
To construct a phylogenetic tree, we used the predicted protein files
from the S. rosmarinus genome and 23 other species
(Antirrhinum majus , Arabidopsis thaliana , Daucus
carota , Boea hygrometrica , Coffea canephora ,Amborella trichopoda , Erythranthe guttata , Sesamum
indicum , Scutellaria baicalensis , Glycine max ,Handroanthus impetiginosus , Olea europaea , Oryza
sativa , Populus trichocarpa , Beta vulgaris , Striga
asiatica , Solanum lycopersicum , Vitis vinifera , Zea
mays , Ocimum tenuiflorum , Salvia miltiorrhiza ,Salvia splendens , Tectona grandis ).. Based on 465
single-copy genes, MUSCLE was used for the sequence alignments and
matrix construction. A maximum-likelihood phylogenetic tree was then
constructed by IQtree2 (v20151210) with the ‘MFP+MERGE’ model. The
divergence time of among 24 plants was predicted using BEAST2 (v2.5.4)
(http://www.beast2.org/) with a strict molecular clock model, and
time scales were calibrated by the divergence time of the fossil record
of species from TimeTree (http://www.timetree.org). The results of
OrtherFinder, CAFÉ 5 (https://github.com/hahnlab/CAFE) (Mendes,
Vanderpool, Fulton, & Hahn, 2020) were used to analyze the expansion
and contraction of gene families. Gene families were regarded as
significantly expanded or contracted if the p-value was less than 0.05
in all species. Covariance analysis within genes were performed by jcvi
(Tang et al., 2015). A gene pair was considered to have a covariance
relationship while cscore was greater than 0.7. Homologous gene pairs
were marked with strips and target genes with colorful trips.