*2.6. Divergence of Protein-Coding Gene Sequence*

The cp genomes of four Capparaceae species include 80 protein-coding genes in *C. glandulosa* and 81 genes in other species. To detect the genes under selective pressure, the rates of synonymous (dS) and non-synonymous (dN) substitution and dN/dS ratio were calculated. The results showed that in all of the paired genes of *C. farinosa* vs. *C. glandulosa,* the dN/dS ratio is less than 1, and most of the paired genes are less than 1 except *atpF* in *C. farinosa* vs. *M. crassifolia* and *cemA, psbK* and *rps18* in *C. farinosa* vs. *M. oblongifolia,* having values of 1.16, 1.52 and 1.2, respectively (Figure 8). The result of the dN/dS ratio obtained in this study is consistent with other related studies [52,53]. In all the genes, the synonymous (dS) values range from 0 to 0.32 (Figure 8).

**Figure 8.** The synonymous (dS) and dN/dS ratio values of 81 protein-coding genes from four Capparaceae cp genomes.

## *2.7. Phylogenetic Analysis*

Phylogenetic relationships based on Bayesian analysis and maximum parsimony were congruent and placed all samples into three main clades, with strong support in all the nodes with PP 1.00 (Figure 9). The first clade contains species of the Capparaceae family and is divided into two subclades; the first subclade includes species of genera *Cadaba* and *Maerua*, while the second clade includes species of genus *Capparis*. The second clade comprises Cleomaceae species, while the third clade includes species from the Brassicaceae family. The phylogenetic tree showed that the Capparaceae family is the earliest diverging lineage among the three families and is sister to Cleomaceae and Brassicaceae. It is clear in this phylogenetic result that Cleomaceae was separated from Capparaceae and became a sister to the Brassicaceae family, as reported by [19,20]; this is consistent with some previous classifications of the order Brassicales.

**Figure 9.** Phylogenetic tree reconstruction based on the complete chloroplast genome of 21 taxa inferred from Bayesian inference (BI) methods, showing relationships within Brassicales. Numbers in the clade represent posterior probability (PP) values.
