*2.3. Selective Pressure Analysis*

To reflect the selective pressure of PCGs, we calculated the nonsynonymous (Ka) and synonymous (Ks) substitution rates of each PCG between *P. vulgaris* and other higher plants. *Arabidopsis thaliana* (*A. thaliana*; Brassicaceae) is a popular model organism in plant biology and genetics. *Citrullus lanatus* (*C. lanatus*; Cucurbitaceae) and *Vitis vinifera* (*V. vinifera*; Vitaceae) are highly cultivated fruits worldwide and belong to the Rosids clade, like leguminous plants. Therefore, we selected the mitogenomes of *A. thaliana*, *V. vinifera*, and *C. lanatus* as references to infer the direction and magnitude of natural selection acting on PCGs during the evolution of *P. vulgaris*. The orthologous gene pairs from *P. vulgaris*, *A. thaliana*, *V. vinifera*, and *C. lanatus* were aligned and formatted by ParaAT2.0 with default parameters [43]. The Ka, Ks, and Ka/Ks values were calculated using KaKs\_Calculator v.2.0 based on the YN method, and Fisher's exact test was performed to justify the validity of the Ka and Ks values [44,45].

**Figure 1.** The master genome and two isomeric genomes observed from *P. vulgaris* mitogenome mediated by two pairs of large repeats (Contig15 and Contig40). The mt contigs were generated and selected from Newbler assembly software. MC and ISO mean the master and isomeric conformations, respectively. Arrows denote the sequence orientation of assembled contigs.
