**4. Conclusions**

In this study, we first assembled and characterized the complete mitogenome of *P. vulgaris*. By aligning the PacBio sequencing reads to the draft mitogenome, one master circle and two isomeric molecules were assembled based on two large repeats. Selective-pressure analysis of PCGs indicates that *ccmB*, *ccmFC*, *rps1*, *rps10*, and *rps14* genes with Ka/Ks ratios > 1 might play important roles during evolution, whereas all Complex I–V genes with Ka/Ks ratios < 1 were highly conserved in the evolutionary process of higher plants. The C-to-U conversions may generate initiation, termination, or internal codons with completely unpredictable functions. The prediction of RNA editing sites in *P. vulgaris* mt PCGs will provide important clues for the investigation of gene functions with novel codons. The comparison of genomic features in all sequenced leguminous plants should contribute to a comprehensive understanding of the evolutionary process of legumes. The sequencing of the *P. vulgaris* mitogenome not only provides an important opportunity to conduct further genomic breeding studies in the common bean, it also provides valuable information for future evolutionary and molecular studies of leguminous plants.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/1422-0067/21/11/3778/s1, Figure S1: The flowchart of *P. vulgaris* mitogenome assembly and annotation, Table S1: PacBio reads of spanning repetitive contigs, Table S2: The abbreviations and genome sizes of studied mitogenomes, Table S3: The relative synonymous codon usage (RSCU) of mitogenome genome across seven higher plants, Table S4: Comparison of dispersed repeats within six mitogenomes of Papilionaceae subfamily.

**Author Contributions:** Conceptualization, C.H.; Formal analysis, C.B. and N.L.; Funding acquisition, Z.L.; Methodology, C.B.; Project administration, Z.L.; C.B., N.L., and Y.X.; Writing—original draft, C.B.; Writing—review and editing, C.H. and Z.L. All authors have read and agreed to the published version of the manuscript.

**Funding:** This work was funded by the National Science and Technology Major Project of China (6307030004) and Jiangsu Basic Research Program (Natural Science Foundation) Project (no. BK20191393).

**Conflicts of Interest:** The authors declare no conflict of interest.
