**Changwei Bi 1, Na Lu 1, Yiqing Xu 2, Chunpeng He 1,\* and Zuhong Lu 1,\***


Received: 6 May 2020; Accepted: 25 May 2020; Published: 27 May 2020

**Abstract:** The common bean (*Phaseolus vulgaris*) is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of *P. vulgaris*, its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Among the 31 PCGs, four genes (*mttB*, *nad1*, *nad4L*, and *rps10*) use ACG as initiation codons, which are altered to standard initiation codons by RNA editing. In addition, the termination codon CGA in the *ccmFC* gene is converted to UGA. Selective pressure analysis indicates that the *ccmB*, *ccmFC*, *rps1*, *rps10*, and *rps14* genes were under evolutionary positive selection. The proportions of five amino acids (Phe, Leu, Pro, Arg, and Ser) in the whole amino acid profile of the proteins in each mitogenome can be used to distinguish angiosperms from gymnosperms. Phylogenetic analyses show that *P. vulgaris* is evolutionarily closer to the Glycininae than other leguminous plants. The results of the present study not only provide an important opportunity to conduct further genomic breeding studies in the common bean, they also provide valuable information for future evolutionary and molecular studies of leguminous plants.

**Keywords:** common bean; *Phaseolus vulgaris*; mitochondrial genome; comparative genomics; phylogeny
