*3.1. Genomic Features of the P. vulgaris Mitogenome*

The complete genomic sequence of the *P. vulgaris* mitogenome was submitted to the NCBI Genome Database (https://www.ncbi.nlm.nih.gov/genome/browse/) under accession number NC\_045135.1. The mitogenome was assembled into a typical circular molecule 395,516 bp in length (Figure 2), similar to the mitochondria of some papilionoid legumes such as *G. max* (402,558 bp), *G. soja* (402,545 bp), *L. japonicus* (380,861 bp), *V. angularis* (404,466 bp), and *V. radiata* var. *radiata* (401,262 bp; Table S2). In fact, the mitogenome sizes vary considerably among the papilionoid legumes, ranging from 271,618 bp in *Medicago truncatula* to 588,000 bp in *Vicia faba*. Mitogenome sizes can vary greatly in different cultivars of the same species. For example, the mitogenome size of *G. max* Aiganhuang (N21249) is 402,558 bp, whereas that of *G. max* cultivar Zhonghuang 13 is 513,779 bp [51].

The nucleotide composition of the whole mitogenome is A: 27.37%, C: 22.40%, G: 22.71%, and T: 27.52% (Table 1). The overall GC content is 45.11%, which is consistent with other leguminous plants (*G. max*: 45.03%, *V. faba*: 45.04%, and *V. radiata* var. *radiata*: 45.11%). Strikingly, the GC content of the PCGs is very small compared to those of other regions. As shown in Table 2, a total of 49 unique genes were detected in the *P. vulgaris* mitogenome, comprising 31 PCGs, 15 tRNA genes and 3 rRNA genes. However, none of the genes encodes subunits of Complex II (succinate dehydrogenase), which has also been lost in some other leguminous plants. Additionally, two tRNA genes located in repeat sequences were found to contain two or three copies (*trnC-GCA* and *trnfM-CAU*). The total lengths of the PCGs and *cis*-spliced introns comprise 7.26% and 8.24% of the whole mitogenome, while tRNA and rRNA genes only comprise 0.34% and 1.33% of the mitogenome, respectively. Most PCGs have no introns; however, eight genes (Table 2; *nad1*, *nad2*, *nad4*, *nad5*, *nad7*, *ccmFC*, *rps3*, and *rps10*) were found to contain one or more introns. Three genes (*nad1*, *nad2*, and *nad5*) required trans-splicing to assembly fully-translatable mRNA (Figure 2).

**Figure 2.** Circular map of the *P. vulgaris* mitogenome. Genes shown on the outside of the circle are transcribed clockwise, whereas genes on the inside are transcribed counterclockwise. GC content is represented on the inner circle by the dark gray plot. The asterisks besides genes denote intron-containing genes.

**Table 1.** Genomic features of *P. vulgaris* mitogenome.


<sup>a</sup> Protein-coding genes, *cis*-spliced introns, tRNAs, and rRNAs belong to coding regions.


\* The asterisks besides genes denotes intron-containing genes.
