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.
Highlights
Mitochondria are semi-autonomous organelles that are part of almost all eukaryotic cells
In order to accurately infer the phylogenetic relationships of P. vulgaris within the Fabaceae family, maximum likelihood (ML) analysis was performed based on the conserved mitochondrial protein-coding genes (PCGs) of 23 higher plants
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)
Summary
Mitochondria (mt) are semi-autonomous organelles that are part of almost all eukaryotic cells (cells with clearly defined nuclei). Mitochondria are specific to each plant and have complex genome structures [3,4,5], variable genome sizes [6,7], numerous repetitive sequences [8,9], multiple RNA editing modifications [10,11], and frequent gene gains or losses during evolution [9,12,13]. The Fabaceae, commonly known as legumes, is an economically and ecologically important family of flowering plants ranging from small annual herbs to giant trees, most of which are herbaceous perennials This family is the third-largest angiosperm family after the Asteraceae and Orchidaceae [27,28], consisting of about 770 genera and more than 20,000 species. Mitochondrial biogenesis is very important in plant breeding and knowledge of the complete mitogenome provides an opportunity to conduct further important genomic breeding studies in the common bean
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