Characterization of the complete mitochondrial genome of the rice bean (Vigna umbellata)

Background: Rice bean (Vigna umbellata), an underrated legume crop, demonstrates strong adaptability to poor soil fertility and has significant potential to enhance global food security. It is valuable both as a vegetable and fodder crop due to its high protein content, essential fatty acids, and micronutrients. Despite the sequencing of a high-quality genome of rice bean, its mitochondrial genome (mitogenome) sequence has not yet been reported.

Results: For the first time, the rice bean mitogenome was assembled and annotated using PacBio HiFi sequencing and Geseq software. The mitogenome is a circular molecule with a length of 404,493 bp, containing 32 protein-coding genes, 17 tRNAs, and 3 rRNAs. Codon usage and sequence repeats were also determined. Six gene migration events from the chloroplast to the mitogenome were detected in rice bean. A phylogenetic analysis, including the rice bean mitogenome and 25 other taxa (23 of which are Fabales species), clarified the evolutionary and taxonomic status of rice bean. Additionally, a collinearity analysis of seven Fabales mitogenomes revealed high structural variability. In total, 473 RNA editing sites in protein-coding genes were identified.

Conclusions: This study presents the first sequencing, assembly, annotation, and analysis of the rice bean mitogenome, providing valuable background information for understanding the evolution of this species. These findings lay the groundwork for future genetic studies and molecular breeding efforts aimed at improving rice bean.