Characterize the Complete Mitogenome of <i>Semiaquilegia guangxiensis</i> and Assess the Efficiency of the Mitochondrial Genes in Ranunculales Phylogeny

Plant mitochondrial genome (mitogenome) has crucial functions underpinning survive, development, and reproduction of organisms. However, the complete mitogenomes have been far less assembled and annotated than plastomes and even nuclear genomes in plants, due to their highly frequent and long repeat sequences and genomic structural variations. These further hinder the understanding of the mitogenome evolution and restrict potential applications in phylogenetic analyses. In this study, we sequenced, assembled, and annotated the complete mitogenome of <i>Semiaquilegia guangxiensis</i> and explored its evolution and usefulness in phylogenetics. The results showed that the mitogenome was composed of two independent molecules, which had a total length of 522,981 bp, a GC content of 45.69%, and 58 genes including 34 protein-coding genes (PCGs), 21 tRNA genes, and three rRNA genes. A generalized codon usage preference was observed among the mitochondrial PCGs, and a total of 665 potential RNA editing sites were identified across the 34 mitochondrial PCGs, all of which were base C-to-U edits. Moreover, a large number of repetitive mitogenome sequences and chloroplast-sourced sequences transferred to the mitogenome were detected. The largest collinear block identified between <i>S. guangxiensis</i> and <i>Paropyrum anemonoides</i> was 4282 bp in length. The phylogenetic analyses based on the mitochondrial gene sequences resolved the phylogenetic relationships within Ranunculales, in which <i>Semiaquilegia</i> was close to <i>Paropyrum</i>. The 19 PCGs were ranked according to their efficiencies on phylogenetic resolution based on several metrics, and the combined metric suggested <i>mat</i>R, <i>rps</i>3, and <i>nad</i>5 were the top three loci contributing most to phylogeny. As the first reported mitogenome in <i>Semiaquilegia</i>, our findings enrich the limited mitogenome library of plants, reecho the complex evolutionary dynamics of the mitogenome, and highlight the usefulness of mitochondrial gene sequences in phylogenetics.