Characterization and Comparative Analysis of the Complete Mitochondrial Genome of a Limestone-Endemic Endangered Plant Species Hemiboea yongfuensis (Gesneriaceae)

<b>Background</b>: <i>Hemiboea yongfuensis</i> is a recently discovered critically endangered species. It is exclusive to the limestone regions of Yongfu County, Guilin, Guangxi. Currently, there is a lack of mitogenome data for <i>Hemiboea</i> species, hindering the potential of disclosing the evolutionary processes of the mitochondrial genome, which has been far less assembled and shown to be complex in the plant kingdom. Moreover, it prevents potential applications of mitochondrial genome data in phylogenetics and plant adaption, breeding, and conservation. <b>Results</b>: In order to reveal the mitochondrial features and variations and explore the usefulness of mitochondrial genes in phylogenetics, in this study, we assembled the complete mitogenome of <i>H. yongfuensis</i> using PacBio HiFi long reads, and analyzed its codon usage bias, RNA editing sites, repetitive sequences, sequence lateral transfer, phylogenetic relationships, and synteny. The linear mitochondrial genome assembly we obtained has a length of 619,997 bp and a GC content of 43.63%. The assembly encompasses 61 genes, which include 37 protein-coding genes (PCGs), 21 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Importantly, our analysis uncovered a significant presence of repetitive sequences with a high proportion of forward repeats in the mitogenome and significant transposition of sequences from the chloroplast to mitochondrion. Additionally, we revealed the codon usage characteristics of protein-coding genes and identified numerous RNA editing events. Furthermore, we assessed the collinearity of the species in the Gesneriaceae family and found rampant reorganizations. The phylogenetic analyses based on the mitochondrial PCGs for the entire Lamiales order show the monophyly of Gesneriaceae as well as other families and a general high phylogenetic resolution. <b>Conclusions</b>: Our study provides the first mitogenome data for <i>H. yongfuensis</i> and the genus <i>Hemiboea</i>, expanding the rapidly increasing but yet limited plant mitogenome resources. It enhances our understanding of the mitogenome and Lamiales evolution, whereas more potentials of the mitogenome data, such as its possible functions in adaptation to limestone habitats, conservation, and germplasm breeding, remain under-exploited. This first reported <i>Hemiboea</i> mitogenome in addition to more mitogenomes from the same and related species would shed further light on these unresolved issues in future studies.