Abstract
Previously, we resolved the complete sequences of the mitochondrial genomes (mitogenome) of two Salvia species (S. miltiorrhiza and S. officinalis). The major configurations of these two species were two circular chromosomes. In this study, we further studied the mitogenome of a floral species of Salvia (Salvia splendens) to understand the diversity and evolution of the Salvia mitogenomes. We sequenced the total DNAs of S. splendens using the Nanopore and Illumina platforms and assembled the mitogenome using a hybrid assembly strategy. The major configurations of the S. splendens were two circular chromosomes with lengths of 182,239 and 165,055 bp. There were 32 protein-coding genes (PCGs), three rRNA genes, and 18 tRNA genes annotated in the S. splendens mitogenome. We found 56 pairs of repetitive sequences in the S. splendens mitogenome. Three of them (R01, 04, and 07) could mediate recombination, whose products could be identified by the mapping of Nanopore reads, PCR amplifications, and Sanger sequencing of the PCR products. 457 RNA editing sites were identified in the S. splendens mitochondrial RNAs when comparing the RNA-seq data with their corresponding DNA templates. We showed that S. splendens was a sister taxon to S. miltiorrhiza based on the mitogenomes, consistent with the phylogeny determined with the plastome sequences. Crucially, we developed 12 mitochondrial markers sourced from mitochondrial intron regions to facilitate the identification of three Salvia species. Our study offers a comprehensive view of the structure of the Salvia mitogenomes and provides robust mitochondrial markers for Salvia species identification.