Mitochondrial Genome of the Korean Endemic Arabis takesimana (Brassicaceae): Addition to the Genomic Resources and Evolutionary Insights

Brassicaceae is a major model system for studies of plant evolution, systematics, comparative genomics, and speciation; however, mitochondrial genomic resources remain limited compared to plastid genomic resources, constraining investigations of mitochondrial genome evolution. Here, we report the mitogenome of the Korean endemic species Arabis takesimana, representing only the third available mitogenome for the genus Arabis. The mitogenome is 291,633 bp in length with a GC content of 45.3%. It was assembled with an average sequencing depth of 298.9×. It contains 58 annotated genes, including 34 protein-coding genes, three rRNA genes, and 21 tRNA genes. A 5.15 kb mitochondrial plastid DNA insertion (MIPT) region contributes four intact plastid-derived tRNA genes (trnA, trnL-CAA, trnS-GGA, and trnN-GUU) and a partial rrn18 gene. The mitogenome also contains 21.83 kb of transposable element (TE) sequences and 44.03 kb of repetitive DNA, representing 7.48% and 15.09% of the genome, respectively. Comparative analysis of 32 Brassicaceae mitogenomes revealed 30 conserved mitochondrial protein-coding genes shared across the sampled taxa, whereas rpl2, rpl10, rps1, rps10, rps13, rps14, rps19, sdh3, and sdh4 exhibited lineage-specific patterns of truncation, pseudogenization, or loss. Linear regression revealed a strong positive association between mitogenome size and TE content (R2 = 0.7245), whereas MIPT content (R2 = 0.09146) and repetitive DNA (R2 = 0.1896) showed weaker associations with mitogenome size. Nucleotide diversity analyses identified highly variable mitochondrial loci with potential as molecular markers. Phylogenetic analyses based on conserved mitochondrial protein-coding genes resolved sampled Brassicaceae species with strong support and established the phylogenetic placement of A. takesimana, highlighting the utility of mitogenomic data for evolutionary, phylogenetic, and comparative genomic studies within the family.