Mitogenome structural diversification accompanied by rapid repeat-family turnover: a comparative organellar perspective from Salvia

Plant mitochondrial genomes (mitogenomes) are structurally diverse, yet their evolutionary dynamics remain insufficiently understood in recently diversified angiosperm lineages. Salvia , the largest genus in Lamiaceae with approximately 1000 species across 11 subgenera, provides an ideal system for examining how organellar genomes diverge within a shallow phylogenetic framework. Here, we analyzed organellar genomes from 15 Salvia species representing 10 subgenera, focusing on mitogenome dynamics. The plastid genomes (plastomes) retained typical quadripartite structures from 150,604 bp to 151,994 bp, encoding 114 unique genes arranged in highly conserved synteny. In contrast, the mitogenomes ranged from 264,965 bp to 414,058 bp and exhibited single circular, multiple circulars, and linear representative conformations, with 31–34 protein-coding genes, 18–20 transfer RNAs, and three ribosomal RNAs. Despite high sequence similarity, Salvia mitogenomes accumulated pronounced structural heterogeneity, and rearrangement patterns were not fully congruent with sequence-based phylogeny. Phylogenetic inference from genome-wide locally collinear blocks improved support for several relationships relative to conserved mitochondrial protein-coding genes. Comparisons across Salvia , all available Lamiaceae mitogenomes, and representative seed plants showed that short repeats formed a widespread background with relatively conserved size and identity profiles. Genus-level benchmarking, however, revealed strongly lineage-dependent repeat-family turnover, ranging from conserved short-repeat families shared by all sampled congeners to predominantly species-specific repertoires. By comparison, plastid-derived insertion families in mitogenomes were more broadly retained within genera, preserving a clearer historical signal. Collectively, this study provides a shallow-scale comparative case for understanding how mitochondrial structural heterogeneity and repeat landscapes diversify during recent angiosperm lineage diversification.