Comparative chloroplast genomics and RNA editing of Salvia: Implications for species identification and resource utilization

Salvia (Lamiaceae) is the largest genus in its family, includes nearly 1000 species that possess substantial medicinal, ecological, and economic value. However, effective species identification, phylogenetic resolution, and resource utilization in Salvia have been severely hindered by high morphological variability, ambiguous taxonomic boundaries, and insufficient genomic resources. This study assembled and analyzed the chloroplast genomes of 18 Salvia species representing major subgeneric lineages and systematically characterized RNA editing events in the chloroplast genome of Salvia miltiorrhiza f. alba using RNA-seq data. Among the 18 Salvia species, chloroplast genome length varied from 151,039 to 151,727 bp. Each genome contained 131 or 132 annotated genes, including 87 protein-coding genes, 36–37 tRNA genes, and eight rRNA genes. Across these chloroplast genomes, 25–41 simple sequence repeats (SSRs) and 26–50 long repeat elements were detected. Comparative genomic analyses revealed highly conserved structure and gene content, although slight variations existed at inverted repeat (IR) and single-copy region boundaries. Sequence divergence analysis indicated that nucleotide variability was significantly higher in single-copy regions compared to IR regions, identifying several mutation hotspots suitable for molecular marker development. Phylogenetic trees inferred by the maximum-likelihood method from 85 whole chloroplast genomes offered robust resolution of relationships among Salvia species, strongly supporting current subgeneric classifications and clarifying previously unresolved taxonomic issues among closely related subgenera. Furthermore, 26 RNA editing sites were identified in the chloroplast genome of S. miltiorrhiza f. alba , mainly causing nonsynonymous changes in genes related to photosynthesis, energy production, and gene expression, potentially affecting stress adaptation and secondary metabolism. These findings provide comprehensive chloroplast genomic resources and molecular tools for the accurate identification, phylogenetic resolution, and sustainable utilization of Salvia species, while shedding new light on evolutionary dynamics and the functional complexity of RNA editing in this economically important genus. • Complete chloroplast genomes of 18 Salvia species were assembled and compared. • Highly variable regions and SSRs were identified as potential molecular markers. • Plastome-based phylogeny clarified relationships among major Salvia subgenera. • RNA editing sites were systematically detected in S. miltiorrhiza f. alba. • Results provide genomic tools for Salvia species authentication and conservation.