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

Salvia (Lamiaceae) is the largest genus in its family, comprising nearly 1,000 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. In this study, we assembled and analyzed the complete chloroplast genomes of 18 Salvia species representing major subgeneric lineages, and systematically characterized RNA editing sites in the chloroplast genome of Salvia miltiorrhiza f. alba using RNA-seq data. The chloroplast genome sizes of the 18 species ranged from 151,039 to 151,727 bp and exhibited a typical quadripartite structure, encoding 131-132 genes, including 87 protein-coding genes, 36-37 tRNA genes, and 8 rRNA genes. A total of 25-41 simple sequence repeats (SSRs) and 26-50 long repeats were identified across these chloroplast genomes. Comparative genomic analyses revealed highly conserved gene content and structure, 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. Maximum likelihood phylogenetic analysis based on 83 complete chloroplast genomes robustly resolved the relationships within Salvia, strongly supporting current subgeneric classifications and clarifying previously unresolved taxonomic issues among closely related subgenera. Furthermore, we identified 26 RNA editing sites 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.