Comparative Analysis of the Complete Chloroplast Genomes of Eight <i>Salvia</i> Medicinal Species: Insights into the Deep Phylogeny of <i>Salvia</i> in East Asia

<i>Salvia</i>, a medicinally and economically important genus, is widely used in traditional medicine, agriculture, and horticulture. This study compares the chloroplast genomes of eight East Asian <i>Salvia</i> species to assess genetic diversity, structural features, and evolutionary relationships. Complete chloroplast genomes were sequenced, annotated, and analyzed for gene content, codon usage, and repetitive sequences. Phylogenetic relationships were reconstructed using Maximum Likelihood, Maximum Parsimony and Bayesian inference. The genomes exhibited a conserved quadripartite structure (151,081–152,678 bp, GC content 37.9–38.1%), containing 114 unique genes with consistent arrangement. Codon usage favored A/T endings, with leucine (Leu) most frequent and cysteine (Cys) least. We identified 281 long sequence repeats (LSRs) and 345 simple sequence repeats (SSRs), mostly in non-coding regions. Comparative analysis revealed five hypervariable regions (<i>trnH</i>-<i>psbA</i>, <i>rbcL</i>-<i>accD</i>, <i>petA</i>-<i>psbJ</i>, <i>rpl32</i>-<i>trnL</i>, <i>ycf1</i>) as potential molecular markers. Phylogenetic analysis confirmed the monophyly of East Asian <i>Salvia</i>, dividing them into five clades, with Sect. <i>Sonchifoliae</i> basal. While G1, G3, and G8 were monophyletic, G5 and G6 were paraphyletic, and the G7-G8 relationship challenged traditional classifications. The genomic evidence provides crucial insights for resolving long-standing taxonomic uncertainties and refining the classification system of <i>Salvia</i>. These findings suggest a complex evolutionary history involving hybridization and incomplete lineage sorting, providing valuable genomic insights for <i>Salvia</i> phylogeny, taxonomy, and conservation.