Table 1_Comparative plastid genomics reveals phylogenetic relationships and candidate molecular markers in Salvia.xlsx

These compositional features are consistent with previous reports for Salvia and provide the descriptive baseline for the analyses that follow. Comparative analyses indicated that IR regions were more conserved than single-copy regions, whereas several highly variable loci were promising candidates for marker development; the most divergent region was not the most discriminating, and ycf1 separated 99.8% of the 4,753 Salvia species pairs against 97.6% for rbcL.

Phylogenomic reconstruction based on 98 Salvia plastomes, performed after removing one inverted-repeat copy from every genome and trimming ambiguously aligned columns, recovered three major clades broadly consistent with current subgeneric classification, and the same three clades were recovered from a partitioned supermatrix of 50 protein-coding genes. In S. officinalis, 21 plastid RNA editing sites were identified in 10 protein-coding genes; 20 sites were nonsynonymous, and the second codon position was most frequently edited (17 of 21 sites).

Seven nonsynonymous sites were confirmed by Sanger sequencing of genomic DNA and cDNA amplicons, all reported on the coding strand.</p>Discussion<p>The plastid genomes of Salvia are structurally conservative but contain sufficient localized variation for marker development and species discrimination. The expanded plastome phylogeny improves resolution of major evolutionary lineages within the genus, and the RNA editing analysis adds a functional layer to plastid genome evolution in Salvia.

Together, these results provide practical genomic resources for taxonomy, germplasm authentication, phylogenetic inference, and the sustainable utilization of Salvia resources.</p>