Comparative plastid genomics reveals phylogenetic relationships and candidate molecular markers in Salvia

Abstract

Introduction Salvia is the largest genus in Lamiaceae and includes numerous medicinal, ornamental, and aromatic species. Species identification and rational resource utilization in this genus remain difficult because morphological characters are variable, infrageneric boundaries are sometimes ambiguous, and broad comparative genomic resources are still limited. In addition, plastid RNA editing has rarely been characterized in Salvia. Methods We assembled six new plastid genomes, compared complete plastid genomes representing major lineages of Salvia, and characterized plastid RNA editing in Salvia officinalis. Results The Salvia plastid genomes were highly conserved in organization and ranged from 150,604 to 151,994 bp, with 132–134 annotated gene features and GC contents of 37.95%–38.11%. Codon usage showed a clear A/U-ending preference, with AGA being the most strongly preferred codon. A total of 623 SSRs were detected across these plastomes, with 24–45 loci per species; most were A/T-rich mononucleotide repeats and were concentrated in the LSC and intergenic regions. REPuter identified 30–50 nontandem repeats per plastome, and forward and palindromic repeats occurred at comparable frequencies. 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. Discussion 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.