The complete chloroplast genome of Salvia nubicola provides new insights into genome evolution and phylogenetic relationships within Lamiaceae

Salvia nubicola is a medicinal plant traditionally used to treat various life-threatening diseases. A high-quality draft genome (~ 417 Mb) assembly of Salvia nubicola was constructed using Illumina NextSeq500 paired-end sequencing. The chloroplast (cp.) genome of S. nubicola , assembled via reference-guided mapping, spans 153,424 bp and features the typical quadripartite structure: inverted repeats (IRa and IRb; 25,562 bp each), large single-copy (LSC; 84,674 bp), and small single-copy (SSC; 17,626 bp) regions. Genome annotation revealed 107 protein-coding genes, 43 tRNAs, and 10 rRNAs. Maximum likelihood phylogeny placed S. nubicola among Old World S. species, closely related to S. glutinosa and S. chanryoenica , consistent with its geographic origin. The overall tree topology reflects clear continental clustering within the Lamiaceae . Salvia nubicola exhibited a 42 bp extension of rps19 into IRb, representing an IR/LSC junction configuration within the 24–46 bp range observed among the compared Salvia plastomes. The time-calibrated analysis of 39 Salvia species and the outgroup Stachys byzantina using five conserved chloroplast markers ( matK , ndhF , atpH , rbcL and ycf3 ) estimated the root of the sampled Salvia ingroup at approximately 40 Ma; this root predates the younger internal node assigned the 5–23 Ma secondary calibration. This study provides a valuable genomic framework for phylogenetic, evolutionary, and functional investigations in S. nubicola and related species.