Nucleotide diversityin CentralAsian Salvia L.: high variability regions as candidate markers

Accurate species identification and reliable reconstruction of phylogenetic relationships in many plant groups remain challenging because they are often characterized by rapid evolutionary radiations, pronounced geographic structuring, and an uneven distribution of informative plastid variation across the chloroplast genome. In this context, plastome-scale analyses provide an efficient route to identify lineage informative regions that outperform traditional single-locus markers for closely related taxa. Here we profile chloroplast nucleotide diversity (Pi) in Salvia to quantify how variation is partitioned along the chloroplast genome and to define a practical framework for marker selection targeted to Central Asian endemic lineages. Complete chloroplast genomes were aligned and analyzed using a sliding-window approach to quantify Pi across protein-coding genes (CDS) and intergenic spacers (IGS). The results show that nucleotide diversity is concentrated predominantly in non-coding regions, especially intergenic spacers, whereas most protein-coding genes remain comparatively conserved, consistent with functional constraints on plastid gene evolution. High-Pi peaks occur predominantly in non-coding spacers and SSC associated segments, indicating that marker performance can be substantially improved by prioritizing a small panel of hotspot loci rather than relying on widely used but low-variation regions. As the most informative and consistently high-variability candidate markers for Salvia, we identified the intergenic regions ccsA--ndhD, trnG-GCC--trnfM-CAU, trnW-CCA--trnP-UGG, trnH-GUG--psbA, atpI--rps2, rpl32--trnL UAG as well as the protein-coding loci ycf1, matK, rpl16, rpl22, ndhF. Taken together, these findings indicate that plastome nucleotide-diversity profiling offers a robust, data-driven basis for primer development, DNA barcoding, and improved phylogenetic inference in Salvia, supporting future taxonomic and biogeographic studies of Central Asian diversity.

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