Pan-plastome analysis reveals conserved plastome organization, abundant intraspecific variation, and complex population structure in Salvia miltiorrhiza

Salvia miltiorrhiza Bunge (Danshen) is an economically important medicinal plant whose wild genetic resources are increasingly threatened by overharvesting and habitat degradation. Despite well-established genomic resources, the genetic variation in wild populations remains largely unexplored. To uncover plastome-level variation and maternal population structure, we generated the first pan-plastome across Lamiaceae using 70 individuals from 14 wild populations covering the core natural distribution of S. miltiorrhiza in China. The plastomes were highly conserved in structure and gene content, ranging from 151,299 to 152,296 bp and containing 114 unique genes. We identified 3095 simple sequence repeats, 1247 nucleotide variants, 35 haplotypes, and ten hypervariable regions, providing potential resources for germplasm identification and molecular marker development. Genetic variation was predominantly partitioned among populations, whereas province-level grouping explained only a limited component of the observed structure. A significant phylogeographic signal indicated a non-random geographic distribution of related haplotypes. However, genetic differentiation was not significantly correlated with geographic distance, and phylogenetic reconstruction and genetic clustering did not recover a consistent grouping pattern corresponding to provincial boundaries. Our findings confirm extensive plastomic variation and strong population subdivision in S. miltiorrhiza , whose maternal genetic spatial heterogeneity cannot be interpreted by administrative provinces or geographic isolation. This study expands the plastomic resources available for this important medicinal species and highlights the need for genome-wide nuclear data to further resolve its evolutionary history.