Phylogenomics and biogeographic patterns of Scutellaria L. (Lamiaceae): Southern Asian origins and worldwide dispersal

Scutellaria L. (Lamiaceae) is a diverse and pharmacologically important genus with significant species richness in Central Asia. Here, we sequenced and analyzed complete chloroplast genomes of 14 Scutellaria species from Uzbekistan and adjacent regions, integrating them with 184 publicly available plastomes to investigate genome evolution, phylogenetic relationships, and biogeographic history. All plastomes exhibited a conserved quadripartite structure, with limited variation in genome size (151.6–152.3 kb), GC content (38.23–38.34%), and gene content. Codon usage showed a consistent bias toward A/T-ending codons. A total of 32–55 SSRs were identified per genome, with elevated variability in several Central Asian taxa, highlighting their utility as molecular markers. Nucleotide diversity analyses revealed highly variable loci, primarily in noncoding regions, suitable for DNA barcoding and phylogenetic inference. Phylogenomic reconstruction strongly supported the monophyly of Scutellaria and resolved three major evolutionary lineages. Newly sequenced taxa provided strong support for the cohesion of the Anaspis lineage, reinforcing its recognition at the subgeneric level. Ancestral area analyses indicate a southern Asian origin followed by diversification in Central and Eastern Asia and multiple dispersal events into Europe, Africa, and the Americas.