Comparative chloroplast genomics of Teucrium species reveals genome evolution, phylogenetic relationships, and candidate molecular markers.

The genus Teucrium (Lamiaceae) comprises approximately 250 species with significant medicinal and ecological importance. Despite extensive phytochemical studies, molecular data, particularly on chloroplast (cp.) genomes, remain limited for many species, especially those native to Iran. In this study, we sequenced and analyzed the complete cp. genomes of three Iranian Teucrium species, T. chamaedrys, T. flavum, and T. polium, to investigate genome structure, variation, and phylogenetic relationships within the genus. Using high-throughput sequencing, we assembled and annotated the cp. genomes, revealing typical quadripartite structures with sizes ranging from 149,913 bp to 150,026 bp. Comparative genomic analyses, including IR boundary shifts, codon usage, repeat elements, and nucleotide diversity, highlighted structural variations. Sequence divergence analysis using mVISTA revealed several genes, including rpoC2, ycf1, ycf2, ndhF, rpl32, rps16, and accD, displayed notable sequence variation, making them potential phylogenetic markers. Additionally, highly variable intergenic regions, such as trnH-GUG-psbA, rps16-trnQ-UUG, and petG-trnW-CCA, were identified as potential hotspots for species differentiation. Codon usage analysis revealed a strong preference for A/U-ending codons, while nucleotide diversity (Pi) analysis identified highly variable intergenic regions such as trnH-GUG-psbA and rpl32-trnL-UAG. Phylogenetic reconstruction based on cp. genome sequences placed T. chamaedrys, T. flavum, and T. polium in well-supported clades, clarifying evolutionary relationships within Teucrium. This study provides the first complete cp. genome sequences for these Iranian Teucrium species, expanding genomic resources and offering valuable insights into their genetic diversity, evolutionary history, and medicinal potential.