Complete Chloroplast genome of Mentha aquatica reveals hypervariable regions and resolves phylogenetic position within the genus Mentha.

BACKGROUND: The genus Mentha (Lamiaceae) encompasses economically and medicinally important aromatic herbs, yet its taxonomy remains complex due to frequent hybridization, polyploidy, and morphological plasticity. Chloroplast (cp.) genomes emerged as powerful tools for resolving phylogenetic relationships, but no complete cp. genome of Mentha aquatica from Iran has been available. METHODS AND RESULTS: In this study, we sequenced and assembled the first complete cp. genome of M. aquatica from Iran using Illumina sequencing. The resulting circular genome measured 152,077 bp and exhibited a typical quadripartite structure, consisting of a large single-copy region (83,212 bp), a small single-copy region (17,665 bp), and two inverted repeats (25,600 bp each). Annotation revealed 132 functional genes, including 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Comparative analyses with other Mentha species showed conserved gene content but detected structural variations at IR-LSC/SSC boundaries, particularly in the positioning of rps19 and trnN. Nucleotide diversity (Pi) analysis identified hypervariable regions, with ycf1 and *rpl2-trnH* displaying the highest polymorphism, suggesting their potential as DNA barcodes. Phylogenetic reconstruction based on complete cp. genomes placed M. aquatica in a strongly supported clade with M. canadensis, indicating recent divergence, while the broader Mentha lineage formed a monophyletic group distinct from related genera. The ycf1 locus demonstrated high discriminatory power, generating phylogenies consistent with whole-genome analyses, whereas rpl14 provided limited resolution. CONCLUSIONS: This study established a foundational genomic resource for M. aquatica, advancing phylogenetic and biogeographic research within Mentha, and highlighted the utility of cp. genomes and hypervariable loci for species identification and evolutionary studies in this taxonomically challenging genus.