The complete chloroplast genome of Origanum vulgare L. (Lamiaceae) from AL-Madinah, Saudi Arabia, and its phylogenetic relationship.

Abstract

The genus Origanum is taxonomically complex and often considered an underutilized group despite its economic and medicinal significance. Origanum vulgare L., the most variable species within the genus, is widely utilized as a culinary spice and medicinal herb, exhibiting considerable morphological diversity across its six recognized subspecies. In this study, we assembled and annotated the complete chloroplast (cp) genome of a wilt-resistant Saudi Arabian accession of O. vulgare. The cp genome measures 151,826 bp in length and displays the typical circular quadripartite structure, consisting of a large single copy (LSC) region (83,014 bp), a small single copy (SSC) region (17,620 bp), and a pair of inverted repeats (IRs) (25,596 bp each). It contains 129 genes, including 85 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. Notably, the Saudi accession possesses a duplicated rps19 gene, and its cp genome length differs from that of other O. vulgare accessions. Phylogenetic analysis clustered all O. vulgare accessions into a single well-supported clade, revealing considerable genetic divergence among populations. Furthermore, the genus Origanum was strongly supported as sister to Thymus. This study provides a valuable chloroplast genome resource for evolutionary, taxonomic, and conservation studies in O. vulgare and related taxa within the Lamiaceae.