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Members of Lam. (Thymelaeaceae) are evergreen trees that are widely distributed in the Indomalesia region. is highly prized for its unique scented resin, agarwood, which is often the subject of unlawful trade activities. Survival of the tree is heavily threatened by destructive harvesting and agarwood poaching, leading to its protection under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Unfortunately, an efficient species identification method, which is crucial to aid in the conservation efforts of is lacking. Here, we described our search for a suitable specific DNA barcode for species using eight complete plastome sequences. We identified five highly variable regions (HVR) (K-16, F-32, J-A, D, and T-L) in the plastomes. These regions were further analyzed using the neighbor-joining (NJ) method to assess their ability at discriminating the eight species. Coupled with in silico primer design, two potential barcoding regions, J-A and T-L, were identified. Their strengths in species delimitation were evaluated individually and in combination, via DNA barcoding analysis. Our findings showed that the combined dataset, J-A + T-L, effectively resolved members of the genus by clustering all species into their respective clades. In addition, we demonstrated that the newly proposed DNA barcode was capable at identifying the species of origin of six commercial agarwood samples that were included as unknown samples. Such achievement offers a new technical advancement, useful in the combat against illicit agarwood trades and in assisting the conservation of these valuable species in natural populations.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-023-03479-1.