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Aquilaria  Lam. is an important group of trees that produce agarwood, which is widely used for manufacturing medicine, perfumes and incense. The members of the genus  Aquilaria  are close to being extinct due to illegal harvesting and are now protected in many countries. In this study, five DNA barcodes [internal transcribed spacer (ITS), maturase K ( mat K),  psb A- trn H, ribulose bisphosphate carboxylase ( rbc L) and  trn L- trn F] and their combinations were evaluated for the discrimination of the major (16 out of 21) species of  Aquilaria  based on three criteria: sequence variation, genetic distances and the discrimination ability. In addition, we attempted to determine the phylogenetic relationship between  Aquilaria  and  Gyrinops  species using three phylogenetic analysis methods. We observed that the combination barcode ITS+ trn L- trn F had a good discrimination ability based on the best match and best close match methods, provided more genetic information, and clearly indicated the comprehensive phylogenetic relationship between most  Aquilaria  and  Gyrinops  species. Considering the overall performance of these barcodes, the ITS+ trn L- trn F is a suitable barcode for the identification of  Aquilaria  species.

Phylogenetic analysis of Aquilaria Lam. (Thymelaeaceae) based on DNA barcoding