Abstract
Abstract 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 (matK), psbA-trnH, ribulose bisphosphate carboxylase (rbcL) and trnL-trnF] 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+trnL-trnF 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+trnL-trnF is a suitable barcode for the identification of Aquilaria species.
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