Aquilaria species are renowned for producing agarwood, a dark, fragrant resin with significant medicinal and economic value. Due to high market demand, overexploitation, and limited natural availability, the prevalence of counterfeit agarwood products has increased, highlighting the need for accurate species identification to ensure product authenticity and support conservation efforts. Traditional morphological methods are often inadequate for reliable species-level discrimination, particularly in semi-processed or traded materials. In this study, DNA was extracted from 20 commercial Aquilaria wood log samples, and two genomic loci, viz., trnL-trnF (chloroplast) and ITS (nuclear), were PCR-amplified and analysed. Sequence identity was assessed via BLASTn, and phylogenetic relationships were reconstructed using MEGA X. While the ITS region showed limited taxonomic resolution due to high sequence similarity among A. agallochum, A. yunnanensis, and A. malaccensis, the trnL-trnF locus consistently identified most samples as A. agallochum, demonstrating superior species-level resolving power. However, ambiguous cases suggest that single-locus markers may not always be conclusive. These findings underscore the value of trnL-trnF as a practical and reliable molecular marker for agarwood authentication, while also pointing potential of full chloroplast genome strategies for more definitive species identification across the Aquilaria genus.
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