A real-time PCR method for the detection of trnL-trnF sequence in agarwood and products from Aquilaria (Thymelaeaceae)

The trn L- trn F intergenic spacer is used in phylogenetic studies of many plant species including Thymelaeaceae. Members of this family are endangered tropical tree species. Aquilaria produces agarwood that is prized for its fragrance when used directly as incense or processed into essential oil. The goal of the project was to detect DNA sequences from processed samples of Aquilaria malaccensis using real-time PCR (RT-PCR). When using regular PCR, only fresh wood sample yielded a specific band of 465 bp. Samples consisted of fresh wood, different grades of agarwood chips, samples taken at various stages during essential oil processing, and its by-product. Our results revealed lower levels of intact trn L- trn F sequence in samples that had undergone treatments (threshold cycle, C t ≥ 20) when compared to fresh wood (C t = 16 and 18). We demonstrated RT-PCR sensitivity and usefulness in detecting DNA presence in agarwood and processed products derived from agarwood.