DNA barcoding for identification of the endangered species Aquilaria sinensis: comparison of data from heated or aged wood samples

Abstract

Aquilaria sinensis (Lour.) Gilg is an evergreen tree and produces agarwood used for incense and as a uniquely precious medicine. It is in danger of disappearing due to illegal logging and its identification and protection is crucial. However, it is difficult or impossible to distinguish A. sinensis from other species of the genus Aquilaria Lam. and its closely related genus Gyrinops Gaertn. based on wood anatomical characteristics. Probably, DNA barcoding technology might provide an improvement in species identification. In this study, wood samples were tested, which were submitted to high-temperature drying and were stored for a long period in a xylarium. The factors should be identified that hinder the efficiency of wood DNA extraction from this species. The results indicate that the DNA from the wood tissues could be successfully amplified, apart from some DNA regions from the heartwood of the dried samples and the xylarium samples. The DNA sequences from the wood tissues mostly matched with the sequences of A. sinensis deposited in the GenBank. Moreover, analyses of phylogenetic trees based on trnL-trnF and ITS1 regions indicated that the wood tissues in the tests clustered together with the A. sinensis species from the GenBank, with bootstrap values of 74% and 94%, respectively. Consequently, it is feasible to identify A. sinensis wood on a species level based on the DNA barcoding technology.

Tracking the geographical origin of timber by DNA fingerprinting: a study of the endangered species Cinnamomum kanehirae in Taiwan

“…Spreng. (Jiao et al 2014), members of the Meliaceae family (Michael et al 2012), Dalbergia odorifera T.C. Chen (Yu et al 2016), Robinia pseudoacacia L. (De Filippis and Magel 1998), Quercus L. ssp.…”

Comparative analysis of the complete chloroplast genomic sequence and chemical components of Cinnamomum micranthum and Cinnamomum kanehirae

“…The extraction of sapwood DNA followed the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany) protocol according to Jiao et al (2014). The 2-μg DNA sample was subjected to quality checks before next-generation sequencing (NGS) using a Qubit fluorometer with a Quant-iT dsDNA BR assay kit (Thermo Fisher Scientific, Waltham, MA, USA) and agarose gel electrophoresis assay.…”

“…Many studies reported that the less potential inhibitors of DNA isolation and PCR amplification are present in the sapwood (Rachmayanti et al 2006;Tnah et al 2012;Yu et al 2016). There are many more living parenchyma cells in the sapwood than in the heartwood (Jiao et al 2014;Yu et al 2016). Thus, the six InDel primers are useful for wood differentiation between C. micranthum and C. kanehirae and can be helpful in forensic investigations in the court.…”

“…Moreover, their allozyme analysis reveals very different allele patterns (Lin 1993;Lin et al 1997). The use of DNA markers for the identification of similar wood species was intensively discussed in the last decade, and obviously, this approach is also suited for tracing the origin of trees from illegal logging or for the identification of endangered species (Degen and Fladung 2007;Michael et al 2012;Jiao et al 2014Jiao et al , 2015Sandak et al 2015;Yu et al 2016).…”

The phylogenetic analysis of Dalbergia (Fabaceae: Papilionaceae) based on different DNA barcodes

“…Furthermore, the region of nuclear ribosomal internal transcribed spacer (ITS) and the ITS2 region were also suggested as an alternative source of barcoding for flora (Chen et al 2010a;China Plant BOL Group 2011). Single or combined barcodes allows the identification of different species for a number of genera (Ibeiro et al 2007;Gonzalez et al 2009;Chen et al 2014;Jiao et al 2014). Hassold et al (2016) demonstrated that DNA barcoding is efficient to discriminate between Malagasy and non-Malagasy Dalbergia species.…”