Comparison of DNA extraction methods on CITES-listed timber species and application in species authentication of commercial products using DNA barcoding

Abstract

Quality and quantity of DNA extracted from wood is important for molecular identification of wood species, which can serve for conservation of wood species and law enforcement to combat illegal wood trading. Rosewood (Dalbergia and Pterocarpus) and agarwood (Aquilaria) are the most commonly found hardwood in timber seizure incidents. To monitor international trade of timber and commercial wood products and to protect these endangered wood species from further population decline, in this study, we have compared three extraction protocols for DNA extraction from 12 samples of rosewood and agarwood timber logs, and later applied the best DNA extraction protocol on 10 commercial wood products claimed to be rosewood and agarwood. We also demonstrated the applicability of DNA mini-barcoding with multi-loci combination with reference library for identifying the species of timber and commercial wood products. We found that a silica column-based method with guanidine thiocyanate-containing binding buffer served the best in DNA extraction from different parts of wood in all three genera with good quality and quantity. Single barcode region ITS2 or multi-loci combinations including ITS2 barcode region generally provide better discriminatory power for species identification for both rosewood and agarwood. All 10 products were identified to species-level using multi-loci combination. In terms of accuracy in labelling, 80% of them were labelled correctly. Our work has shown the feasibility of extracting good quality of DNA from authentic wood samples and processed wood products and identifying them to species level based on DNA barcoding technology.

An affordable and simple method for DNA extraction from agarose suitable for downstream applications

“…To accomplish this, it is often necessary to visualize the DNA of interest using techniques such as agarose or polyacrylamide gel electrophoresis 10 , Once the relevant DNA bands have been identi ed, they are directly puri ed from the gel. 11 This extraction is typically performed using commercial kits. However, access to these products is not always possible.…”

Appearance, molecule identification, and phylogenetic analysis of the three Leonurus species used for the treatment of gynecological diseases

“…In comparison with the chloroplast genome, Internal Transcribed Spacer2 (ITS2) is the non-coding region of the ribosome components in eukaryotes organisms (But et al, 2023). After annotation and contrast of the ITS2 sequences among the seven Leonurus species including the three studied species, we found that the most of nucleotide differences occur after the 57th base from the beginning of the sequence in a total of 221 bases except the species of L. pseudomacranthus showing the signi cant differentia, agreed with the discovery from the group of Dr. Chao and Yang (Yang et al, 2011) (Fig.…”

DNA barcoding of Andaman Padauk (Pterocarpus dalbergioides Roxb.,) an endemic tree species of Andaman and Nicobar Islands, India

“…Chase et al 2007;Kang et al 2017) DNA extracted from wood of Pterocarpus also shows better ampli cation and high discrimination with ITS2(But et al 2023). In this investigation, a comprehensive analysis was undertaken by comparing the Internal Transcribed Spacer 2 (ITS2) sequences of 30 Andaman padauk accessions with those of 16…”