Wood discrimination of six commonly traded Phoebe and Machilus species using high-resolution plastid and nuclear DNA barcodes

Abstract

Phoebe and Machilus trees, whose wood is known as Nanmu in China, face endangerment owing to long-term manmade destruction and climate change. Therefore, effective and accurate forensic tools to identify Nanmu species are required. This study developed a method for DNA identification of woods from six commonly traded Phoebe and Machilus species. DNA was efficiently extracted from oil cell-rich wood tissues, DNA barcodes were screened, species were compared, and a Nanmu DNA database was constructed. Comparison and analysis involved 26 sets of plastid genomes of Phoebe and Machilus. The five highest variable regions (Pi>0.009; psbA-trnH, psbJ, psbJ-petA, rpl32-trnL, and ycf 1) were identified, and three nuclear regions (ITS, LEAFY, and RPB2) were compared. Among single DNA fragments, the nuclear DNA region LEAFY proved optimal for identifying Nanmu species, while psbA-trnH+psbJ+ycf1 was the optimal plastid combination locus. Compared with distance-based (TaxonDNA) and machine-learning analyses, the tree-based method had a lower success rate for species identification. Four labelled Nanmu samples were selected to validate the method and clustered with P. zhennan and P. sheareri data based on the LEAFY region and plastid combination locus. These findings will contribute to the conservation, classification, architecture maintenance, and trade monitoring of Nanmu natural resources.