Comparative chloroplast genome analysis reveals powerful barcodes for combatting illegal logging of CITES-listed threatened Asian rosewoods (Dalbergia, Leguminosae, Papilionoideae)

Abstract

Rosewoods (Dalbergia) are among the most heavily trafficked natural resources in the illegal global multibillion-dollar wildlife trade. Consequently, many rosewood species experience high extinction threats. To enforce the conservation of rosewood species threatened by illegal logging, reliable identification is required to distinguish between legally and illegally traded rosewood timber. DNA barcoding is considered the most promising approach to achieve rapid and reliable species identification, compared to morphological and biochemical compound analyses. This study was designed to establish a DNA barcoding approach for rosewoods by utilizing whole-chloroplast genome sequences, either as super-barcodes or as sources to identify short but highly informative DNA barcoding regions. To achieve these objectives, 81 rosewood plastomes that cover 28 species were generated de novo. The phylogenomic dataset was further expanded to include a total of 110 accessions representing 31 species of Dalbergia. The chloroplast genome structure and composition were found to be highly conserved across all the species studied. The phylogenetic hypothesis obtained using the coding sequences data were fully resolved and robust, even for closely related species. Five loci were identified as powerful DNA barcodes that corresponded to sequence variation hotspots. In summary, the whole chloroplast genomes were found to be highly powerful super-barcodes, while up to five plastome loci were identified as small barcode regions that can be amplified even for degraded DNA. This study successfully establishes the resources necessary to carry out DNA barcoding for rosewoods, serving as a main tool to provide reliable identification of threatened species traded in the illegal timber market.