DNA Barcodes for the Assessment of Phylogenetic Relationships Based on CpDNA and NrDNA Regions in Vigna Species

The phylogenetic relationships among species and subspecies in the genus Vigna were investigated using sequence data from the chloroplast and nuclear regions as DNA barcodes. We analysed 156 accessions of 56 species of the taxonomically best-known groups in the genus and evaluated the effectiveness of three chloroplast regions and a nuclear dataset currently employed as DNA barcodes using the barcoding gap, applied similarity, and tree-based methods. The chloroplast regions were able to identify fewer than 44% of the species, whereas the nuclear datasets identified more than 62% of the species using the “best match” and “best close match” options in the TaxonDNA software. All species had high interspecific pairwise distances that did not fully overlap with the intraspecific distances, and the tree-based analysis resolved more than 80% of the species. The nuclear ribosomal internal transcribed spacer 2 (ITS2) region was the most useful as a single barcode and the four-barcode combinations that included ITS2 provided the best discriminatory power. Therefore, we suggest that the ITS2 barcoding region should be used as a starting point to identify Vigna species.