DNA barcoding rapidly became a useful complementary tool in floristic investigations particularly for identifying specimens that lack diagnostic characters. Here we assess the capability of three DNA barcode markers (chloroplast rpoB, accD and nuclear ITS) in correctly species assignment in a floristic survey on Caucasus. We focused on two herbal groups with potential for ornamental applications, namely orchids and asterids. On these two plant groups we tested whether our selection of barcode markers allows identification of the “barcoding gap” in sequence identity and to distinguish between monophyletic species when employing distance-based methods. All markers successfully amplified most specimens, but we found that rate of species-level resolution among selected markers largely varied in the two plant groups. Overall, for both lineages, plastid markers had a species-level assignment success rate lower that nuclear ITS marker. The latter confirmed in orchids both the existence of a barcoding gap and that all accessions of same species clustered together in monophyletic groups. Further, it also allowed the detection of a phylogeographic signal. ITS marker resulted to be the best performing barcode for asterids; however, none of the three tested markers showed high discriminatory ability. Even if ITS revealed as the most promising plant barcode marker we argue that the ability of this barcode for species assignment is strongly dependent on the evolutionary history of the investigated plant lineage.

Generated sequences were aligned by using MUSCLE program in Mega X.