Date Published: February 9, 2017
Publisher: Public Library of Science
Author(s): De-Yi Wang, Qiang Wang, Ying-Li Wang, Xiao-Guo Xiang, Lu-Qi Huang, Xiao-Hua Jin, Zhong-Jian Liu.
DNA barcoding is expected to be one of the most promising tools in biological taxonomy. However, there have been no agreements on which core barcode should be used in plants, especially in species-rich genera with wide geographical distributions. To evaluate their discriminatory power in large genera, four of the most widely used DNA barcodes, including three plastid regions (matK, rbcL, trnH-psbA) and nuclear internal transcribed spacer (nrITS), were tested in seven species-rich genera (Ficus, Pedicularis, Rhodiola, Rhododendron,Viburnum, Dendrobium and Lysimachia) and a moderate size genus, Codonopsis. All of the sequences from the aforementioned seven large genera were downloaded from NCBI. The related barcodes for Codonopsis were newly generated in this study. Genetics distances, DNA barcoding gaps and phylogenetic trees of the four single barcodes and their combinations were calculated and compared in the seven genera. As for single barcode, nrITS has the most variable sites, the clearest intra- and inter-specific divergences and the highest discrimination rates in the seven genera. Among the combinations of barcodes, ITS+matK performed better than all the single barcodes in most cases and even the three- and four-loci combinations in the seven genera. Therefore, we recommend ITS+matK as the core barcodes for large plant genera.
DNA barcoding, the use of a short gene sequence from a standardized region of the genome as a tool for species identification, provides new tools for use in biological taxonomy [1–5]. It has shown promise in providing a practical, standardized, species-level identification tool that can be used for taxonomic research, population genetics , phylogenetics , biodiversity assessment , and ecological studies [9–11]. An ideal DNA barcode should be variable enough to resolve closely related species and short enough for easy experimental manipulation at low cost . The cytochrome oxidase I (COI) for the zoological community appears to generally fulfill these criteria [11, 13–15]. In contrast, there is no universally accepted counterpart barcode for plants yet . In the past decade, four loci widely used in plant molecular systematics, namely, ITS, matK, rbcL and trnH-psbA, have been extensively evaluated [3, 16–19]. The lack of resolving power for single barcodes has led to the transition from a single- to a multi-region barcoding system [3, 4, 20–24]. Specifically, the combined use of short segments of the chloroplast genes matK and rbcL was proposed by the Plant Working Group of the Consortium for Barcodes of Life [3, 14].
The synthetic analyses of identification ability for all barcodes in the seven species-rich genera (Codonopsis, Dendrobium, Ficus, Pedicularis, Rhodiola, Rhododendron, and Viburnum) agreed with previous studies that ‘ITS+matK’ may be the best core barcode combination for large genera in angiosperms [21, 51, 61, 62]. The ITS and matK exhibited more variable and informative sites for species identification. The combination of ITS and matK performs much better than other single barcode, and was almost equal to the discriminatory power of the three- or four-locus barcodes. Therefore, we propose the combined ‘ITS + matK’ as the core barcode for large plant genera.