Evaluation of DNA barcodes in Codonopsis (Campanulaceae) and in some large angiosperm plant genera

DNA barcoding is expected to be one of the most promising tools in biological taxonomy

De-Yi Wang 1,2, Qiang Wang1, Ying-Li Wang 3, Xiao-Guo Xiang 1, Lu-Qi Huang 4*, XiaoHua Jin1,5*
1 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China,
2 University of Chinese Academy of Sciences, Beijing, China,
3 Baotou MedicalCollege, Donghe District, Baotou City, Inner Mongolia, China,
4 National Resource Centre for Chinese Materia Medica, China Academy of Chinese Medical Science, Beijing, China,
5 Southeast Asia Biodiversity Research Institute, Chinese Academy of Science (CAS-SEABRI), Menglun, Mengla, Yunnan, China

PubYear : 2017
Volume : 12(2)
Publication Name :PLOS ONE
Page number : e0170286. doi:10.1371/journal

Abstract:
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.