J Syst Evol ›› 2011, Vol. 49 ›› Issue (5): 425-437.doi: 10.1111/j.1759-6831.2011.00154.x

• Research Articles • Previous Articles     Next Articles

DNA barcoding of Pedicularis L. (Orobanchaceae): Evaluating four universal barcode loci in a large and hemiparasitic genus

1,2Wen-Bin YU 1,2Pan-Hui HUANG 3Richard H. REE 1,2Min-Lu LIU 1De-Zhu LI 1Hong WANG*   

  1. 1(Key Laboratory of Biodiversity and Biogeography, and Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China)
    2(Graduate University of Chinese Academy of Sciences, Beijing 100049, China)
    3(Department of Botany, Field Museum of Natural History, Chicago, Illinois 60605, USA)
  • Received:2011-01-23 Online:2011-05-30 Published:2011-08-19

Abstract: One application of DNA barcoding is species identification based on sequences of a short and standardized DNA region. In plants, various DNA regions, alone or in combination, have been proposed and investigated, but consensus on a universal plant barcode remains elusive. In this study, we tested the utility of four candidate barcoding regions (rbcL, matK, trnH-psbA, and internal transcribed spacer (ITS)) as DNA barcodes for discriminating species in a large and hemiparasitic genus Pedicularis (Orobanchaceae). Amplification and sequencing was successful using single primer pairs for rbcL, trnH-psbA, and ITS, whereas two primer pairs were required for matK. Patterns of sequence divergence commonly showed a “barcoding gap”, that is, a bimodal frequency distribution of pairwise distances representing genetic diversity within and between species, respectively. Considering primer universality, ease of amplification and sequencing, and performance in discriminating species, we found the most effective single-region barcode for Pedicularis to be ITS, and the most effective two-region barcode to be rbcL + ITS. Both discriminated at least 78% of the 88 species and correctly identified at least 89% of the sequences in our sample, and were effective in placing unidentified samples in known species groups. Our results suggest that DNA barcoding has the potential to aid taxonomic research in Pedicularis, a species-rich cosmopolitan clade much in need of revision, as well as ecological studies in its center of diversity, the Hengduan Mountains region of China.

Key words: DNA barcode, Hengduan Mountains region, ITS, Pedicularis, rbcL, species identification.

[1] Luiz Henrique M. Fonseca and Lúcia G. Lohmann. Exploring the potential of nuclear and mitochondrial sequencing data generated through genome‐skimming for plant phylogenetics: A case study from a clade of neotropical lianas . J Syst Evol, 2020, 58(1): 18-32.
[2] Jose L. Villar, M. Ángeles Alonso, Ana Juan, John F. Gaskin, and Manuel B. Crespo. Out of the Middle East: New phylogenetic insights in the genus Tamarix (Tamaricaceae) . J Syst Evol, 2019, 57(5): 488-507.
[3] Nerea Larranaga, Federico J. Albertazzi, and Jose I. Hormaza. Phylogenetics of Annona cherimola (Annonaceae) and some of its closest relatives . J Syst Evol, 2019, 57(3): 211-221.
[4] W. John Kress. Plant DNA barcodes: Applications today and in the future . J Syst Evol, 2017, 55(4): 291-307.
[5] Xiang-Ping Wang, Shuang-Quan Huang. Interspecific and intraspecific variation in corolla tube length in Pedicularis species achieved by both cell anisotropy and division . J Syst Evol, 2017, 55(3): 208-214.
[6] Wen-Kui Dai, Edwin Luguba Kadiori, Qing-Feng Wang, Chun-Feng Yang. Pollen limitation, plasticity in floral traits, and mixed mating system in an alpine plant Pedicularis siphonantha (Orobanchaceae) from different altitudes . J Syst Evol, 2017, 55(3): 192-199.
[7] Partha Sarathi Saha, Mainak Sengupta, Sumita Jha. Ribosomal DNA ITS1, 5.8S and ITS2 secondary structure, nuclear DNA content and phytochemical analyses reveal distinctive characteristics of four subclades of Protasparagus . J Syst Evol, 2017, 55(1): 54-70.
[8] Yi-Xuan Kou, Kun Xiao, Xiao-Rong Lai, Yu-Jin Wang, Zhi-Yong Zhang. Natural hybridization between Torreya jackii and T. grandis (Taxaceae) in southeast China . J Syst Evol, 2017, 55(1): 25-33.
[9] Prashant Singh, Robin Anigo Minz, Kikku Kunui, Zaid Muneef Shaikh, Archana Suradkar, Yogesh S Shouche, Arun Kumar Mishra, Satya Shila Singh. A new species of Scytonema isolated from Bilaspur, Chhattisgarh, India . J Syst Evol, 2016, 54(5): 519-527.
[10] Gezahegn Girma, Charles Spillane, Melaku Gedil. DNA barcoding of the main cultivated yams and selected wild species in the genus Dioscorea . J Syst Evol, 2016, 54(3): 228-237.
[11] Paul M Peterson, Konstantin Romaschenko, Yolanda Herrera Arrieta. Phylogeny and subgeneric classification of Bouteloua with a new species, B. herrera-arrietae (Poaceae: Chloridoideae: Cynodonteae: Boutelouinae) . J Syst Evol, 2015, 53(4): 351-366.
[12] Zi-Yi CHEN, Zhu-Jun XIONG, Xiao-Yun PAN, Su-Qin SHEN, Yu-Peng GENG, Cheng-Yuan XU, Jia-Kuan CHEN, Wen-Ju ZHANG. Variation of genome size and the ribosomal DNA ITS region of Alternanthera philoxeroides (Amaranthaceae) in Argentina, the USA, and China . J Syst Evol, 2015, 53(1): 82-87.
[13] Szilvia STRANCZINGER, Aniko GALAMBOS, Dalma SZENASY, Balint SZALONTAI. Phylogenetic relationships in the Neotropical tribe Hamelieae (Rubiaceae, Cinchonoideae) and comments on its generic limits . J Syst Evol, 2014, 52(5): 643-650.
[14] De-Qing HUANG   Qin-Qin LI   Chun-Jing ZHOU   Song-Dong ZHOU   Xing-Jin HE. Intraspecific differentiation of Allium wallichii (Amaryllidaceae) inferred from chloroplast DNA and internal transcribed spacer fragments . J Syst Evol, 2014, 52(3): 341-354.
[15] Xin-Hui LI, Xin-Xin ZHU, Yang NIU, Hang SUN. Phylogenetic clustering and overdispersion for alpine plants along elevational gradient in the Hengduan Mountains Region, southwest China . J Syst Evol, 2014, 52(3): 280-288.
Full text



No Suggested Reading articles found!