J Syst Evol ›› 2014, Vol. 52 ›› Issue (4): 487-499.doi: 10.1111/jse.12076

• Research Articles • Previous Articles     Next Articles

Developing DNA barcodes for species identification in Podophylloideae (Berberidaceae)

1Yun-Rui MAO 1Yong-Hua ZHANG 2Koh NAKAMURA 3Bi-Cai GUAN 1Ying-Xiong QIU*   

  1. 1(Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China)
    2(Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Nangang, Taiwan, China)
    3(College of Life Sciences and Food Engineering, Nanchang University, Nanchang, China)
  • Received:2013-06-19 Online:2013-12-19 Published:2014-07-10

Abstract: Species of Podophyllum, Dysosma, Sinopodophyllum, and Diphylleia, genera from Podophylloideae of Berberidaceae, have long been used in traditional herbal medicine in East Asia and/or North America. Accurate identification of the species of these four genera is crucial to their medicinal uses. In this study, we tested the utility of nine barcodes (matK, rbcL, atpH-atpI, rpl32-trnLUAG, rps18-clpp, trnL-trnF, trnL-ndhJ, trnS-trnfM, and internal transcribed spacer (ITS)) to discriminate different species of Podophylloideae. Thirty-six individuals representing 12 species of Podophylloideae were collected from different locations in China, Japan, and North America. We assessed the feasibility of amplification and sequencing of all markers, examined the levels of the barcoding gap based on DNA sequence divergence between ranges of intra- and interspecific variation using pairwise distances, and further evaluated successful identifications using each barcode by similarity-based and tree-based methods. Results showed that nine barcodes, except rps18-clpp, have a high level of primer universality and sequencing success. As a single barcode, ITS has the most variable sites, greater intra- and interspecific divergences, and the highest species discrimination rate (83%), followed by matKwhich has moderate variation and also high species discrimination rates. However, these species can also be discriminated by ITS alone, except Dysosma versipellis (Hance) M. Cheng ex T. S. Ying and D. pleiantha (Hance) Woodson. The combination of ITS + matK did not improve species resolution over ITS alone. Thus, we propose that ITS may be used as a sole region for identification of most species in Podophylloideae. The failure of ITS to distinguish D. versipellis and D. pleiantha is likely attributed to incomplete lineage sorting due to recent divergence of the two species.

Key words: DNA barcoding, Podophylloideae, species identification, traditional Chinese medicine.

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[1] . [J]. Chin Bull Bot, 1994, 11(专辑): 41 .
[2] Wang Hong Jian Ling-cheng Sun Long-hua. The Roles of the Cold-Resister for Accelerating the Growth and Development, and the Cold-Stability of the Tissue and Cell Structure of Plant Leaves[J]. Chin Bull Bot, 1994, 11(特辑): 163 -167 .
[3] Hong Jian-ming;Yin Li-ping and Qiu Ze-sheng. Progress of Genetic Engineering for Plant Diseases Resistance[J]. Chin Bull Bot, 1997, 14(03): 40 -46 .
[4] Lin liang-qiu;Zhang Qing-qi and Wu Wen-shan. A Study on Pollen Morphology of Rosa laevigata and Its Nutrition Composition[J]. Chin Bull Bot, 1994, 11(04): 43 -44 .
[5] Wen Ye-chun;Jin Bao-qi;Li En-shi and Chen Yu-qun. Identification of the Major Components of Stevia rebaudina[J]. Chin Bull Bot, 1984, 2(23): 55 -56 .
[6] . [J]. Chin Bull Bot, 2004, 21(02): 254 -255 .
[7] Ding Bing- yang;He Yao-hua;Miao Jing and Huang Tao. The Germinating Experiment of the Seeds of Rhododendromn huadingense[J]. Chin Bull Bot, 1997, 14(01): 53 -54 .
[8] Li Ai-ming and Wu Qi. The Shoot Differentiation and Plant Regeneration of Peanut Cotyledon[J]. Chin Bull Bot, 1988, 5(03): 143 -145 .
[9] Jie Dong;Fenghui Qi;Yaguang Zhan. Establishment of the Suspension Culture System and Optimization of Biosynthesis of Gallic Acid in Acer ginnala[J]. Chin Bull Bot, 2008, 25(06): 734 -740 .
[10] Lubin Li;Xiaojun Guo;Zhenhua Peng;Guanshui Liu;Hongshui Yuan;Baocheng Zhu;Kai Yang*. Effect of the Quantity of AFLP Primer Combinations on Accurately Identifying Bamboo Genetic Relationships[J]. Chin Bull Bot, 2008, 25(04): 449 -454 .