DNA barcoding the Dioscorea in China, a vital group in the evolution of monocotyledon

Use of matk gene for species discrimination

Xiao Qin Sun, Yingjie Zhu, Jian Lin Guo, Bin Peng, Ming Ming Bai, Yue Yu Hang

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

Background: Dioscorea is an important plant genus in terms of food supply and pharmaceutical applications. However, its classification and identification are controversial. DNA barcoding is a recent aid to taxonomic identification and uses a short standardized DNA region to discriminate plant species. In this study, the applicability of three candidate DNA barcodes (rbcL, matK, and psbA-trnH) to identify species within Dioscorea was tested. Methodology/Principal Findings: One-hundred and forty-eight individual plant samples of Dioscorea, encompassing 38 species, seven varieties and one subspecies, representing majority species distributed in China of this genus, were collected from its main distributing areas. Samples were assessed by PCR amplification, sequence quality, extent of specific genetic divergence, DNA barcoding gap, and the ability to discriminate between species. matK successfully identified 23.26% of all species, compared with 9.30% for rbcL and 11.63% for psbA-trnH. Therefore, matK is recommended as the best DNA barcoding candidate. We found that the combination of two or three loci achieved a higher success rate of species discrimination than one locus alone. However, experimental cost would be much higher if two or three loci, rather than a single locus, were assessed. Conclusions: We conclude that matK is a strong, although not perfect, candidate as a DNA barcode for Dioscorea identification. This assessment takes into account both its ability for species discrimination and the cost of experiments.

Original languageEnglish (US)
Article numbere32057
JournalPLoS One
Volume7
Issue number2
DOIs
StatePublished - Feb 20 2012
Externally publishedYes

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Dioscorea
DNA barcoding
Liliopsida
China
Genes
DNA
loci
genes
Food supply
Costs and Cost Analysis
Food Supply
Amplification
Costs
taxonomy
sampling
drugs
genetic variation
Polymerase Chain Reaction
Pharmaceutical Preparations

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

DNA barcoding the Dioscorea in China, a vital group in the evolution of monocotyledon : Use of matk gene for species discrimination. / Sun, Xiao Qin; Zhu, Yingjie; Guo, Jian Lin; Peng, Bin; Bai, Ming Ming; Hang, Yue Yu.

In: PLoS One, Vol. 7, No. 2, e32057, 20.02.2012.

Research output: Contribution to journalArticle

Sun, Xiao Qin ; Zhu, Yingjie ; Guo, Jian Lin ; Peng, Bin ; Bai, Ming Ming ; Hang, Yue Yu. / DNA barcoding the Dioscorea in China, a vital group in the evolution of monocotyledon : Use of matk gene for species discrimination. In: PLoS One. 2012 ; Vol. 7, No. 2.
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