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 FindingsOne-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.ConclusionsWe 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.
Highlights
Dioscorea is a genus of more than 600 plant species in the family Dioscoreaceae [1], which contains approximately 70 sections
We conclude that matK is a strong, not perfect, candidate as a DNA barcode for Dioscorea identification
This study focuses on Dioscorea species distributed in China, and three candidate DNA barcode regions in the plastid genome were evaluated for identification
Summary
Dioscorea is a genus of more than 600 plant species in the family Dioscoreaceae [1], which contains approximately 70 sections. These species are mainly found in Southeast Asia, Africa, Central America, South America, and in other tropical or subtropical regions where some Dioscorea species are an economically important supply of starch in the staple diet. The importance of Dioscorea in terms of food supply and pharmaceutical use, together with the controversy over classification [5,6,7,8], has given impetus to improve the identification of this genus. Dioscorea is an important plant genus in terms of food supply and pharmaceutical applications. The applicability of three candidate DNA barcodes (rbcL, matK, and psbA-trnH) to identify species within Dioscorea was tested
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