Choosing and Using a Plant DNA Barcode

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Abstract

The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 ( CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.

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Most cited references 115

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Universal primers for amplification of three non-coding regions of chloroplast DNA.

Pierre Taberlet, Ludovic Gielly, Guy Pautou … (1991)

Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.

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A DNA barcode for land plants.

Peter M. Hollingsworth, Laura L. Forrest, John Spouge … (2009)

DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

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Use of DNA barcodes to identify flowering plants.

W. John Kress, Kenneth J Wurdack, Elizabeth Zimmer … (2005)

Methods for identifying species by using short orthologous DNA sequences, known as "DNA barcodes," have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short ( approximately 450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.

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Author and article information

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: Role: Editor

Journal

Journal ID (nlm-ta): PLoS One

Journal ID (publisher-id): plos

Journal ID (pmc): plosone

Title: PLoS ONE

Publisher: Public Library of Science (San Francisco, USA )

ISSN (Electronic): 1932-6203

Publication date Collection: 2011

Publication date (Electronic): 26 May 2011

Publication date (Corrected, electronic): 30 June 2011

Volume: 6

Issue: 5

Electronic Location Identifier: e19254

Affiliations

[1 ]Genetics and Conservation Section, Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom

[2 ]University of British Columbia Botanical Garden and Centre for Plant Research, Faculty of Land and Food Systems, and Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada

[3 ]Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, New York, United States of America

Biodiversity Insitute of Ontario - University of Guelph, Canada

Author notes

* E-mail: P.Hollingsworth@ 123456rbge.org.uk

Conceived and designed the experiments: PMH SWG DPL. Analyzed the data: PMH SWG DPL. Wrote the paper: PMH SWG DPL.

Article

Publisher ID: PONE-D-11-03466

DOI: 10.1371/journal.pone.0019254

PMC ID: 3102656

PubMed ID: 21637336

SO-VID: 9bcc2407-4925-4a65-9b25-56c7ec0525a5

Copyright © Hollingsworth et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Choosing and Using a Plant DNA Barcode

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Most cited references 115

Universal primers for amplification of three non-coding regions of chloroplast DNA.

A DNA barcode for land plants.

Use of DNA barcodes to identify flowering plants.

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