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      Choosing and Using a Plant DNA Barcode

      1 , * , 2 , 3

      PLoS ONE

      Public Library of Science

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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 123

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          Biological identifications through DNA barcodes.

          Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
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            bold: The Barcode of Life Data System (http://www.barcodinglife.org)

            The Barcode of Life Data System (bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.
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              Universal primers for amplification of three non-coding regions of chloroplast DNA.

              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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                Author and article information

                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

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

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2011
                26 May 2011
                30 June 2011
                : 6
                : 5
                3102656
                21637336
                PONE-D-11-03466
                10.1371/journal.pone.0019254
                (Editor)
                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.
                Counts
                Pages: 13
                Categories
                Review
                Biology
                Evolutionary Biology
                Evolutionary Systematics
                Taxonomy
                Plant Taxonomy
                Molecular Systematics
                Organismal Evolution
                Plant Evolution
                Plant Science
                Botany
                Plant Taxonomy
                Plant Taxonomy

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