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      A DNA barcode for land plants

      1 , 1 , 2 , 3 , 3 , 4 , 5 , 5 , 6 , 7 , 8 , 9 , 10 , 6 , 9 , 5 , 11 , 12 , 13 , 11 , 14 , 15 , 9 , 16 , 1 , 5 , 17 , 5 , 18 , 19 , 1 , 7 , 1 , 5 , 7 , 10 , 20 , 4 , 10 , 1 , 16 , 4 , 3 , 7 , 21 , 8 , 22 , 1 , 23 , 5 , 24 , 22 , 18 , 10 , 25 , CBOL Plant Working Group1
      Proceedings of the National Academy of Sciences
      Proceedings of the National Academy of Sciences

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          Abstract

          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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          Most cited references24

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

          We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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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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              Use of DNA barcodes to identify flowering plants.

              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

                Journal
                Proceedings of the National Academy of Sciences
                Proc. Natl. Acad. Sci. U.S.A.
                Proceedings of the National Academy of Sciences
                0027-8424
                1091-6490
                August 04 2009
                August 04 2009
                August 04 2009
                : 106
                : 31
                : 12794-12797
                Affiliations
                [1 ]Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom;
                [2 ]National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Computational Biology Branch, Bethesda, MD 20894;
                [3 ]Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, ON, Canada N1G 2W1;
                [4 ]Department of Botany and Plant Biotechnology, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa;
                [5 ]Royal Botanic Gardens, Kew, Richmond TW9 3DS, United Kingdom;
                [6 ]Department of Botany, Smithsonian Institution, Washington DC, 20013-7012;
                [7 ]Department of Integrative Biology, University of Guelph, Guelph, ON, Canada N1G 2W1;
                [8 ]UBC Botanical Garden and Centre for Plant Research, Faculty of Land and Food Systems, and Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4;
                [9 ]Botany Department, Natural History Museum, London SW7 5BD, United Kingdom;
                [10 ]School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea;
                [11 ]Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2;
                [12 ]Laboratório de Sistemática Molecular de Plantas, Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, 44031-460, Feira de Santana, Bahia, Brazil;
                [13 ]Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, Costa Rica;
                [14 ]Department of Biology, Columbus State University, Columbus, GA 31907-5645;
                [15 ]Department of Botany, University of Wisconsin, Madison, WI 53508;
                [16 ]Universidad de los Andes, Apartado Aéreo 4976, Bogotá, D.C., Colombia;
                [17 ]Leslie Hill Molecular Systematics Laboratory, SANBI, Kirstenbosch Research Centre, Claremont 7735, Cape Town, South Africa;
                [18 ]Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion SY23 3DA, United Kingdom;
                [19 ]Department of Botany, University of Cape Town, Rondebosch 7700, South Africa;
                [20 ]Department of Life Sciences, Hallym University, Chuncheon 200-702, Korea;
                [21 ]School of Biological Sciences, Seoul National University, Seoul 151-742, Korea;
                [22 ]Natural History Museum of Denmark, University of Copenhagen, 1307 Copenhagen K, Denmark;
                [23 ]Instituto de Biología, Universidad Nacional Autónoma de México, 04510 México, D.F., Mexico;
                [24 ]Imperial College London, Silwood Park Campus, Ascot SL5 7PY, United Kingdom; and
                [25 ]Cullman Program for Molecular Systematics, New York Botanical Garden, Bronx, NY, 10458-5126
                Article
                10.1073/pnas.0905845106
                2722355
                19666622
                88a7d66e-e1b3-4419-bb1d-d181ed1be176
                © 2009
                History

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