How Effective Are DNA Barcodes in the Identification of African Rainforest Trees?
Identifieur interne : 000021 ( France/Analysis ); précédent : 000020; suivant : 000022How Effective Are DNA Barcodes in the Identification of African Rainforest Trees?
Auteurs : Ingrid Parmentier [Belgique] ; Jérôme Duminil [Belgique, Cameroun] ; Maria Kuzmina [Canada] ; Morgane Philippe [Belgique] ; Duncan W. Thomas [États-Unis] ; David Kenfack [États-Unis] ; George B. Chuyong [Cameroun] ; Corinne Cruaud [France] ; Olivier J. Hardy [Belgique]Source :
- PLoS ONE [ 1932-6203 ] ; 2013.
Abstract
DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of
We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95–100% success), but less for species identification (71–88%). Using a single marker, best results for species identification were obtained with
Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.
Url:
DOI: 10.1371/journal.pone.0054921
PubMed: 23565134
PubMed Central: 3615068
Affiliations:
- Belgique, Cameroun, Canada, France, États-Unis
- Oregon, Région de Bruxelles-Capitale, Île-de-France
- Bruxelles, Évry (Essonne)
- Université libre de Bruxelles
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PMC:3615068Le document en format XML
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of <italic>rbcL</italic>
, <italic>matK</italic>
and <italic>trnH</italic>
-<italic>psbA</italic>
plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species.</p>
</sec>
<sec><title>Methodology/Principal Findings</title>
<p>We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95–100% success), but less for species identification (71–88%). Using a single marker, best results for species identification were obtained with <italic>trnH-psbA</italic>
. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84–90%. The GD method performed best but a global multiple sequence alignment is not applicable on <italic>trnH-psbA</italic>
.</p>
</sec>
<sec><title>Conclusions/Significance</title>
<p>Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.</p>
</sec>
</div>
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<li>Cameroun</li>
<li>Canada</li>
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<region><li>Oregon</li>
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<settlement><li>Bruxelles</li>
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<country name="Cameroun"><noRegion><name sortKey="Duminil, Jerome" sort="Duminil, Jerome" uniqKey="Duminil J" first="Jérôme" last="Duminil">Jérôme Duminil</name>
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<name sortKey="Chuyong, George B" sort="Chuyong, George B" uniqKey="Chuyong G" first="George B." last="Chuyong">George B. Chuyong</name>
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<name sortKey="Kenfack, David" sort="Kenfack, David" uniqKey="Kenfack D" first="David" last="Kenfack">David Kenfack</name>
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<country name="France"><region name="Île-de-France"><name sortKey="Cruaud, Corinne" sort="Cruaud, Corinne" uniqKey="Cruaud C" first="Corinne" last="Cruaud">Corinne Cruaud</name>
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