ScienceDaily (Nov. 6, 2009) — In foods, soil samples or customs checks, plant fragments sometimes need to be quickly identified. The use of DNA "barcodes" to itemize plant biodiversity was proposed during the 1992 Rio de Janeiro Summit. Jérôme Chave's team from the Evolution et diversité biologique (1) laboratory has tested this method in the tropical forest where the CNRS Nouragues, French Guiana (2) research station is located.
Their study, published in PLoS One, shows that while the identification of plant species has improved considerably, some aspects of this method remain problematic, especially for tropical species.
Climbing to the canopy: the uppermost part of trees, an area with particularly rich biodiversity near the CNRS Nouragues Station in French Guiana. (Credit: Copyright J.CHAVE/CNRS)
Creating a large-scale inventory of plant biodiversity is essential for the development of conservation strategies. Within the framework of the Convention on Biological Diversity(3), the use of DNA barcoding was proposed for the identification of plant and animal species. This method consists of using tissue to sequence short DNA fragments which contain a substantial amount of information. These fragments are then compared to a reference collection to identify their origin. In August 2009, after several years of debate, an international consensus headed by the Plant Working Group of the Consortium for the Barcode of Life (CBoL) was reached, according to which two DNA markers (two gene regions dubbed rbcL and matK) would suffice to characterize 250,000 plant species.
The team from the Toulouse Evolution et diversité biologique(1) laboratory, in collaboration with Guyanese partners, conducted the first test of this DNA barcoding method in a tropical forest environment. A total of eight candidate barcodes were tested on over 200 tree species sampled at the CNRS Nouragues research station in French Guiana(2). More than 2,000 DNA sequences were thus generated for this project. The study yielded significant progress in species discrimination. However, identification success did not exceed 70% and one of the two markers proposed by CBoL proved very difficult to sequence.
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Identification of Amazonian Trees with DNA Barcodes
Mailyn Adriana Gonzalez 1, Christopher Baraloto 2, Julien Engel 1, Scott A. Mori 3, Pascal Pétronelli 4, Bernard Riéra 5, Aurélien Roger 1, Christophe Thébaud 1, Jérôme Chave 1*
1 Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier and CNRS, UMR 5174, Toulouse, France, 2 INRA, UMR Ecologie des Forêts de Guyane, Kourou, French Guiana, France, 3 Institute of Systematic Botany, New York Botanical Garden, Bronx, New York, United States of America, 4 CIRAD, UMR Ecologie des Forêts de Guyane, Kourou, French Guiana, France, 5 Laboratoire Fonctionnement, Evolution et Mécanismes Régulateurs des Ecosystèmes Forestiers, CNRS, UMR 5176, Brunoy, France
Abstract Top
Background
Large-scale plant diversity inventories are critical to develop informed conservation strategies. However, the workload required for classic taxonomic surveys remains high and is particularly problematic for megadiverse tropical forests.
Methodology/Principal Findings
Based on a comprehensive census of all trees in two hectares of a tropical forest in French Guiana, we examined whether plant DNA barcoding could contribute to increasing the quality and the pace of tropical plant biodiversity surveys. Of the eight plant DNA markers we tested (rbcLa, rpoC1, rpoB, matK, ycf5, trnL, psbA-trnH, ITS), matK and ITS had a low rate of sequencing success. More critically, none of the plastid markers achieved a rate of correct plant identification greater than 70%, either alone or combined. The performance of all barcoding markers was noticeably low in few species-rich clades, such as the Laureae, and the Sapotaceae. A field test of the approach enabled us to detect 130 molecular operational taxonomic units in a sample of 252 juvenile trees. Including molecular markers increased the identification rate of juveniles from 72% (morphology alone) to 96% (morphology and molecular) of the individuals assigned to a known tree taxon.
Conclusion/Significance
We conclude that while DNA barcoding is an invaluable tool for detecting errors in identifications and for identifying plants at juvenile stages, its limited ability to identify collections will constrain the practical implementation of DNA-based tropical plant biodiversity programs.
Citation: Gonzalez MA, Baraloto C, Engel J, Mori SA, Pétronelli P, et al. (2009) Identification of Amazonian Trees with DNA Barcodes. PLoS ONE 4(10): e7483. doi:10.1371/journal.pone.0007483
Editor: Andy Hector, University of Zurich, Switzerland
Received: August 28, 2009; Accepted: September 28, 2009; Published: October 16, 2009
Copyright: © 2009 Gonzalez 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.
Funding: Funding from Agence Nationale pour la Recherche and CNRS are acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: Author Jerome Chave is on the editorial board.
* E-mail: chave@cict.fr
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