Nucleic Acids Research Advance Access originally published online on December 14, 2006
Nucleic Acids Research 2007 35(3):e14; doi:10.1093/nar/gkl938
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Nucleic Acids Research, 2007, Vol. 35, No. 3 e14
© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Methods Online |
Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding
1 Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier BP 53, 38041 Grenoble Cedex 9, France 2 Laboratoire Adaptation et Pathogénie des Microorganismes, CNRS UMR 5163, Université Joseph Fourier BP 170, 38042 Grenoble Cedex 9, France 3 INRIA Rhône-Alpes, Hélix Project 655 Avenue de l'Europe, 38334 Montbonnot Cedex, France 4 Dipartimento di Ecologia e Sviluppo Economico Sostenibile, Università degli Studi della Tuscia via S. Giovanni Decollato 1, 01100 Viterbo, Italy 5 Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences PO Box 5003, No-1432 Ås, Norway 6 Bioinformatics, GENOME Express 11 Chemin des Prés, 38944 Meylan, France 7 UR 910 Ecologie et Physiologie du Système Digestif, INRA Domaine de Vilvert 78352 Jouy-en-Josas Cedex, France 8 National Centre for Biosystematics, Natural History Museum, University of Oslo PO Box 1172 Blindern, NO-0318 Oslo, Norway 9 Center for Ancient Genetics, Niels Bohr Institute & Biological Institutes, University of Copenhagen Juliane Maries vej 30, DK-2100 Copenhagen, Denmark
*To whom correspondence should be addressed. Tel: +33 476 51 45 24; Fax: +33 476 51 42 79; Email: pierre.taberlet{at}ujf-grenoble.fr
Received June 29, 2006. Revised September 21, 2006. Accepted October 16, 2006.
DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trnL (UAA) intron (254–767 bp) and of a shorter fragment of this intron (the P6 loop, 10–143 bp) amplified with highly conserved primers. The main limitation of the whole trnL intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trnL intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies.
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