Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding

• Published in: Nucleic Acids Research
• Main Authors: Taberlet, P., Coissac, Eric, Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., Corthier, G., Brochmann, C., Willerslev, E.
• Other Authors: Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry ), Computer science and genomics (HELIX), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Ecologia e Sviluppo Economico Sostenibile (DECOS), Università degli studi della Tuscia Viterbo, Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences (NMBU), GENOME Express (GENOME Express), GENOME Express, Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), National Centre for Biosystematics (NCB), University of Oslo (UiO), Center for Ancient Genetics, University of Copenhagen = Københavns Universitet (KU)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2007
• Subjects: [SDE.BE]Environmental Sciences/Biodiversity and Ecology; [SDV.BID]Life Sciences [q-bio]/Biodiversity; [SDV.EE]Life Sciences [q-bio]/Ecology; environment; permafrost
• Online Access: https://hal.archives-ouvertes.fr/halsde-00276494; https://hal.archives-ouvertes.fr/halsde-00276494/document; https://hal.archives-ouvertes.fr/halsde-00276494/file/2007_Taberlet_Nucleid%20Acids%20reseach_1.pdf; https://doi.org/10.1093/nar/gkl938

Times Cited: 4 International audience 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.