Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding
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 chloro...
Published in: | Nucleic Acids Research |
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Main Authors: | , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2007
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Subjects: | |
Online Access: | https://hal.science/halsde-00276494 https://hal.science/halsde-00276494/document https://hal.science/halsde-00276494/file/2007_Taberlet_Nucleid%20Acids%20reseach_1.pdf https://doi.org/10.1093/nar/gkl938 |
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HAL Lyon 1 (University Claude Bernard Lyon 1) |
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English |
topic |
[SDE.BE]Environmental Sciences/Biodiversity and Ecology [SDV.BID]Life Sciences [q-bio]/Biodiversity [SDV.EE]Life Sciences [q-bio]/Ecology environment |
spellingShingle |
[SDE.BE]Environmental Sciences/Biodiversity and Ecology [SDV.BID]Life Sciences [q-bio]/Biodiversity [SDV.EE]Life Sciences [q-bio]/Ecology environment Taberlet, P. Coissac, Eric Pompanon, F. Gielly, L. Miquel, C. Valentini, A. Vermat, T. Corthier, G. Brochmann, C. Willerslev, E. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding |
topic_facet |
[SDE.BE]Environmental Sciences/Biodiversity and Ecology [SDV.BID]Life Sciences [q-bio]/Biodiversity [SDV.EE]Life Sciences [q-bio]/Ecology environment |
description |
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. |
author2 |
Laboratoire d'Ecologie Alpine (LECA) Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry )-Centre National de la Recherche Scientifique (CNRS) 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-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 (UCPH) |
format |
Article in Journal/Newspaper |
author |
Taberlet, P. Coissac, Eric Pompanon, F. Gielly, L. Miquel, C. Valentini, A. Vermat, T. Corthier, G. Brochmann, C. Willerslev, E. |
author_facet |
Taberlet, P. Coissac, Eric Pompanon, F. Gielly, L. Miquel, C. Valentini, A. Vermat, T. Corthier, G. Brochmann, C. Willerslev, E. |
author_sort |
Taberlet, P. |
title |
Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding |
title_short |
Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding |
title_full |
Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding |
title_fullStr |
Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding |
title_full_unstemmed |
Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding |
title_sort |
power and limitations of the chloroplast trnl (uaa) intron for plant dna barcoding |
publisher |
HAL CCSD |
publishDate |
2007 |
url |
https://hal.science/halsde-00276494 https://hal.science/halsde-00276494/document https://hal.science/halsde-00276494/file/2007_Taberlet_Nucleid%20Acids%20reseach_1.pdf https://doi.org/10.1093/nar/gkl938 |
genre |
permafrost |
genre_facet |
permafrost |
op_source |
ISSN: 0305-1048 EISSN: 1362-4962 Nucleic Acids Research https://hal.science/halsde-00276494 Nucleic Acids Research, 2007, 35 (3), pp.e14. ⟨10.1093/nar/gkl938⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkl938 info:eu-repo/semantics/altIdentifier/pmid/17169982 halsde-00276494 https://hal.science/halsde-00276494 https://hal.science/halsde-00276494/document https://hal.science/halsde-00276494/file/2007_Taberlet_Nucleid%20Acids%20reseach_1.pdf doi:10.1093/nar/gkl938 PRODINRA: 318411 PUBMED: 17169982 |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1093/nar/gkl938 |
container_title |
Nucleic Acids Research |
container_volume |
35 |
container_issue |
3 |
container_start_page |
e14 |
op_container_end_page |
e14 |
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1802649033112551424 |
spelling |
ftunivlyon1:oai:HAL:halsde-00276494v1 2024-06-23T07:56:08+00:00 Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding Taberlet, P. Coissac, Eric Pompanon, F. Gielly, L. Miquel, C. Valentini, A. Vermat, T. Corthier, G. Brochmann, C. Willerslev, E. Laboratoire d'Ecologie Alpine (LECA) Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry )-Centre National de la Recherche Scientifique (CNRS) 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-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 (UCPH) 2007 https://hal.science/halsde-00276494 https://hal.science/halsde-00276494/document https://hal.science/halsde-00276494/file/2007_Taberlet_Nucleid%20Acids%20reseach_1.pdf https://doi.org/10.1093/nar/gkl938 en eng HAL CCSD Oxford University Press info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkl938 info:eu-repo/semantics/altIdentifier/pmid/17169982 halsde-00276494 https://hal.science/halsde-00276494 https://hal.science/halsde-00276494/document https://hal.science/halsde-00276494/file/2007_Taberlet_Nucleid%20Acids%20reseach_1.pdf doi:10.1093/nar/gkl938 PRODINRA: 318411 PUBMED: 17169982 info:eu-repo/semantics/OpenAccess ISSN: 0305-1048 EISSN: 1362-4962 Nucleic Acids Research https://hal.science/halsde-00276494 Nucleic Acids Research, 2007, 35 (3), pp.e14. ⟨10.1093/nar/gkl938⟩ [SDE.BE]Environmental Sciences/Biodiversity and Ecology [SDV.BID]Life Sciences [q-bio]/Biodiversity [SDV.EE]Life Sciences [q-bio]/Ecology environment info:eu-repo/semantics/article Journal articles 2007 ftunivlyon1 https://doi.org/10.1093/nar/gkl938 2024-05-27T14:39:54Z 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. Article in Journal/Newspaper permafrost HAL Lyon 1 (University Claude Bernard Lyon 1) Nucleic Acids Research 35 3 e14 e14 |