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

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 trn L (UAA) intron (254–767 bp)...

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Published in:Nucleic Acids Research
Main Authors: Taberlet, Pierre, Coissac, Eric, Pompanon, François, Gielly, Ludovic, Miquel, Christian, Valentini, Alice, Vermat, Thierry, Corthier, Gérard, Brochmann, Christian, Willerslev, Eske
Format: Text
Language:English
Published: Oxford University Press 2007
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Online Access:http://nar.oxfordjournals.org/cgi/content/short/35/3/e14
https://doi.org/10.1093/nar/gkl938
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spelling fthighwire:oai:open-archive.highwire.org:nar:35/3/e14 2023-05-15T17:57:53+02:00 Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding Taberlet, Pierre Coissac, Eric Pompanon, François Gielly, Ludovic Miquel, Christian Valentini, Alice Vermat, Thierry Corthier, Gérard Brochmann, Christian Willerslev, Eske 2007-02-16 00:00:00.0 text/html http://nar.oxfordjournals.org/cgi/content/short/35/3/e14 https://doi.org/10.1093/nar/gkl938 en eng Oxford University Press http://nar.oxfordjournals.org/cgi/content/short/35/3/e14 http://dx.doi.org/10.1093/nar/gkl938 Copyright (C) 2007, Oxford University Press Methods Online TEXT 2007 fthighwire https://doi.org/10.1093/nar/gkl938 2013-05-26T16:01:10Z 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 trn L (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 trn L 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 trn L 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. Text permafrost HighWire Press (Stanford University) Nucleic Acids Research 35 3 e14 e14
institution Open Polar
collection HighWire Press (Stanford University)
op_collection_id fthighwire
language English
topic Methods Online
spellingShingle Methods Online
Taberlet, Pierre
Coissac, Eric
Pompanon, François
Gielly, Ludovic
Miquel, Christian
Valentini, Alice
Vermat, Thierry
Corthier, Gérard
Brochmann, Christian
Willerslev, Eske
Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding
topic_facet Methods Online
description 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 trn L (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 trn L 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 trn L 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.
format Text
author Taberlet, Pierre
Coissac, Eric
Pompanon, François
Gielly, Ludovic
Miquel, Christian
Valentini, Alice
Vermat, Thierry
Corthier, Gérard
Brochmann, Christian
Willerslev, Eske
author_facet Taberlet, Pierre
Coissac, Eric
Pompanon, François
Gielly, Ludovic
Miquel, Christian
Valentini, Alice
Vermat, Thierry
Corthier, Gérard
Brochmann, Christian
Willerslev, Eske
author_sort Taberlet, Pierre
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 Oxford University Press
publishDate 2007
url http://nar.oxfordjournals.org/cgi/content/short/35/3/e14
https://doi.org/10.1093/nar/gkl938
genre permafrost
genre_facet permafrost
op_relation http://nar.oxfordjournals.org/cgi/content/short/35/3/e14
http://dx.doi.org/10.1093/nar/gkl938
op_rights Copyright (C) 2007, Oxford University Press
op_doi https://doi.org/10.1093/nar/gkl938
container_title Nucleic Acids Research
container_volume 35
container_issue 3
container_start_page e14
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