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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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 |
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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 |
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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 |
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35 |
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3 |
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e14 |
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e14 |
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1766166389452701696 |