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 trnL (UAA) intron (254–767 bp) a...
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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1807943 http://www.ncbi.nlm.nih.gov/pubmed/17169982 https://doi.org/10.1093/nar/gkl938 |
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ftpubmed:oai:pubmedcentral.nih.gov:1807943 2023-05-15T17:57:49+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 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1807943 http://www.ncbi.nlm.nih.gov/pubmed/17169982 https://doi.org/10.1093/nar/gkl938 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1807943 http://www.ncbi.nlm.nih.gov/pubmed/17169982 http://dx.doi.org/10.1093/nar/gkl938 © 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. CC-BY-NC Methods Online Text 2007 ftpubmed https://doi.org/10.1093/nar/gkl938 2013-08-31T18:03:32Z 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. Text permafrost PubMed Central (PMC) 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 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. |
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://www.ncbi.nlm.nih.gov/pmc/articles/PMC1807943 http://www.ncbi.nlm.nih.gov/pubmed/17169982 https://doi.org/10.1093/nar/gkl938 |
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permafrost |
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permafrost |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1807943 http://www.ncbi.nlm.nih.gov/pubmed/17169982 http://dx.doi.org/10.1093/nar/gkl938 |
op_rights |
© 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. |
op_rightsnorm |
CC-BY-NC |
op_doi |
https://doi.org/10.1093/nar/gkl938 |
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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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1766166319457107968 |