DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match.
Identifieur interne : 003704 ( PubMed/Checkpoint ); précédent : 003703; suivant : 003705DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match.
Auteurs : Bruce E. Deagle [Australie] ; Simon N. Jarman [Australie] ; Eric Coissac [France] ; François Pompanon [France] ; Pierre Taberlet [France]Source :
- Biology letters [ 1744-957X ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA Primers, Electron Transport Complex IV.
- methods : DNA Barcoding, Taxonomic, Sequence Analysis, DNA.
- Animals, Biodiversity, Species Specificity.
Abstract
DNA metabarcoding enables efficient characterization of species composition in environmental DNA or bulk biodiversity samples, and this approach is making significant and unique contributions in the field of ecology. In metabarcoding of animals, the cytochrome c oxidase subunit I (COI) gene is frequently used as the marker of choice because no other genetic region can be found in taxonomically verified databases with sequences covering so many taxa. However, the accuracy of metabarcoding datasets is dependent on recovery of the targeted taxa using conserved amplification primers. We argue that COI does not contain suitably conserved regions for most amplicon-based metabarcoding applications. Marker selection deserves increased scrutiny and available marker choices should be broadened in order to maximize potential in this exciting field of research.
DOI: 10.1098/rsbl.2014.0562
PubMed: 25209199
Affiliations:
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pubmed:25209199Le document en format XML
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Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine, F-38000 Grenoble, France Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine, F-38000 Grenoble</wicri:regionArea><wicri:noRegion>38000 Grenoble</wicri:noRegion><orgName type="university">Université Grenoble-Alpes</orgName><placeName><settlement type="city">Grenoble</settlement><region type="region" nuts="2">Auvergne-Rhône-Alpes</region><region type="old region" nuts="2">Rhône-Alpes</region></placeName></affiliation></author></analytic><series><title level="j">Biology letters</title><idno type="eISSN">1744-957X</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Biodiversity</term><term>DNA Barcoding, Taxonomic (methods)</term><term>DNA Primers (genetics)</term><term>Electron Transport Complex IV (genetics)</term><term>Sequence Analysis, DNA (methods)</term><term>Species Specificity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Amorces ADN (génétique)</term><term>Analyse de séquence d'ADN ()</term><term>Animaux</term><term>Biodiversité</term><term>Codage à barres de l'ADN pour la taxonomie ()</term><term>Complexe IV de la chaîne respiratoire (génétique)</term><term>Spécificité d'espèce</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA Primers</term><term>Electron Transport Complex IV</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Amorces ADN</term><term>Complexe IV de la chaîne respiratoire</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>DNA Barcoding, Taxonomic</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Biodiversity</term><term>Species 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In metabarcoding of animals, the cytochrome c oxidase subunit I (COI) gene is frequently used as the marker of choice because no other genetic region can be found in taxonomically verified databases with sequences covering so many taxa. However, the accuracy of metabarcoding datasets is dependent on recovery of the targeted taxa using conserved amplification primers. We argue that COI does not contain suitably conserved regions for most amplicon-based metabarcoding applications. Marker selection deserves increased scrutiny and available marker choices should be broadened in order to maximize potential in this exciting field of research.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25209199</PMID><DateCreated><Year>2014</Year><Month>09</Month><Day>11</Day></DateCreated><DateCompleted><Year>2015</Year><Month>05</Month><Day>19</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1744-957X</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>9</Issue><PubDate><Year>2014</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Biology letters</Title><ISOAbbreviation>Biol. Lett.</ISOAbbreviation></Journal><ArticleTitle>DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1098/rsbl.2014.0562</ELocationID><ELocationID EIdType="pii" ValidYN="Y">20140562</ELocationID><Abstract><AbstractText>DNA metabarcoding enables efficient characterization of species composition in environmental DNA or bulk biodiversity samples, and this approach is making significant and unique contributions in the field of ecology. In metabarcoding of animals, the cytochrome c oxidase subunit I (COI) gene is frequently used as the marker of choice because no other genetic region can be found in taxonomically verified databases with sequences covering so many taxa. However, the accuracy of metabarcoding datasets is dependent on recovery of the targeted taxa using conserved amplification primers. We argue that COI does not contain suitably conserved regions for most amplicon-based metabarcoding applications. Marker selection deserves increased scrutiny and available marker choices should be broadened in order to maximize potential in this exciting field of research.</AbstractText><CopyrightInformation>© 2014 The Author(s) Published by the Royal Society. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Deagle</LastName><ForeName>Bruce E</ForeName><Initials>BE</Initials><AffiliationInfo><Affiliation>203, Channel Highway, Kingston, Tasmania, Australia bruce.deagle@aad.gov.au.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jarman</LastName><ForeName>Simon N</ForeName><Initials>SN</Initials><AffiliationInfo><Affiliation>203, Channel Highway, Kingston, Tasmania, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Coissac</LastName><ForeName>Eric</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine, F-38000 Grenoble, France Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine, F-38000 Grenoble, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pompanon</LastName><ForeName>François</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine, F-38000 Grenoble, France Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine, F-38000 Grenoble, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Taberlet</LastName><ForeName>Pierre</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine, F-38000 Grenoble, France Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine, F-38000 Grenoble, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Biol Lett</MedlineTA><NlmUniqueID>101247722</NlmUniqueID><ISSNLinking>1744-9561</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D017931">DNA Primers</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.9.3.1</RegistryNumber><NameOfSubstance UI="D003576">Electron Transport Complex IV</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Appl Environ Microbiol. 2008 Mar;74(5):1660-3</RefSource><PMID Version="1">18192413</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Ecol Resour. 2014 Nov;14(6):1160-70</RefSource><PMID Version="1">24751203</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Genomics. 2010;11:434</RefSource><PMID Version="1">20637073</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2013 Jan 7;41(1):e1</RefSource><PMID Version="1">22933715</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Ecol Resour. 2014 Mar;14(2):306-23</RefSource><PMID Version="1">24128180</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>PLoS One. 2011;6(8):e20552</RefSource><PMID Version="1">21857897</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Ecol Lett. 2013 Oct;16(10):1245-57</RefSource><PMID Version="1">23910579</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>PLoS One. 2011;6(12):e27310</RefSource><PMID Version="1">22194782</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Ecol Resour. 2014 Sep;14(5):892-901</RefSource><PMID Version="1">24641208</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Front Zool. 2013 Jun 14;10:34</RefSource><PMID Version="1">23767809</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Ecol Resour. 2013 Sep;13(5):851-61</RefSource><PMID Version="1">23848937</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Gigascience. 2013 Mar 27;2(1):4</RefSource><PMID Version="1">23587339</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Ecol. 2012 Apr;21(8):1789-93</RefSource><PMID Version="1">22486819</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Ecol. 2009 May;18(9):2022-38</RefSource><PMID Version="1">19317847</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D044822" MajorTopicYN="N">Biodiversity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058893" MajorTopicYN="N">DNA Barcoding, 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Grenoble-Alpes</li></orgName></list><tree><country name="Australie"><noRegion><name sortKey="Deagle, Bruce E" sort="Deagle, Bruce E" uniqKey="Deagle B" first="Bruce E" last="Deagle">Bruce E. Deagle</name></noRegion><name sortKey="Jarman, Simon N" sort="Jarman, Simon N" uniqKey="Jarman S" first="Simon N" last="Jarman">Simon N. Jarman</name></country><country name="France"><region name="Auvergne-Rhône-Alpes"><name sortKey="Coissac, Eric" sort="Coissac, Eric" uniqKey="Coissac E" first="Eric" last="Coissac">Eric Coissac</name></region><name sortKey="Pompanon, Francois" sort="Pompanon, Francois" uniqKey="Pompanon F" first="François" last="Pompanon">François Pompanon</name><name sortKey="Taberlet, Pierre" sort="Taberlet, Pierre" uniqKey="Taberlet P" first="Pierre" last="Taberlet">Pierre Taberlet</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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