Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle
Identifieur interne : 000743 ( Istex/Corpus ); précédent : 000742; suivant : 000744Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle
Auteurs : Amanda D. Roe ; Adrianne V. Rice ; Sean E. Bromilow ; Janice E. K. Cooke ; Felix A. H. SperlingSource :
- Molecular Ecology Resources [ 1755-098X ] ; 2010-11.
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Abstract
There is strong community‐wide interest in applying molecular techniques to fungal species delimitation and identification, but selection of a standardized region or regions of the genome has not been finalized. A single marker, the ribosomal DNA internal transcribed spacer region, has frequently been suggested as the standard for fungi. We used a group of closely related blue stain fungi associated with the mountain pine beetle (Dendroctonus ponderosae Hopkins) to examine the success of such single‐locus species identification, comparing the internal transcribed spacer with four other nuclear markers. We demonstrate that single loci varied in their utility for identifying the six fungal species examined, while use of multiple loci was consistently successful. In a literature survey of 21 similar studies, individual loci were also highly variable in their ability to provide consistent species identifications and were less successful than multilocus diagnostics. Accurate species identification is the essence of any molecular diagnostic system, and this consideration should be central to locus selection. Moreover, our study and the literature survey demonstrate the value of using closely related species as the proving ground for developing a molecular identification system. We advocate use of a multilocus barcode approach that is similar to the practice employed by the plant barcode community, rather than reliance on a single locus.
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DOI: 10.1111/j.1755-0998.2010.02844.x
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A single marker, the ribosomal DNA internal transcribed spacer region, has frequently been suggested as the standard for fungi. We used a group of closely related blue stain fungi associated with the mountain pine beetle (Dendroctonus ponderosae Hopkins) to examine the success of such single‐locus species identification, comparing the internal transcribed spacer with four other nuclear markers. We demonstrate that single loci varied in their utility for identifying the six fungal species examined, while use of multiple loci was consistently successful. In a literature survey of 21 similar studies, individual loci were also highly variable in their ability to provide consistent species identifications and were less successful than multilocus diagnostics. Accurate species identification is the essence of any molecular diagnostic system, and this consideration should be central to locus selection. Moreover, our study and the literature survey demonstrate the value of using closely related species as the proving ground for developing a molecular identification system. We advocate use of a multilocus barcode approach that is similar to the practice employed by the plant barcode community, rather than reliance on a single locus.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>AMANDA D. ROE</name><affiliations><json:string>CW 405 – Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada</json:string></affiliations></json:item><json:item><name>ADRIANNE V. RICE</name><affiliations><json:string>CW 405 – Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada</json:string></affiliations></json:item><json:item><name>SEAN E. 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A single marker, the ribosomal DNA internal transcribed spacer region, has frequently been suggested as the standard for fungi. We used a group of closely related blue stain fungi associated with the mountain pine beetle (Dendroctonus ponderosae Hopkins) to examine the success of such single‐locus species identification, comparing the internal transcribed spacer with four other nuclear markers. We demonstrate that single loci varied in their utility for identifying the six fungal species examined, while use of multiple loci was consistently successful. In a literature survey of 21 similar studies, individual loci were also highly variable in their ability to provide consistent species identifications and were less successful than multilocus diagnostics. Accurate species identification is the essence of any molecular diagnostic system, and this consideration should be central to locus selection. Moreover, our study and the literature survey demonstrate the value of using closely related species as the proving ground for developing a molecular identification system. We advocate use of a multilocus barcode approach that is similar to the practice employed by the plant barcode community, rather than reliance on a single locus.</p></abstract><textClass xml:lang="en"><keywords scheme="keyword"><list><head>keywords</head><item><term>Dendroctonus ponderosae</term></item><item><term>DNA barcoding</term></item><item><term>fungi</term></item><item><term>identification</term></item><item><term>molecular diagnostics</term></item><item><term>Ophiostomataceae</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2010-11">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/A8C5866F05A723AE688565A1247329A2FA98C1EB/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Publishing Ltd</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1755-0998</doi><issn type="print">1755-098X</issn><issn type="electronic">1755-0998</issn><idGroup><id type="product" value="MEN"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="MOLECULAR ECOLOGY RESOURCES">Molecular Ecology Resources</title></titleGroup></publicationMeta><publicationMeta level="part" position="11106"><doi origin="wiley">10.1111/men.2010.10.issue-6</doi><numberingGroup><numbering type="journalVolume" number="10">10</numbering><numbering type="journalIssue" number="6">6</numbering></numberingGroup><coverDate startDate="2010-11">November 2010</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="4" status="forIssue"><doi origin="wiley">10.1111/j.1755-0998.2010.02844.x</doi><idGroup><id type="unit" value="MEN2844"></id></idGroup><countGroup><count type="pageTotal" number="14"></count></countGroup><titleGroup><title type="tocHeading1">DNA BARCODING</title></titleGroup><copyright>© 2010 Blackwell Publishing Ltd</copyright><eventGroup><event type="firstOnline" date="2010-03-08"></event><event type="publishedOnlineAcceptedOrEarlyUnpaginated" date="2010-03-08"></event><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:2.10 mode:FullText" date="2011-09-22"></event><event type="publishedOnlineFinalForm" date="2010-03-08"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:4.0.1" date="2014-03-20"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.1.7 mode:FullText,remove_FC" date="2014-10-31"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="946">946</numbering><numbering type="pageLast" number="959">959</numbering></numberingGroup><correspondenceTo>Amanda D. Roe, Fax: 780 492 9234; E‐mail: <email>amandaroe5@gmail.com</email></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:MEN.MEN2844.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 28 October 2009; revision received 10 January 2010; accepted 24 January 2010</unparsedEditorialHistory><countGroup><count type="figureTotal" number="6"></count><count type="tableTotal" number="3"></count></countGroup><titleGroup><title type="main">Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle</title><title type="short">DNA BARCODING</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#aff-1-1"><personName><givenNames>AMANDA D.</givenNames><familyName>ROE</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#aff-1-1"><personName><givenNames>ADRIANNE V.</givenNames><familyName>RICE</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#aff-1-1"><personName><givenNames>SEAN E.</givenNames><familyName>BROMILOW</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#aff-1-1"><personName><givenNames>JANICE E. K.</givenNames><familyName>COOKE</familyName></personName></creator><creator creatorRole="author" xml:id="cr5" affiliationRef="#aff-1-1"><personName><givenNames>FELIX A. H.</givenNames><familyName>SPERLING</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="aff-1-1" countryCode="CA"><unparsedAffiliation>CW 405 – Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada</unparsedAffiliation></affiliation></affiliationGroup><keywordGroup xml:lang="en"><keyword xml:id="k1"><i>Dendroctonus ponderosae</i></keyword><keyword xml:id="k2">DNA barcoding</keyword><keyword xml:id="k3">fungi</keyword><keyword xml:id="k4">identification</keyword><keyword xml:id="k5">molecular diagnostics</keyword><keyword xml:id="k6">Ophiostomataceae</keyword></keywordGroup><supportingInformation><p><b>Appendix S1</b> Table of specimen collection data, voucher information, and haplotype assignments.</p><p><b>Appendix S2</b> Representative GenBank sequences from closely related <i>Grosmannia</i> species.</p><p><b>Appendix S3</b> Literature survey of multilocus data for pairs of closely related ascomycete fungi (methodology described in Materials and Methods).</p><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:1755098X:media:men2844:MEN_2844_sm_Appendix1"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:1755098X:media:men2844:MEN_2844_sm_Appendix2"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:1755098X:media:men2844:MEN_2844_sm_Appendix3"></mediaResource><caption>Supporting info item</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title><p>There is strong community‐wide interest in applying molecular techniques to fungal species delimitation and identification, but selection of a standardized region or regions of the genome has not been finalized. A single marker, the ribosomal DNA internal transcribed spacer region, has frequently been suggested as the standard for fungi. We used a group of closely related blue stain fungi associated with the mountain pine beetle (<i>Dendroctonus ponderosae</i> Hopkins) to examine the success of such single‐locus species identification, comparing the internal transcribed spacer with four other nuclear markers. We demonstrate that single loci varied in their utility for identifying the six fungal species examined, while use of multiple loci was consistently successful. In a literature survey of 21 similar studies, individual loci were also highly variable in their ability to provide consistent species identifications and were less successful than multilocus diagnostics. Accurate species identification is the essence of any molecular diagnostic system, and this consideration should be central to locus selection. Moreover, our study and the literature survey demonstrate the value of using closely related species as the proving ground for developing a molecular identification system. We advocate use of a multilocus barcode approach that is similar to the practice employed by the plant barcode community, rather than reliance on a single locus.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>DNA BARCODING</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle</title></titleInfo><name type="personal"><namePart type="given">AMANDA D.</namePart><namePart type="family">ROE</namePart><affiliation>CW 405 – Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">ADRIANNE V.</namePart><namePart type="family">RICE</namePart><affiliation>CW 405 – Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">SEAN E.</namePart><namePart type="family">BROMILOW</namePart><affiliation>CW 405 – Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">JANICE E. K.</namePart><namePart type="family">COOKE</namePart><affiliation>CW 405 – Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">FELIX A. H.</namePart><namePart type="family">SPERLING</namePart><affiliation>CW 405 – Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article"></genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2010-11</dateIssued><edition>Received 28 October 2009; revision received 10 January 2010; accepted 24 January 2010</edition><copyrightDate encoding="w3cdtf">2010</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType><extent unit="figures">6</extent><extent unit="tables">3</extent></physicalDescription><abstract lang="en">There is strong community‐wide interest in applying molecular techniques to fungal species delimitation and identification, but selection of a standardized region or regions of the genome has not been finalized. A single marker, the ribosomal DNA internal transcribed spacer region, has frequently been suggested as the standard for fungi. We used a group of closely related blue stain fungi associated with the mountain pine beetle (Dendroctonus ponderosae Hopkins) to examine the success of such single‐locus species identification, comparing the internal transcribed spacer with four other nuclear markers. We demonstrate that single loci varied in their utility for identifying the six fungal species examined, while use of multiple loci was consistently successful. In a literature survey of 21 similar studies, individual loci were also highly variable in their ability to provide consistent species identifications and were less successful than multilocus diagnostics. Accurate species identification is the essence of any molecular diagnostic system, and this consideration should be central to locus selection. Moreover, our study and the literature survey demonstrate the value of using closely related species as the proving ground for developing a molecular identification system. We advocate use of a multilocus barcode approach that is similar to the practice employed by the plant barcode community, rather than reliance on a single locus.</abstract><subject lang="en"><genre>keywords</genre><topic>Dendroctonus ponderosae</topic><topic>DNA barcoding</topic><topic>fungi</topic><topic>identification</topic><topic>molecular diagnostics</topic><topic>Ophiostomataceae</topic></subject><relatedItem type="host"><titleInfo><title>Molecular Ecology Resources</title></titleInfo><genre type="journal">journal</genre><note type="content"> Appendix S1 Table of specimen collection data, voucher information, and haplotype assignments. Appendix S2 Representative GenBank sequences from closely related Grosmannia species. Appendix S3 Literature survey of multilocus data for pairs of closely related ascomycete fungi (methodology described in Materials and Methods). Appendix S1 Table of specimen collection data, voucher information, and haplotype assignments. Appendix S2 Representative GenBank sequences from closely related Grosmannia species. Appendix S3 Literature survey of multilocus data for pairs of closely related ascomycete fungi (methodology described in Materials and Methods). Appendix S1 Table of specimen collection data, voucher information, and haplotype assignments. Appendix S2 Representative GenBank sequences from closely related Grosmannia species. Appendix S3 Literature survey of multilocus data for pairs of closely related ascomycete fungi (methodology described in Materials and Methods).Supporting Info Item: Supporting info item - Supporting info item - Supporting info item - </note><identifier type="ISSN">1755-098X</identifier><identifier type="eISSN">1755-0998</identifier><identifier type="DOI">10.1111/(ISSN)1755-0998</identifier><identifier type="PublisherID">MEN</identifier><part><date>2010</date><detail type="volume"><caption>vol.</caption><number>10</number></detail><detail type="issue"><caption>no.</caption><number>6</number></detail><extent unit="pages"><start>946</start><end>959</end><total>14</total></extent></part></relatedItem><identifier type="istex">A8C5866F05A723AE688565A1247329A2FA98C1EB</identifier><identifier type="DOI">10.1111/j.1755-0998.2010.02844.x</identifier><identifier type="ArticleID">MEN2844</identifier><accessCondition type="use and reproduction" contentType="copyright">© 2010 Blackwell Publishing Ltd</accessCondition><recordInfo><recordContentSource>WILEY</recordContentSource><recordOrigin>Blackwell Publishing Ltd</recordOrigin></recordInfo></mods></metadata><enrichments><json:item><type>multicat</type><uri>https://api.istex.fr/document/A8C5866F05A723AE688565A1247329A2FA98C1EB/enrichments/multicat</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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