DNA barcoding of Mycosphaerella species of quarantine importance to Europe
Identifieur interne : 001360 ( Main/Exploration ); précédent : 001359; suivant : 001361DNA barcoding of Mycosphaerella species of quarantine importance to Europe
Auteurs : W. Quaedvlieg [Pays-Bas] ; J. Z. Groenewald ; M. De Jesús Yá Ez-Morales ; P. W. Crous [Pays-Bas]Source :
- Persoonia : Molecular Phylogeny and Evolution of Fungi [ 0031-5850 ] ; 2012.
Abstract
The EU 7th Framework Program provided funds for Quarantine Barcoding of Life (QBOL) to develop a quick, reliable and accurate DNA barcode-based diagnostic tool for selected species on the European and Mediterranean Plant Protection Organization (EPPO) A1/A2 quarantine lists. Seven nuclear genomic loci were evaluated to determine those best suited for identifying species of
Url:
DOI: 10.3767/003158512X661282
PubMed: 23606768
PubMed Central: 3589787
Affiliations:
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Quaedvlieg</name><affiliation><nlm:aff id="A1"> CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; corresponding author e-mail:<email>w.quaedvlieg@cbs.knaw.nl</email>.</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="A2"> Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea> Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht</wicri:regionArea><orgName type="university">Université d'Utrecht</orgName><placeName><settlement type="city">Utrecht</settlement><region nuts="2">Utrecht (province)</region></placeName></affiliation></author><author><name sortKey="Groenewald, J Z" sort="Groenewald, J Z" uniqKey="Groenewald J" first="J. Z." last="Groenewald">J. Z. Groenewald</name><affiliation><nlm:aff id="A1"> CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; corresponding author e-mail:<email>w.quaedvlieg@cbs.knaw.nl</email>.</nlm:aff></affiliation></author><author><name sortKey="De Jesus Ya Ez Morales, M" sort="De Jesus Ya Ez Morales, M" uniqKey="De Jesus Ya Ez Morales M" first="M." last="De Jesús Yá Ez-Morales">M. De Jesús Yá Ez-Morales</name></author><author><name sortKey="Crous, P W" sort="Crous, P W" uniqKey="Crous P" first="P. W." last="Crous">P. W. Crous</name><affiliation><nlm:aff id="A1"> CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; corresponding author e-mail:<email>w.quaedvlieg@cbs.knaw.nl</email>.</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="A2"> Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea> Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht</wicri:regionArea><orgName type="university">Université d'Utrecht</orgName><placeName><settlement type="city">Utrecht</settlement><region nuts="2">Utrecht (province)</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A4"> Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea> Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen</wicri:regionArea><wicri:noRegion>6708 PB Wageningen</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23606768</idno><idno type="pmc">3589787</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589787</idno><idno type="RBID">PMC:3589787</idno><idno type="doi">10.3767/003158512X661282</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">001238</idno><idno type="wicri:Area/Pmc/Curation">001237</idno><idno type="wicri:Area/Pmc/Checkpoint">000D33</idno><idno type="wicri:Area/Ncbi/Merge">001281</idno><idno type="wicri:Area/Ncbi/Curation">001281</idno><idno type="wicri:Area/Ncbi/Checkpoint">001281</idno><idno type="wicri:doubleKey">0031-5850:2012:Quaedvlieg W:dna:barcoding:of</idno><idno type="wicri:Area/Main/Merge">001375</idno><idno type="wicri:Area/Main/Curation">001360</idno><idno type="wicri:Area/Main/Exploration">001360</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">DNA barcoding of <italic>Mycosphaerella</italic> species of quarantine importance to Europe</title><author><name sortKey="Quaedvlieg, W" sort="Quaedvlieg, W" uniqKey="Quaedvlieg W" first="W." last="Quaedvlieg">W. Quaedvlieg</name><affiliation><nlm:aff id="A1"> CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; corresponding author e-mail:<email>w.quaedvlieg@cbs.knaw.nl</email>.</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="A2"> Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea> Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht</wicri:regionArea><orgName type="university">Université d'Utrecht</orgName><placeName><settlement type="city">Utrecht</settlement><region nuts="2">Utrecht (province)</region></placeName></affiliation></author><author><name sortKey="Groenewald, J Z" sort="Groenewald, J Z" uniqKey="Groenewald J" first="J. Z." last="Groenewald">J. Z. Groenewald</name><affiliation><nlm:aff id="A1"> CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; corresponding author e-mail:<email>w.quaedvlieg@cbs.knaw.nl</email>.</nlm:aff></affiliation></author><author><name sortKey="De Jesus Ya Ez Morales, M" sort="De Jesus Ya Ez Morales, M" uniqKey="De Jesus Ya Ez Morales M" first="M." last="De Jesús Yá Ez-Morales">M. De Jesús Yá Ez-Morales</name></author><author><name sortKey="Crous, P W" sort="Crous, P W" uniqKey="Crous P" first="P. W." last="Crous">P. W. Crous</name><affiliation><nlm:aff id="A1"> CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; corresponding author e-mail:<email>w.quaedvlieg@cbs.knaw.nl</email>.</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="A2"> Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea> Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht</wicri:regionArea><orgName type="university">Université d'Utrecht</orgName><placeName><settlement type="city">Utrecht</settlement><region nuts="2">Utrecht (province)</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A4"> Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea> Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen</wicri:regionArea><wicri:noRegion>6708 PB Wageningen</wicri:noRegion></affiliation></author></analytic><series><title level="j">Persoonia : Molecular Phylogeny and Evolution of Fungi</title><idno type="ISSN">0031-5850</idno><idno type="eISSN">1878-9080</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The EU 7th Framework Program provided funds for Quarantine Barcoding of Life (QBOL) to develop a quick, reliable and accurate DNA barcode-based diagnostic tool for selected species on the European and Mediterranean Plant Protection Organization (EPPO) A1/A2 quarantine lists. Seven nuclear genomic loci were evaluated to determine those best suited for identifying species of <italic>Mycosphaerella</italic> and/or its associated anamorphs. These genes included β-tubulin (Btub), internal transcribed spacer regions of the nrDNA operon (ITS), 28S nrDNA (LSU), Actin (Act), Calmodulin (Cal), Translation elongation factor 1-alpha (EF-1α) and RNA polymerase II second largest subunit (RPB2). Loci were tested on their Kimura-2-parameter-based inter- and intraspecific variation, PCR amplification success rate and ability to distinguish between quarantine species and closely related taxa. Results showed that none of these loci was solely suited as a reliable barcoding locus for the tested fungi. A combination of a primary and secondary barcoding locus was found to compensate for individual weaknesses and provide reliable identification. A combination of ITS with either EF-1α or Btub was reliable as barcoding loci for EPPO A1/A2-listed <italic>Mycosphaerella</italic> species. Furthermore, <italic>Lecanosticta acicola</italic> was shown to represent a species complex, revealing two novel species described here, namely <italic>L. brevispora</italic> sp. nov. on <italic>Pinus</italic> sp. from Mexico and <italic>L. guatemalensis</italic> sp. nov. on <italic>Pinus oocarpa</italic> from Guatemala. Epitypes were also designated for <italic>L. acicola</italic> and <italic>L. longispora</italic> to resolve the genetic application of these names.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Barnes, I" uniqKey="Barnes I">I Barnes</name></author><author><name sortKey="Crous, Pw" uniqKey="Crous P">PW Crous</name></author><author><name sortKey="Wingfield, Bd" uniqKey="Wingfield B">BD Wingfield</name></author><author><name sortKey="Wingfield, Mj" uniqKey="Wingfield M">MJ Wingfield</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bier, Je" uniqKey="Bier J">JE Bier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bonants, P" uniqKey="Bonants P">P Bonants</name></author><author><name sortKey="Groenewald, E" uniqKey="Groenewald E">E Groenewald</name></author><author><name sortKey="Rasplus, Jy" uniqKey="Rasplus J">JY Rasplus</name></author><author><name 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uniqKey="Verkley G">GJM Verkley</name></author><author><name sortKey="Seifbarghi, S" uniqKey="Seifbarghi S">S Seifbarghi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rayner, Rw" uniqKey="Rayner R">RW Rayner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schoch, Cl" uniqKey="Schoch C">CL Schoch</name></author><author><name sortKey="Seifert, Ka" uniqKey="Seifert K">KA Seifert</name></author><author><name sortKey="Huhndorf, S" uniqKey="Huhndorf S">S Huhndorf</name></author><author><name sortKey="Robert, V" uniqKey="Robert V">V Robert</name></author><author><name sortKey="Spouge, Jl" uniqKey="Spouge J">JL Spouge</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schubert, K" uniqKey="Schubert K">K Schubert</name></author><author><name sortKey="Groenewald, Jz" uniqKey="Groenewald J">JZ Groenewald</name></author><author><name sortKey="Braun, U" uniqKey="Braun U">U Braun</name></author><author><name sortKey="Dijksterhuis, J" uniqKey="Dijksterhuis J">J Dijksterhuis</name></author><author><name sortKey="Starink, Ms" uniqKey="Starink M">MS Starink</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stevenson, Wr" uniqKey="Stevenson W">WR Stevenson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stukenbrock, Eh" uniqKey="Stukenbrock E">EH Stukenbrock</name></author><author><name sortKey="Quaedvlieg, W" uniqKey="Quaedvlieg W">W Quaedvlieg</name></author><author><name sortKey="Javan Nikhah, M" uniqKey="Javan Nikhah M">M Javan-Nikhah</name></author><author><name sortKey="Zala, M" uniqKey="Zala M">M Zala</name></author><author><name sortKey="Crous, Pw" uniqKey="Crous P">PW Crous</name></author><author><name sortKey="Mcdonald, Ba" uniqKey="Mcdonald B">BA McDonald</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K Tamura</name></author><author><name sortKey="Dudley, J" uniqKey="Dudley J">J Dudley</name></author><author><name sortKey="Nei, M" uniqKey="Nei M">M Nei</name></author><author><name sortKey="Kumar, S" uniqKey="Kumar S">S Kumar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Timmer, Lw" uniqKey="Timmer L">LW Timmer</name></author><author><name sortKey="Garnsey, Sm" uniqKey="Garnsey S">SM Garnsey</name></author><author><name sortKey="Graham, Jh" uniqKey="Graham J">JH Graham</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Verkley, Gjm" uniqKey="Verkley G">GJM Verkley</name></author><author><name sortKey="Starink Willemse, M" uniqKey="Starink Willemse M">M Starink-Willemse</name></author><author><name sortKey="Iperen, A Van" uniqKey="Iperen A">A van Iperen</name></author><author><name sortKey="Abeln, Eca" uniqKey="Abeln E">ECA Abeln</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vilgalys, R" uniqKey="Vilgalys R">R Vilgalys</name></author><author><name sortKey="Hester, M" uniqKey="Hester M">M Hester</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Waterman, Am" uniqKey="Waterman A">AM Waterman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="White, Tj" uniqKey="White T">TJ White</name></author><author><name sortKey="Bruns, T" uniqKey="Bruns T">T Bruns</name></author><author><name sortKey="Lee, S" uniqKey="Lee S">S Lee</name></author><author><name sortKey="Taylor, Jw" uniqKey="Taylor J">JW Taylor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wingfield, Mj" uniqKey="Wingfield M">MJ Wingfield</name></author><author><name sortKey="Beer, Zw De" uniqKey="Beer Z">ZW de Beer</name></author><author><name sortKey="Slippers, B" uniqKey="Slippers B">B Slippers</name></author><author><name sortKey="Wingfield, Bd" uniqKey="Wingfield B">BD Wingfield</name></author><author><name sortKey="Groenewald, Jz" uniqKey="Groenewald J">JZ Groenewald</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Pays-Bas</li></country><region><li>Utrecht (province)</li></region><settlement><li>Utrecht</li></settlement><orgName><li>Université d'Utrecht</li></orgName></list><tree><noCountry><name sortKey="De Jesus Ya Ez Morales, M" sort="De Jesus Ya Ez Morales, M" uniqKey="De Jesus Ya Ez Morales M" first="M." last="De Jesús Yá Ez-Morales">M. De Jesús Yá Ez-Morales</name><name sortKey="Groenewald, J Z" sort="Groenewald, J Z" uniqKey="Groenewald J" first="J. Z." last="Groenewald">J. Z. Groenewald</name></noCountry><country name="Pays-Bas"><region name="Utrecht (province)"><name sortKey="Quaedvlieg, W" sort="Quaedvlieg, W" uniqKey="Quaedvlieg W" first="W." last="Quaedvlieg">W. Quaedvlieg</name></region><name sortKey="Crous, P W" sort="Crous, P W" uniqKey="Crous P" first="P. W." last="Crous">P. W. Crous</name><name sortKey="Crous, P W" sort="Crous, P W" uniqKey="Crous P" first="P. W." last="Crous">P. W. Crous</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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