Application of direct PCR in rapid rDNA ITS haplotype determination of the hyperparasitic fungus Sphaeropsis visci (Botryosphaeriaceae)
Identifieur interne : 000B88 ( Main/Exploration ); précédent : 000B87; suivant : 000B89Application of direct PCR in rapid rDNA ITS haplotype determination of the hyperparasitic fungus Sphaeropsis visci (Botryosphaeriaceae)
Auteurs : Ildik Varga [Finlande] ; Péter Poczai [Finlande] ; István Cernák ; Jaakko Hyvönen [Finlande]Source :
- SpringerPlus [ 2193-1801 ] ; 2014.
Abstract
The plant pathogenic fungus,
Most isolates of
The diPCR approach allowed amplification of ITS rRNA gene directly from small amounts of fungal samples without prior DNA extraction. This simple bioassay in plant disease management enables collection of genomic data from fungal plant pathogen populations.
Url:
DOI: 10.1186/2193-1801-3-569
PubMed: 25332869
PubMed Central: 4193967
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Application of direct PCR in rapid rDNA ITS haplotype determination of the hyperparasitic fungus <italic>Sphaeropsis visci</italic> (Botryosphaeriaceae)</title><author><name sortKey="Varga, Ildik" sort="Varga, Ildik" uniqKey="Varga I" first="Ildik" last="Varga">Ildik Varga</name><affiliation wicri:level="4"><nlm:aff id="Aff7">Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, Helsinki, FI-00014 Finland</nlm:aff><orgName type="university">Université d'Helsinki</orgName><country>Finlande</country><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author><author><name sortKey="Poczai, Peter" sort="Poczai, Peter" uniqKey="Poczai P" first="Péter" last="Poczai">Péter Poczai</name><affiliation wicri:level="4"><nlm:aff id="Aff7">Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, Helsinki, FI-00014 Finland</nlm:aff><orgName type="university">Université d'Helsinki</orgName><country>Finlande</country><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="Aff9">Botanical Museum, University of Helsinki, PO Box 7, Helsinki, FI-00014 Finland</nlm:aff><orgName type="university">Université d'Helsinki</orgName><country>Finlande</country><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author><author><name sortKey="Cernak, Istvan" sort="Cernak, Istvan" uniqKey="Cernak I" first="István" last="Cernák">István Cernák</name><affiliation><nlm:aff id="Aff8">Potato Research Centre, Centre of Agricultural Sciences, University of Pannonia, Festetics u. 7, Keszthely, H-8360 Hungary</nlm:aff><wicri:noCountry code="subfield">H-8360 Hungary</wicri:noCountry></affiliation></author><author><name sortKey="Hyvonen, Jaakko" sort="Hyvonen, Jaakko" uniqKey="Hyvonen J" first="Jaakko" last="Hyvönen">Jaakko Hyvönen</name><affiliation wicri:level="4"><nlm:aff id="Aff7">Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, Helsinki, FI-00014 Finland</nlm:aff><orgName type="university">Université d'Helsinki</orgName><country>Finlande</country><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25332869</idno><idno type="pmc">4193967</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4193967</idno><idno type="RBID">PMC:4193967</idno><idno type="doi">10.1186/2193-1801-3-569</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000697</idno><idno type="wicri:Area/Pmc/Curation">000696</idno><idno type="wicri:Area/Pmc/Checkpoint">000898</idno><idno type="wicri:Area/Ncbi/Merge">001872</idno><idno type="wicri:Area/Ncbi/Curation">001872</idno><idno type="wicri:Area/Ncbi/Checkpoint">001872</idno><idno type="wicri:Area/Main/Merge">000B91</idno><idno type="wicri:Area/Main/Curation">000B88</idno><idno type="wicri:Area/Main/Exploration">000B88</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Application of direct PCR in rapid rDNA ITS haplotype determination of the hyperparasitic fungus <italic>Sphaeropsis visci</italic> (Botryosphaeriaceae)</title><author><name sortKey="Varga, Ildik" sort="Varga, Ildik" uniqKey="Varga I" first="Ildik" last="Varga">Ildik Varga</name><affiliation wicri:level="4"><nlm:aff id="Aff7">Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, Helsinki, FI-00014 Finland</nlm:aff><orgName type="university">Université d'Helsinki</orgName><country>Finlande</country><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author><author><name sortKey="Poczai, Peter" sort="Poczai, Peter" uniqKey="Poczai P" first="Péter" last="Poczai">Péter Poczai</name><affiliation wicri:level="4"><nlm:aff id="Aff7">Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, Helsinki, FI-00014 Finland</nlm:aff><orgName type="university">Université d'Helsinki</orgName><country>Finlande</country><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="Aff9">Botanical Museum, University of Helsinki, PO Box 7, Helsinki, FI-00014 Finland</nlm:aff><orgName type="university">Université d'Helsinki</orgName><country>Finlande</country><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author><author><name sortKey="Cernak, Istvan" sort="Cernak, Istvan" uniqKey="Cernak I" first="István" last="Cernák">István Cernák</name><affiliation><nlm:aff id="Aff8">Potato Research Centre, Centre of Agricultural Sciences, University of Pannonia, Festetics u. 7, Keszthely, H-8360 Hungary</nlm:aff><wicri:noCountry code="subfield">H-8360 Hungary</wicri:noCountry></affiliation></author><author><name sortKey="Hyvonen, Jaakko" sort="Hyvonen, Jaakko" uniqKey="Hyvonen J" first="Jaakko" last="Hyvönen">Jaakko Hyvönen</name><affiliation wicri:level="4"><nlm:aff id="Aff7">Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, Helsinki, FI-00014 Finland</nlm:aff><orgName type="university">Université d'Helsinki</orgName><country>Finlande</country><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author></analytic><series><title level="j">SpringerPlus</title><idno type="eISSN">2193-1801</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The plant pathogenic fungus, <italic>Sphaeropsis visci</italic> a dark-spored species of Botryosphaeriaceae, which causes the leaf spot disease of the European mistletoe (<italic>Viscum album</italic>). This species seems to have potential as a tool for biological control of the hemiparasite. For the rapid detection of <italic>S. visci</italic> haplotypes we tested a direct PCR assay without prior DNA purification. This approach was based on a polymerase enzyme from the crenarchaeon <italic>Sulfolobus solfataricus</italic> engineered by fusion protein technology, which linked the polymerase domain to a sequence non-specific DNA binding protein (Sso7d)<italic>.</italic></p></sec><sec><title>Findings</title><p>Most isolates of <italic>Sphaeropsis visci</italic> grouped together in our phylogenetic analyses, indicating that isolates had a previously reported haplotype sequence, which is commonly found in the analyzed Hungarian population. This haplotype was also reported from diseased mistletoe bushes from other European countries. We further identified unique single nucleotide polymorphisms (SNPs) in the ITS region, which were specific to the only well resolved clade in the phylogenetic analysis.</p></sec><sec><title>Conclusions</title><p>The diPCR approach allowed amplification of ITS rRNA gene directly from small amounts of fungal samples without prior DNA extraction. 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Economou</name></author><author><name sortKey="Soulioti, N" uniqKey="Soulioti N">N Soulioti</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Varga, I" uniqKey="Varga I">I Varga</name></author><author><name sortKey="Taller, J" uniqKey="Taller J">J Taller</name></author><author><name sortKey="Baltazar, T" uniqKey="Baltazar T">T Baltazár</name></author><author><name sortKey="Hyvonen, J" uniqKey="Hyvonen J">J Hyvönen</name></author><author><name sortKey="Poczai, P" uniqKey="Poczai P">P Poczai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Varga, I" uniqKey="Varga I">I Varga</name></author><author><name sortKey="Nagy, V" uniqKey="Nagy V">V Nagy</name></author><author><name sortKey="Baltazar, T" uniqKey="Baltazar T">T Baltazár</name></author><author><name sortKey="Matyas, Kk" uniqKey="Matyas K">KK Mátyás</name></author><author><name sortKey="Poczai, P" uniqKey="Poczai P">P Poczai</name></author><author><name 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sortKey="Tiborcz, V" uniqKey="Tiborcz V">V Tiborcz</name></author><author><name sortKey="Aranyi, Nr" uniqKey="Aranyi N">NR Aranyi</name></author><author><name sortKey="Baltazar, T" uniqKey="Baltazar T">T Baltazár</name></author><author><name sortKey="Bartha, D" uniqKey="Bartha D">D Bartha</name></author><author><name sortKey="Pejchal, M" uniqKey="Pejchal M">M Pejchal</name></author><author><name sortKey="Hvvonen, J" uniqKey="Hvvonen J">J Hvvönen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Von Tubeuf, Kf" uniqKey="Von Tubeuf K">KF von Tubeuf</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name></author><author><name sortKey="Prosen, De" uniqKey="Prosen D">DE Prosen</name></author><author><name sortKey="Mei, L" uniqKey="Mei L">L Mei</name></author><author><name sortKey="Sullivan, Jc" uniqKey="Sullivan J">JC Sullivan</name></author><author><name sortKey="Finney, M" uniqKey="Finney M">M Finney</name></author><author><name sortKey="Vander Horn, Pb" uniqKey="Vander Horn P">PB Vander Horn</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></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zillig, W" uniqKey="Zillig W">W Zillig</name></author><author><name sortKey="Stetter, Ko" uniqKey="Stetter K">KO Stetter</name></author><author><name sortKey="Wunderl, S" uniqKey="Wunderl S">S Wunderl</name></author><author><name sortKey="Schultz, W" uniqKey="Schultz W">W Schultz</name></author><author><name sortKey="Priess, H" uniqKey="Priess H">H Priess</name></author><author><name sortKey="Scholz, I" uniqKey="Scholz I">I Scholz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zuber, D" uniqKey="Zuber D">D Zuber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zuber, D" uniqKey="Zuber D">D Zuber</name></author><author><name sortKey="Widmer, A" uniqKey="Widmer A">A Widmer</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Finlande</li></country><region><li>Uusimaa</li></region><settlement><li>Helsinki</li></settlement><orgName><li>Université d'Helsinki</li></orgName></list><tree><noCountry><name sortKey="Cernak, Istvan" sort="Cernak, Istvan" uniqKey="Cernak I" first="István" last="Cernák">István Cernák</name></noCountry><country name="Finlande"><region name="Uusimaa"><name sortKey="Varga, Ildik" sort="Varga, Ildik" uniqKey="Varga I" first="Ildik" last="Varga">Ildik Varga</name></region><name sortKey="Hyvonen, Jaakko" sort="Hyvonen, Jaakko" uniqKey="Hyvonen J" first="Jaakko" last="Hyvönen">Jaakko Hyvönen</name><name sortKey="Poczai, Peter" sort="Poczai, Peter" uniqKey="Poczai P" first="Péter" last="Poczai">Péter Poczai</name><name sortKey="Poczai, Peter" sort="Poczai, Peter" uniqKey="Poczai P" first="Péter" last="Poczai">Péter Poczai</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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