Optimization of a real-time PCR assay for the detection of the quarantine pathogen Melampsora medusae f. sp. deltoidae.
Identifieur interne : 000052 ( Main/Exploration ); précédent : 000051; suivant : 000053Optimization of a real-time PCR assay for the detection of the quarantine pathogen Melampsora medusae f. sp. deltoidae.
Auteurs : Anne-Laure Boutigny [France] ; Cécile Guinet ; Agathe Vialle ; Richard C. Hamelin ; Axelle Andrieux ; Pascal Frey ; Claude Husson ; Renaud IoosSource :
- Fungal biology [ 1878-6146 ] ; 2013.
Descripteurs français
- KwdFr :
- ARN fongique (génétique), ARN ribosomique 28S (génétique), Amorces ADN (génétique), Basidiomycota (génétique), Basidiomycota (isolement et purification), Europe (MeSH), Maladies des plantes (microbiologie), Mycologie (méthodes), Populus (microbiologie), Quarantaine (MeSH), Reproductibilité des résultats (MeSH), Réaction de polymérisation en chaine en temps réel (méthodes), Sensibilité et spécificité (MeSH), Sondes oligonucléotidiques (génétique).
- MESH :
- génétique : ARN fongique, ARN ribosomique 28S, Amorces ADN, Basidiomycota, Sondes oligonucléotidiques.
- isolement et purification : Basidiomycota.
- microbiologie : Maladies des plantes, Populus.
- méthodes : Mycologie, Réaction de polymérisation en chaine en temps réel.
- Europe, Quarantaine, Reproductibilité des résultats, Sensibilité et spécificité.
English descriptors
- KwdEn :
- Basidiomycota (genetics), Basidiomycota (isolation & purification), DNA Primers (genetics), Europe (MeSH), Mycology (methods), Oligonucleotide Probes (genetics), Plant Diseases (microbiology), Populus (microbiology), Quarantine (MeSH), RNA, Fungal (genetics), RNA, Ribosomal, 28S (genetics), Real-Time Polymerase Chain Reaction (methods), Reproducibility of Results (MeSH), Sensitivity and Specificity (MeSH).
- MESH :
- chemical , genetics : DNA Primers, Oligonucleotide Probes, RNA, Fungal, RNA, Ribosomal, 28S.
- geographic : Europe.
- genetics : Basidiomycota.
- isolation & purification : Basidiomycota.
- methods : Mycology, Real-Time Polymerase Chain Reaction.
- microbiology : Plant Diseases, Populus.
- Quarantine, Reproducibility of Results, Sensitivity and Specificity.
Abstract
Melampsora medusae (Mm), one of the causal agents of poplar rust, is classified as an A2 quarantine pest for European Plant Protection Organization (EPPO) and its presence in Europe is strictly controlled. Two formae speciales have been described within Mm, Melampsora medusae f. sp. deltoidae (Mmd), and Melampsora medusae f. sp. tremuloidae (Mmt) on the basis of their pathogenicity on Populus species from the section Aigeiros (e.g. Populus deltoides) or Populus (e.g. Populus tremuloides), respectively. In this study, a real-time polymerase chain reaction (PCR) assay was developed allowing the detection of Mmd, the forma specialis that is economically harmful. A set of primers and hydrolysis probe were designed based on sequence polymorphisms in the large ribosomal RNA subunit (28S). The real-time PCR assay was optimized and performance criteria of the detection method, i.e. sensitivity, specificity, repeatability, reproducibility, and robustness, were assessed. The real-time PCR method was highly specific and sensitive and allowed the detection of one single urediniospore of Mmd in a mixture of 2 mg of urediniospores of other Melampsora species. This test offers improved specificity over currently existing conventional PCR tests and can be used for specific surveys in European nurseries and phytosanitary controls, in order to avoid introduction and spread of this pathogen in Europe.
DOI: 10.1016/j.funbio.2013.04.001
PubMed: 23809649
Affiliations:
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Two formae speciales have been described within Mm, Melampsora medusae f. sp. deltoidae (Mmd), and Melampsora medusae f. sp. tremuloidae (Mmt) on the basis of their pathogenicity on Populus species from the section Aigeiros (e.g. Populus deltoides) or Populus (e.g. Populus tremuloides), respectively. In this study, a real-time polymerase chain reaction (PCR) assay was developed allowing the detection of Mmd, the forma specialis that is economically harmful. A set of primers and hydrolysis probe were designed based on sequence polymorphisms in the large ribosomal RNA subunit (28S). The real-time PCR assay was optimized and performance criteria of the detection method, i.e. sensitivity, specificity, repeatability, reproducibility, and robustness, were assessed. The real-time PCR method was highly specific and sensitive and allowed the detection of one single urediniospore of Mmd in a mixture of 2 mg of urediniospores of other Melampsora species. This test offers improved specificity over currently existing conventional PCR tests and can be used for specific surveys in European nurseries and phytosanitary controls, in order to avoid introduction and spread of this pathogen in Europe. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23809649</PMID><DateCompleted><Year>2014</Year><Month>01</Month><Day>06</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1878-6146</ISSN><JournalIssue CitedMedium="Internet"><Volume>117</Volume><Issue>6</Issue><PubDate><Year>2013</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Fungal biology</Title><ISOAbbreviation>Fungal Biol</ISOAbbreviation></Journal><ArticleTitle>Optimization of a real-time PCR assay for the detection of the quarantine pathogen Melampsora medusae f. sp. deltoidae.</ArticleTitle><Pagination><MedlinePgn>389-98</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.funbio.2013.04.001</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S1878-6146(13)00052-4</ELocationID><Abstract><AbstractText>Melampsora medusae (Mm), one of the causal agents of poplar rust, is classified as an A2 quarantine pest for European Plant Protection Organization (EPPO) and its presence in Europe is strictly controlled. Two formae speciales have been described within Mm, Melampsora medusae f. sp. deltoidae (Mmd), and Melampsora medusae f. sp. tremuloidae (Mmt) on the basis of their pathogenicity on Populus species from the section Aigeiros (e.g. Populus deltoides) or Populus (e.g. Populus tremuloides), respectively. In this study, a real-time polymerase chain reaction (PCR) assay was developed allowing the detection of Mmd, the forma specialis that is economically harmful. A set of primers and hydrolysis probe were designed based on sequence polymorphisms in the large ribosomal RNA subunit (28S). The real-time PCR assay was optimized and performance criteria of the detection method, i.e. sensitivity, specificity, repeatability, reproducibility, and robustness, were assessed. The real-time PCR method was highly specific and sensitive and allowed the detection of one single urediniospore of Mmd in a mixture of 2 mg of urediniospores of other Melampsora species. This test offers improved specificity over currently existing conventional PCR tests and can be used for specific surveys in European nurseries and phytosanitary controls, in order to avoid introduction and spread of this pathogen in Europe. </AbstractText><CopyrightInformation>Copyright © 2013 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Boutigny</LastName><ForeName>Anne-Laure</ForeName><Initials>AL</Initials><AffiliationInfo><Affiliation>ANSES Laboratoire de la Santé des Végétaux, Unité de Mycologie, IFR110 EFABA, Domaine de Pixérécourt, BP 90059, 54220 Malzéville, France. anne-laure.boutigny@anses.fr</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guinet</LastName><ForeName>Cécile</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Vialle</LastName><ForeName>Agathe</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Hamelin</LastName><ForeName>Richard C</ForeName><Initials>RC</Initials></Author><Author ValidYN="Y"><LastName>Andrieux</LastName><ForeName>Axelle</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Frey</LastName><ForeName>Pascal</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Husson</LastName><ForeName>Claude</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Ioos</LastName><ForeName>Renaud</ForeName><Initials>R</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D023362">Evaluation Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>04</Month><Day>19</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Fungal Biol</MedlineTA><NlmUniqueID>101524465</NlmUniqueID></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D017931">DNA Primers</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015345">Oligonucleotide Probes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012331">RNA, Fungal</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012339">RNA, Ribosomal, 28S</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001487" MajorTopicYN="N">Basidiomycota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017931" MajorTopicYN="N">DNA Primers</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005060" MajorTopicYN="N" Type="Geographic">Europe</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009172" MajorTopicYN="N">Mycology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015345" MajorTopicYN="N">Oligonucleotide Probes</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011790" MajorTopicYN="N">Quarantine</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012331" MajorTopicYN="N">RNA, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012339" MajorTopicYN="N">RNA, Ribosomal, 28S</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D060888" MajorTopicYN="N">Real-Time Polymerase Chain Reaction</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012680" MajorTopicYN="N">Sensitivity and Specificity</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>10</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2013</Year><Month>01</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2013</Year><Month>04</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>7</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>7</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>1</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">23809649</ArticleId><ArticleId IdType="pii">S1878-6146(13)00052-4</ArticleId><ArticleId IdType="doi">10.1016/j.funbio.2013.04.001</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Grand Est</li><li>Lorraine (région)</li></region><settlement><li>Malzéville</li></settlement></list><tree><noCountry><name sortKey="Andrieux, Axelle" sort="Andrieux, Axelle" uniqKey="Andrieux A" first="Axelle" last="Andrieux">Axelle Andrieux</name><name sortKey="Frey, Pascal" sort="Frey, Pascal" uniqKey="Frey P" first="Pascal" last="Frey">Pascal Frey</name><name sortKey="Guinet, Cecile" sort="Guinet, Cecile" uniqKey="Guinet C" first="Cécile" last="Guinet">Cécile Guinet</name><name sortKey="Hamelin, Richard C" sort="Hamelin, Richard C" uniqKey="Hamelin R" first="Richard C" last="Hamelin">Richard C. Hamelin</name><name sortKey="Husson, Claude" sort="Husson, Claude" uniqKey="Husson C" first="Claude" last="Husson">Claude Husson</name><name sortKey="Ioos, Renaud" sort="Ioos, Renaud" uniqKey="Ioos R" first="Renaud" last="Ioos">Renaud Ioos</name><name sortKey="Vialle, Agathe" sort="Vialle, Agathe" uniqKey="Vialle A" first="Agathe" last="Vialle">Agathe Vialle</name></noCountry><country name="France"><region name="Grand Est"><name sortKey="Boutigny, Anne Laure" sort="Boutigny, Anne Laure" uniqKey="Boutigny A" first="Anne-Laure" last="Boutigny">Anne-Laure Boutigny</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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