Detection of the Genus Phytophthora and the Species Phytophthora nicotianae by LAMP with a QProbe.
Identifieur interne : 000247 ( Main/Exploration ); précédent : 000246; suivant : 000248Detection of the Genus Phytophthora and the Species Phytophthora nicotianae by LAMP with a QProbe.
Auteurs : Ayaka Hieno [Japon] ; Mingzhu Li [République populaire de Chine] ; Auliana Afandi [Indonésie] ; Kayoko Otsubo [Japon] ; Haruhisa Suga [Japon] ; Koji Kageyama [Japon]Source :
- Plant disease [ 0191-2917 ] ; 2020.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Phytophthora.
- Amorces ADN, Japon, Pythium, Techniques d'amplification d'acides nucléiques.
- Wicri :
- geographic : Japon.
English descriptors
- KwdEn :
- MESH :
- chemical : DNA Primers.
- geographic : Japan.
- genetics : Phytophthora.
- Nucleic Acid Amplification Techniques, Pythium.
Abstract
Phytophthora is an oomycete genus with worldwide distribution, and many of its species cause destructive diseases. In Japan, Phytophthora species are listed as quarantine organisms with the exception of Phytophthora nicotianae. For effective quarantine control, we designed a Phytophthora genus-specific loop-mediated isothermal amplification (LAMP) primer set and a P. nicotianae species-specific quenching probe (QProbe) to establish a simultaneous LAMP-based detection method. We confirmed the specificity of the genus-specific primers, and all 161 taxa were detected. No other species in the closely related genera Pythium and Phytopythium gave positive results with the exception of two species, Phytopythium delawarense and Phytopythium fagopyri. These two species gave inconsistent results. We used annealing curve analysis with the QProbe to demonstrate that P. nicotianae could be distinguished from other species. DNA from inoculated and naturally infected plants was extracted using a time-saving extraction kit and subjected to the simultaneous detection method. We confirmed that all Phytophthora DNAs in the plant samples were detected, and P. nicotianae was specifically identified. This simultaneous detection method will make quarantine inspections faster and easier.
DOI: 10.1094/PDIS-12-19-2523-RE
PubMed: 32628090
Affiliations:
- Indonésie, Japon, République populaire de Chine
- Préfecture de Gifu, Région du Chūbu
- Gifu (ville)
- Université de Gifu
Links toward previous steps (curation, corpus...)
Le document en format XML
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Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193</wicri:regionArea><orgName type="university">Université de Gifu</orgName><placeName><settlement type="city">Gifu (ville)</settlement><region type="province">Région du Chūbu</region><region type="prefecture">Préfecture de Gifu</region></placeName></affiliation></author><author><name sortKey="Li, Mingzhu" sort="Li, Mingzhu" uniqKey="Li M" first="Mingzhu" last="Li">Mingzhu Li</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Sciences, Shaanxi Normal University, Xi'an, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Shaanxi Normal University, Xi'an</wicri:regionArea><wicri:noRegion>Xi'an</wicri:noRegion></affiliation></author><author><name sortKey="Afandi, Auliana" sort="Afandi, Auliana" uniqKey="Afandi A" first="Auliana" last="Afandi">Auliana Afandi</name><affiliation wicri:level="1"><nlm:affiliation>Biotechnology Research Center, Universitas Gadjah Mada, Yogyakarta, Indonesia.</nlm:affiliation><country xml:lang="fr">Indonésie</country><wicri:regionArea>Biotechnology Research Center, Universitas Gadjah Mada, Yogyakarta</wicri:regionArea><wicri:noRegion>Yogyakarta</wicri:noRegion></affiliation></author><author><name sortKey="Otsubo, Kayoko" sort="Otsubo, Kayoko" uniqKey="Otsubo K" first="Kayoko" last="Otsubo">Kayoko Otsubo</name><affiliation wicri:level="4"><nlm:affiliation>River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193</wicri:regionArea><orgName type="university">Université de Gifu</orgName><placeName><settlement type="city">Gifu (ville)</settlement><region type="province">Région du Chūbu</region><region type="prefecture">Préfecture de Gifu</region></placeName></affiliation></author><author><name sortKey="Suga, Haruhisa" sort="Suga, Haruhisa" uniqKey="Suga H" first="Haruhisa" last="Suga">Haruhisa Suga</name><affiliation wicri:level="4"><nlm:affiliation>Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193</wicri:regionArea><orgName type="university">Université de Gifu</orgName><placeName><settlement type="city">Gifu (ville)</settlement><region type="province">Région du Chūbu</region><region type="prefecture">Préfecture de Gifu</region></placeName></affiliation></author><author><name sortKey="Kageyama, Koji" sort="Kageyama, Koji" uniqKey="Kageyama K" first="Koji" last="Kageyama">Koji Kageyama</name><affiliation wicri:level="4"><nlm:affiliation>River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193</wicri:regionArea><orgName type="university">Université de Gifu</orgName><placeName><settlement type="city">Gifu (ville)</settlement><region type="province">Région du Chūbu</region><region type="prefecture">Préfecture de Gifu</region></placeName></affiliation></author></analytic><series><title level="j">Plant disease</title><idno type="ISSN">0191-2917</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA Primers (MeSH)</term><term>Japan (MeSH)</term><term>Nucleic Acid Amplification Techniques (MeSH)</term><term>Phytophthora (genetics)</term><term>Pythium (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Amorces ADN (MeSH)</term><term>Japon (MeSH)</term><term>Phytophthora (génétique)</term><term>Pythium (MeSH)</term><term>Techniques d'amplification d'acides nucléiques (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA Primers</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Japan</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Phytophthora</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Nucleic Acid Amplification Techniques</term><term>Pythium</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Amorces ADN</term><term>Japon</term><term>Pythium</term><term>Techniques d'amplification d'acides nucléiques</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Japon</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Phytophthora</i> is an oomycete genus with worldwide distribution, and many of its species cause destructive diseases. In Japan, <i>Phytophthora</i> species are listed as quarantine organisms with the exception of <i>Phytophthora nicotianae</i>. For effective quarantine control, we designed a <i>Phytophthora</i> genus-specific loop-mediated isothermal amplification (LAMP) primer set and a <i>P. nicotianae</i> species-specific quenching probe (QProbe) to establish a simultaneous LAMP-based detection method. We confirmed the specificity of the genus-specific primers, and all 161 taxa were detected. No other species in the closely related genera <i>Pythium</i> and <i>Phytopythium</i> gave positive results with the exception of two species, <i>Phytopythium delawarense</i> and <i>Phytopythium fagopyri</i>. These two species gave inconsistent results. We used annealing curve analysis with the QProbe to demonstrate that <i>P. nicotianae</i> could be distinguished from other species. DNA from inoculated and naturally infected plants was extracted using a time-saving extraction kit and subjected to the simultaneous detection method. We confirmed that all <i>Phytophthora</i> DNAs in the plant samples were detected, and <i>P. nicotianae</i> was specifically identified. This simultaneous detection method will make quarantine inspections faster and easier.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Automated" Owner="NLM"><PMID Version="1">32628090</PMID><DateCompleted><Year>2020</Year><Month>08</Month><Day>28</Day></DateCompleted><DateRevised><Year>2020</Year><Month>08</Month><Day>28</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0191-2917</ISSN><JournalIssue CitedMedium="Print"><Volume>104</Volume><Issue>9</Issue><PubDate><Year>2020</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Plant disease</Title><ISOAbbreviation>Plant Dis</ISOAbbreviation></Journal><ArticleTitle>Detection of the Genus <i>Phytophthora</i> and the Species <i>Phytophthora nicotianae</i> by LAMP with a QProbe.</ArticleTitle><Pagination><MedlinePgn>2469-2480</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/PDIS-12-19-2523-RE</ELocationID><Abstract><AbstractText><i>Phytophthora</i> is an oomycete genus with worldwide distribution, and many of its species cause destructive diseases. In Japan, <i>Phytophthora</i> species are listed as quarantine organisms with the exception of <i>Phytophthora nicotianae</i>. For effective quarantine control, we designed a <i>Phytophthora</i> genus-specific loop-mediated isothermal amplification (LAMP) primer set and a <i>P. nicotianae</i> species-specific quenching probe (QProbe) to establish a simultaneous LAMP-based detection method. We confirmed the specificity of the genus-specific primers, and all 161 taxa were detected. No other species in the closely related genera <i>Pythium</i> and <i>Phytopythium</i> gave positive results with the exception of two species, <i>Phytopythium delawarense</i> and <i>Phytopythium fagopyri</i>. These two species gave inconsistent results. We used annealing curve analysis with the QProbe to demonstrate that <i>P. nicotianae</i> could be distinguished from other species. DNA from inoculated and naturally infected plants was extracted using a time-saving extraction kit and subjected to the simultaneous detection method. We confirmed that all <i>Phytophthora</i> DNAs in the plant samples were detected, and <i>P. nicotianae</i> was specifically identified. This simultaneous detection method will make quarantine inspections faster and easier.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hieno</LastName><ForeName>Ayaka</ForeName><Initials>A</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-5019-2336</Identifier><AffiliationInfo><Affiliation>River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Mingzhu</ForeName><Initials>M</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-8078-333X</Identifier><AffiliationInfo><Affiliation>College of Life Sciences, Shaanxi Normal University, Xi'an, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Afandi</LastName><ForeName>Auliana</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Biotechnology Research Center, Universitas Gadjah Mada, Yogyakarta, Indonesia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Otsubo</LastName><ForeName>Kayoko</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Suga</LastName><ForeName>Haruhisa</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kageyama</LastName><ForeName>Koji</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193, Japan.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>07</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Plant Dis</MedlineTA><NlmUniqueID>9882809</NlmUniqueID><ISSNLinking>0191-2917</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D017931">DNA Primers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017931" MajorTopicYN="N">DNA Primers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007564" MajorTopicYN="N" Type="Geographic">Japan</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D021141" MajorTopicYN="N">Nucleic Acid Amplification Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011775" MajorTopicYN="Y">Pythium</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Phytophthora</Keyword><Keyword MajorTopicYN="N">Phytophthora nicotianae</Keyword><Keyword MajorTopicYN="N">loop-mediated isothermal amplification</Keyword><Keyword MajorTopicYN="N">oomycetes</Keyword><Keyword MajorTopicYN="N">pathogen detection</Keyword><Keyword MajorTopicYN="N">quenching probe</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>7</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>8</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>7</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32628090</ArticleId><ArticleId IdType="doi">10.1094/PDIS-12-19-2523-RE</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Indonésie</li><li>Japon</li><li>République populaire de Chine</li></country><region><li>Préfecture de Gifu</li><li>Région du Chūbu</li></region><settlement><li>Gifu (ville)</li></settlement><orgName><li>Université de Gifu</li></orgName></list><tree><country name="Japon"><region name="Région du Chūbu"><name sortKey="Hieno, Ayaka" sort="Hieno, Ayaka" uniqKey="Hieno A" first="Ayaka" last="Hieno">Ayaka Hieno</name></region><name sortKey="Kageyama, Koji" sort="Kageyama, Koji" uniqKey="Kageyama K" first="Koji" last="Kageyama">Koji Kageyama</name><name sortKey="Otsubo, Kayoko" sort="Otsubo, Kayoko" uniqKey="Otsubo K" first="Kayoko" last="Otsubo">Kayoko Otsubo</name><name sortKey="Suga, Haruhisa" sort="Suga, Haruhisa" uniqKey="Suga H" first="Haruhisa" last="Suga">Haruhisa Suga</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Li, Mingzhu" sort="Li, Mingzhu" uniqKey="Li M" first="Mingzhu" last="Li">Mingzhu Li</name></noRegion></country><country name="Indonésie"><noRegion><name sortKey="Afandi, Auliana" sort="Afandi, Auliana" uniqKey="Afandi A" first="Auliana" last="Afandi">Auliana Afandi</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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