A Novel LAMP Assay for the Detection of Phytophthora cinnamomi Utilizing a New Target Gene Identified From Genome Sequences.
Identifieur interne : 000598 ( Main/Exploration ); précédent : 000597; suivant : 000599A Novel LAMP Assay for the Detection of Phytophthora cinnamomi Utilizing a New Target Gene Identified From Genome Sequences.
Auteurs : Tingting Dai [République populaire de Chine] ; Xiao Yang [États-Unis] ; Tao Hu [République populaire de Chine] ; Zhongyan Li [République populaire de Chine] ; Yue Xu [République populaire de Chine] ; Chenchen Lu [République populaire de Chine]Source :
- Plant disease [ 0191-2917 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Phytophthora.
- méthodes : Agriculture.
- parasitologie : Maladies des plantes.
- Génome de protozoaire, Plantes, Rhizosphère, Sensibilité et spécificité, Techniques d'amplification d'acides nucléiques.
English descriptors
- KwdEn :
- MESH :
- genetics : Phytophthora.
- methods : Agriculture.
- parasitology : Plant Diseases.
- Genome, Protozoan, Nucleic Acid Amplification Techniques, Plants, Rhizosphere, Sensitivity and Specificity.
Abstract
Phytophthora cinnamomi is an ecologically and agriculturally significant plant pathogen. Early and accurate detection of P. cinnamomi is paramount to disease prevention and management. In this study, a loop-mediated isothermal amplification (LAMP) assay utilizing a new target gene Pcinn100006 identified from genomic sequence data was developed and evaluated for the detection of P. cinnamomi. This Pcinn100006 LAMP assay was found highly specific to P. cinnamomi. All 10 tested isolates of P. cinnamomi yielded positive results, whereas 50 isolates belonging to 16 other Phytophthora species, Globisporangium ultimum, and 14 fungal species lacked detection. This assay was 10 times more sensitive (100 pg in a 25-µl reaction mixture) than a conventional PCR assay (2 ng in a 50-µl reaction mixture) for detecting the genomic DNA of P. cinnamomi. In addition, it detected P. cinnamomi from artificially inoculated leaves of Cedrus deodara. Moreover, detection rates of P. cinnamomi using environmental DNAs extracted from 13 naturally infested rhizosphere samples were 100% in the Pcinn100006 LAMP assay versus 46% in the conventional PCR assay. Considering its higher accuracy and shorter time span, this Pcinn100006 LAMP assay is a promising diagnostic tool to replace conventional PCR-based and culture-dependent assays for screening of P. cinnamomi in regions at risk of infection or contamination.
DOI: 10.1094/PDIS-04-19-0781-RE
PubMed: 31613192
Affiliations:
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first="Zhongyan" last="Li">Zhongyan Li</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Yue" sort="Xu, Yue" uniqKey="Xu Y" first="Yue" last="Xu">Yue Xu</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, 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Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Xiao" sort="Yang, Xiao" uniqKey="Yang X" first="Xiao" last="Yang">Xiao Yang</name><affiliation wicri:level="2"><nlm:affiliation>Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA</wicri:regionArea><placeName><region type="state">Virginie</region></placeName></affiliation></author><author><name sortKey="Hu, Tao" sort="Hu, Tao" uniqKey="Hu T" first="Tao" last="Hu">Tao Hu</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Li, Zhongyan" sort="Li, Zhongyan" uniqKey="Li Z" first="Zhongyan" last="Li">Zhongyan Li</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Yue" sort="Xu, Yue" uniqKey="Xu Y" first="Yue" last="Xu">Yue Xu</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Lu, Chenchen" sort="Lu, Chenchen" uniqKey="Lu C" first="Chenchen" last="Lu">Chenchen Lu</name><affiliation wicri:level="1"><nlm:affiliation>Lianyungang Customs (formerly Lianyungang Entry-Exit Inspection and Quarantine Bureau), Lianyungang, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Lianyungang Customs (formerly Lianyungang Entry-Exit Inspection and Quarantine Bureau), Lianyungang</wicri:regionArea><wicri:noRegion>Lianyungang</wicri:noRegion></affiliation></author></analytic><series><title level="j">Plant disease</title><idno type="ISSN">0191-2917</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Agriculture (methods)</term><term>Genome, Protozoan (MeSH)</term><term>Nucleic Acid Amplification Techniques (MeSH)</term><term>Phytophthora (genetics)</term><term>Plant Diseases (parasitology)</term><term>Plants (MeSH)</term><term>Rhizosphere (MeSH)</term><term>Sensitivity and Specificity (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Agriculture (méthodes)</term><term>Génome de protozoaire (MeSH)</term><term>Maladies des plantes (parasitologie)</term><term>Phytophthora (génétique)</term><term>Plantes (MeSH)</term><term>Rhizosphère (MeSH)</term><term>Sensibilité et spécificité (MeSH)</term><term>Techniques d'amplification d'acides nucléiques (MeSH)</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" qualifier="methods" xml:lang="en"><term>Agriculture</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Agriculture</term></keywords><keywords scheme="MESH" qualifier="parasitologie" xml:lang="fr"><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Plant Diseases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Protozoan</term><term>Nucleic Acid Amplification Techniques</term><term>Plants</term><term>Rhizosphere</term><term>Sensitivity and Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Génome de protozoaire</term><term>Plantes</term><term>Rhizosphère</term><term>Sensibilité et spécificité</term><term>Techniques d'amplification d'acides nucléiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Phytophthora cinnamomi</i> is an ecologically and agriculturally significant plant pathogen. Early and accurate detection of <i>P. cinnamomi</i> is paramount to disease prevention and management. In this study, a loop-mediated isothermal amplification (LAMP) assay utilizing a new target gene <i>Pcinn100006</i> identified from genomic sequence data was developed and evaluated for the detection of <i>P. cinnamomi</i>. This <i>Pcinn100006</i> LAMP assay was found highly specific to <i>P. cinnamomi</i>. All 10 tested isolates of <i>P. cinnamomi</i> yielded positive results, whereas 50 isolates belonging to 16 other <i>Phytophthora</i> species, <i>Globisporangium ultimum</i>, and 14 fungal species lacked detection. This assay was 10 times more sensitive (100 pg in a 25-µl reaction mixture) than a conventional PCR assay (2 ng in a 50-µl reaction mixture) for detecting the genomic DNA of <i>P. cinnamomi</i>. In addition, it detected <i>P. cinnamomi</i> from artificially inoculated leaves of <i>Cedrus deodara</i>. Moreover, detection rates of <i>P. cinnamomi</i> using environmental DNAs extracted from 13 naturally infested rhizosphere samples were 100% in the <i>Pcinn100006</i> LAMP assay versus 46% in the conventional PCR assay. Considering its higher accuracy and shorter time span, this <i>Pcinn100006</i> LAMP assay is a promising diagnostic tool to replace conventional PCR-based and culture-dependent assays for screening of <i>P. cinnamomi</i> in regions at risk of infection or contamination.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">31613192</PMID><DateCompleted><Year>2019</Year><Month>11</Month><Day>27</Day></DateCompleted><DateRevised><Year>2019</Year><Month>11</Month><Day>27</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0191-2917</ISSN><JournalIssue CitedMedium="Print"><Volume>103</Volume><Issue>12</Issue><PubDate><Year>2019</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Plant disease</Title><ISOAbbreviation>Plant Dis</ISOAbbreviation></Journal><ArticleTitle>A Novel LAMP Assay for the Detection of <i>Phytophthora cinnamomi</i> Utilizing a New Target Gene Identified From Genome Sequences.</ArticleTitle><Pagination><MedlinePgn>3101-3107</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/PDIS-04-19-0781-RE</ELocationID><Abstract><AbstractText><i>Phytophthora cinnamomi</i> is an ecologically and agriculturally significant plant pathogen. Early and accurate detection of <i>P. cinnamomi</i> is paramount to disease prevention and management. In this study, a loop-mediated isothermal amplification (LAMP) assay utilizing a new target gene <i>Pcinn100006</i> identified from genomic sequence data was developed and evaluated for the detection of <i>P. cinnamomi</i>. This <i>Pcinn100006</i> LAMP assay was found highly specific to <i>P. cinnamomi</i>. All 10 tested isolates of <i>P. cinnamomi</i> yielded positive results, whereas 50 isolates belonging to 16 other <i>Phytophthora</i> species, <i>Globisporangium ultimum</i>, and 14 fungal species lacked detection. This assay was 10 times more sensitive (100 pg in a 25-µl reaction mixture) than a conventional PCR assay (2 ng in a 50-µl reaction mixture) for detecting the genomic DNA of <i>P. cinnamomi</i>. In addition, it detected <i>P. cinnamomi</i> from artificially inoculated leaves of <i>Cedrus deodara</i>. Moreover, detection rates of <i>P. cinnamomi</i> using environmental DNAs extracted from 13 naturally infested rhizosphere samples were 100% in the <i>Pcinn100006</i> LAMP assay versus 46% in the conventional PCR assay. Considering its higher accuracy and shorter time span, this <i>Pcinn100006</i> LAMP assay is a promising diagnostic tool to replace conventional PCR-based and culture-dependent assays for screening of <i>P. cinnamomi</i> in regions at risk of infection or contamination.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Dai</LastName><ForeName>Tingting</ForeName><Initials>T</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-0534-6724</Identifier><AffiliationInfo><Affiliation>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xiao</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Tao</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Zhongyan</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Yue</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Chenchen</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Lianyungang Customs (formerly Lianyungang Entry-Exit Inspection and Quarantine Bureau), Lianyungang, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>10</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Plant Dis</MedlineTA><NlmUniqueID>9882809</NlmUniqueID><ISSNLinking>0191-2917</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000383" MajorTopicYN="Y">Agriculture</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018503" MajorTopicYN="Y">Genome, Protozoan</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D021141" MajorTopicYN="Y">Nucleic Acid Amplification Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="Y">Phytophthora</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="N">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058441" MajorTopicYN="N">Rhizosphere</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012680" MajorTopicYN="N">Sensitivity and Specificity</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Phytophthora dieback</Keyword><Keyword MajorTopicYN="N">Phytophthora root rot</Keyword><Keyword MajorTopicYN="N">disease diagnosis</Keyword><Keyword MajorTopicYN="N">hydroxynaphthol blue</Keyword><Keyword MajorTopicYN="N">oomycetes</Keyword><Keyword MajorTopicYN="N">plant destroyers</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>10</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>11</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>10</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31613192</ArticleId><ArticleId IdType="doi">10.1094/PDIS-04-19-0781-RE</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Virginie</li></region></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Dai, Tingting" sort="Dai, Tingting" uniqKey="Dai T" first="Tingting" last="Dai">Tingting Dai</name></noRegion><name sortKey="Hu, Tao" sort="Hu, Tao" uniqKey="Hu T" first="Tao" last="Hu">Tao Hu</name><name sortKey="Li, Zhongyan" sort="Li, Zhongyan" uniqKey="Li Z" first="Zhongyan" last="Li">Zhongyan Li</name><name sortKey="Lu, Chenchen" sort="Lu, Chenchen" uniqKey="Lu C" first="Chenchen" last="Lu">Chenchen Lu</name><name sortKey="Xu, Yue" sort="Xu, Yue" uniqKey="Xu Y" first="Yue" last="Xu">Yue Xu</name></country><country name="États-Unis"><region name="Virginie"><name sortKey="Yang, Xiao" sort="Yang, Xiao" uniqKey="Yang X" first="Xiao" last="Yang">Xiao Yang</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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