Multiplex detection, distribution, and genetic diversity of Hop stunt viroid and Citrus exocortis viroid infecting citrus in Taiwan
Identifieur interne : 000531 ( Main/Exploration ); précédent : 000530; suivant : 000532Multiplex detection, distribution, and genetic diversity of Hop stunt viroid and Citrus exocortis viroid infecting citrus in Taiwan
Auteurs : Chun-Yi Lin [Taïwan] ; Meng-Ling Wu [Taïwan] ; Tang-Long Shen [Taïwan] ; Hsin-Hung Yeh [Taïwan] ; Ting-Hsuan Hung [Taïwan]Source :
- Virology Journal [ 1743-422X ] ; 2015.
Abstract
Two citrus viroids,
Multiplex RT-PCR was used to detect the two viroids for the first time in seven main cultivars of citrus. Multiplex real-time RT-PCR quantified the distributions of two viroids in four citrus tissues. Sequence alignment and phylogenetic analysis were performed using the ClustalW and MEGA6 (neighbor-joining with p-distance model), respectively.
HSVd was found more prevalent than CEVd (32.2% vs. 30.4%). Both CEVd and HSVd were commonly found simultaneously in the different citrus cultivars (up to 55%). Results of the multiplex quantitative analysis suggested that uneven distributions of both viroids with twig bark as the most appropriate material for studies involving viroid sampling such as quarantine inspection.
Sequence alignment against Taiwanese isolates, along with analysis of secondary structure, revealed the existence of 10 and 5 major mutation sites in CEVd and HSVd, respectively. The mutation sites in CEVd were located at both ends of terminal and variability domains, whereas those in HSVd were situated in left terminal and pathogenicity domains. A phylogenetic analysis incorporating worldwide viroid isolates indicated three and two clusters for the Taiwanese isolates of CEVd and HSVd, respectively.
Moderately high infection and co-infection rates of two viroids in certain citrus cultivars suggest that different citrus cultivars may play important roles in viroid infection and evolution. These data also demonstrate that two multiplex molecular detection methods developed in the present study provide powerful tools to understand the genetic diversities among viroid isolates and quantify viroids in citrus host. Our field survey can help clarify citrus-viroid relationships as well as develop proper prevention strategies.
Url:
DOI: 10.1186/s12985-015-0247-y
PubMed: 25645458
PubMed Central: 4340875
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Multiplex detection, distribution, and genetic diversity of <italic>Hop stunt viroid</italic> and <italic>Citrus exocortis viroid</italic> infecting citrus in Taiwan</title><author><name sortKey="Lin, Chun Yi" sort="Lin, Chun Yi" uniqKey="Lin C" first="Chun-Yi" last="Lin">Chun-Yi Lin</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Plant Pathology and Microbiology, National Taiwan University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Meng Ling" sort="Wu, Meng Ling" uniqKey="Wu M" first="Meng-Ling" last="Wu">Meng-Ling Wu</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Division of Forest Protection, Taiwan Forestry Research Institute, Taipei, 10066 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Division of Forest Protection, Taiwan Forestry Research Institute, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Shen, Tang Long" sort="Shen, Tang Long" uniqKey="Shen T" first="Tang-Long" last="Shen">Tang-Long Shen</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Plant Pathology and Microbiology, National Taiwan University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Yeh, Hsin Hung" sort="Yeh, Hsin Hung" uniqKey="Yeh H" first="Hsin-Hung" last="Yeh">Hsin-Hung Yeh</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Hung, Ting Hsuan" sort="Hung, Ting Hsuan" uniqKey="Hung T" first="Ting-Hsuan" last="Hung">Ting-Hsuan Hung</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Plant Pathology and Microbiology, National Taiwan University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25645458</idno><idno type="pmc">4340875</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340875</idno><idno type="RBID">PMC:4340875</idno><idno type="doi">10.1186/s12985-015-0247-y</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000706</idno><idno type="wicri:Area/Pmc/Curation">000705</idno><idno type="wicri:Area/Pmc/Checkpoint">000416</idno><idno type="wicri:Area/Ncbi/Merge">001993</idno><idno type="wicri:Area/Ncbi/Curation">001993</idno><idno type="wicri:Area/Ncbi/Checkpoint">001993</idno><idno type="wicri:Area/Main/Merge">000531</idno><idno type="wicri:Area/Main/Curation">000531</idno><idno type="wicri:Area/Main/Exploration">000531</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Multiplex detection, distribution, and genetic diversity of <italic>Hop stunt viroid</italic> and <italic>Citrus exocortis viroid</italic> infecting citrus in Taiwan</title><author><name sortKey="Lin, Chun Yi" sort="Lin, Chun Yi" uniqKey="Lin C" first="Chun-Yi" last="Lin">Chun-Yi Lin</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Plant Pathology and Microbiology, National Taiwan University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Meng Ling" sort="Wu, Meng Ling" uniqKey="Wu M" first="Meng-Ling" last="Wu">Meng-Ling Wu</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Division of Forest Protection, Taiwan Forestry Research Institute, Taipei, 10066 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Division of Forest Protection, Taiwan Forestry Research Institute, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Shen, Tang Long" sort="Shen, Tang Long" uniqKey="Shen T" first="Tang-Long" last="Shen">Tang-Long Shen</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Plant Pathology and Microbiology, National Taiwan University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Yeh, Hsin Hung" sort="Yeh, Hsin Hung" uniqKey="Yeh H" first="Hsin-Hung" last="Yeh">Hsin-Hung Yeh</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Hung, Ting Hsuan" sort="Hung, Ting Hsuan" uniqKey="Hung T" first="Ting-Hsuan" last="Hung">Ting-Hsuan Hung</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Plant Pathology and Microbiology, National Taiwan University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author></analytic><series><title level="j">Virology Journal</title><idno type="eISSN">1743-422X</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Two citrus viroids, <italic>Citrus exocortis viroid</italic> (CEVd) and <italic>Hop stunt viroid</italic> (HSVd), have been reported and become potential threats to the citrus industry in Taiwan. The distributions and infection rates of two viroids have not been investigated since the two diseases were presented decades ago. The genetic diversities and evolutionary relationships of two viroids also remain unclear in the mix citrus planted region.</p></sec><sec><title>Methods</title><p>Multiplex RT-PCR was used to detect the two viroids for the first time in seven main cultivars of citrus. Multiplex real-time RT-PCR quantified the distributions of two viroids in four citrus tissues. Sequence alignment and phylogenetic analysis were performed using the ClustalW and MEGA6 (neighbor-joining with p-distance model), respectively.</p></sec><sec><title>Results</title><p>HSVd was found more prevalent than CEVd (32.2% vs. 30.4%). Both CEVd and HSVd were commonly found simultaneously in the different citrus cultivars (up to 55%). Results of the multiplex quantitative analysis suggested that uneven distributions of both viroids with twig bark as the most appropriate material for studies involving viroid sampling such as quarantine inspection.</p><p>Sequence alignment against Taiwanese isolates, along with analysis of secondary structure, revealed the existence of 10 and 5 major mutation sites in CEVd and HSVd, respectively. The mutation sites in CEVd were located at both ends of terminal and variability domains, whereas those in HSVd were situated in left terminal and pathogenicity domains. A phylogenetic analysis incorporating worldwide viroid isolates indicated three and two clusters for the Taiwanese isolates of CEVd and HSVd, respectively.</p></sec><sec><title>Conclusions</title><p>Moderately high infection and co-infection rates of two viroids in certain citrus cultivars suggest that different citrus cultivars may play important roles in viroid infection and evolution. These data also demonstrate that two multiplex molecular detection methods developed in the present study provide powerful tools to understand the genetic diversities among viroid isolates and quantify viroids in citrus host. Our field survey can help clarify citrus-viroid relationships as well as develop proper prevention strategies.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Diener, To" uniqKey="Diener T">TO Diener</name></author><author><name sortKey="Maramorosch, K" uniqKey="Maramorosch K">K Maramorosch</name></author><author><name sortKey="Murphy, Fa" uniqKey="Murphy F">FA Murphy</name></author><author><name sortKey="Shatkin, Aj" uniqKey="Shatkin A">AJ Shatkin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Flores, R" uniqKey="Flores R">R Flores</name></author><author><name sortKey="Hernandez, C" uniqKey="Hernandez C">C Hernandez</name></author><author><name sortKey="De Alba Ae, M" uniqKey="De Alba Ae M">M de Alba AE</name></author><author><name sortKey="Dar S, Ja" uniqKey="Dar S J">JA Daròs</name></author><author><name sortKey="Di Serio, F" uniqKey="Di Serio F">F Di 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Edgar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K Tamura</name></author><author><name sortKey="Peterson, D" uniqKey="Peterson D">D Peterson</name></author><author><name sortKey="Peterson, N" uniqKey="Peterson N">N Peterson</name></author><author><name sortKey="Stecher, G" uniqKey="Stecher G">G Stecher</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></listBibl></div1></back></TEI><affiliations><list><country><li>Taïwan</li></country></list><tree><country name="Taïwan"><noRegion><name sortKey="Lin, Chun Yi" sort="Lin, Chun Yi" uniqKey="Lin C" first="Chun-Yi" last="Lin">Chun-Yi Lin</name></noRegion><name sortKey="Hung, Ting Hsuan" sort="Hung, Ting Hsuan" uniqKey="Hung T" first="Ting-Hsuan" last="Hung">Ting-Hsuan Hung</name><name sortKey="Shen, Tang Long" sort="Shen, Tang Long" uniqKey="Shen T" first="Tang-Long" last="Shen">Tang-Long Shen</name><name sortKey="Wu, Meng Ling" sort="Wu, Meng Ling" uniqKey="Wu M" first="Meng-Ling" last="Wu">Meng-Ling Wu</name><name sortKey="Yeh, Hsin Hung" sort="Yeh, Hsin Hung" uniqKey="Yeh H" first="Hsin-Hung" last="Yeh">Hsin-Hung Yeh</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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