Development of a Multiple Loci Variable Number of Tandem Repeats Analysis (MLVA) to Unravel the Intra-Pathovar Structure of Pseudomonas syringae pv. actinidiae Populations Worldwide
Identifieur interne : 000175 ( Pmc/Curation ); précédent : 000174; suivant : 000176Development of a Multiple Loci Variable Number of Tandem Repeats Analysis (MLVA) to Unravel the Intra-Pathovar Structure of Pseudomonas syringae pv. actinidiae Populations Worldwide
Auteurs : Serena Ciarroni [Italie] ; Lorenzo Gallipoli [Italie] ; Maria C. Taratufolo [Italie] ; Margi I. Butler [Nouvelle-Zélande] ; Russell T. M. Poulter [Nouvelle-Zélande] ; Christine Pourcel [France] ; Gilles Vergnaud [France] ; Giorgio M. Balestra [Italie] ; Angelo Mazzaglia [Italie]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
The bacterial canker of kiwifruit by
Url:
DOI: 10.1371/journal.pone.0135310
PubMed: 26262683
PubMed Central: 4532359
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PMC:4532359Le document en format XML
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pv. <italic>actinidiae</italic>
Populations Worldwide</title>
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pv. <italic>actinidiae</italic>
Populations Worldwide</title>
<author><name sortKey="Ciarroni, Serena" sort="Ciarroni, Serena" uniqKey="Ciarroni S" first="Serena" last="Ciarroni">Serena Ciarroni</name>
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<country xml:lang="fr">Italie</country>
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<author><name sortKey="Gallipoli, Lorenzo" sort="Gallipoli, Lorenzo" uniqKey="Gallipoli L" first="Lorenzo" last="Gallipoli">Lorenzo Gallipoli</name>
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</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Institute for Integrative Biology of the Cell, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay</wicri:regionArea>
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<author><name sortKey="Vergnaud, Gilles" sort="Vergnaud, Gilles" uniqKey="Vergnaud G" first="Gilles" last="Vergnaud">Gilles Vergnaud</name>
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</nlm:aff>
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<author><name sortKey="Balestra, Giorgio M" sort="Balestra, Giorgio M" uniqKey="Balestra G" first="Giorgio M." last="Balestra">Giorgio M. Balestra</name>
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<author><name sortKey="Mazzaglia, Angelo" sort="Mazzaglia, Angelo" uniqKey="Mazzaglia A" first="Angelo" last="Mazzaglia">Angelo Mazzaglia</name>
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</nlm:aff>
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<front><div type="abstract" xml:lang="en"><p>The bacterial canker of kiwifruit by <italic>Pseudomonas syringae</italic>
pv. <italic>actinidiae</italic>
is an emblematic example of a catastrophic disease of fruit crops. In 2008 a new, extremely virulent form of the pathogen emerged and rapidly devastated many <italic>Actinidia</italic>
spp. orchards all over the world. In order to understand differences in populations within this pathovar and to elucidate their diffusion and movements on world scale, it is necessary to be able to quickly and on a routine basis compare new isolates with previous records. In this report a worldwide collection of 142 strains was analyzed by MLVA, chosen as investigative technique for its efficacy, reproducibility, simplicity and low cost. A panel of 13 Variable Number of Tandem Repeats (VNTR) loci was identified and used to describe the pathogen population. The MLVA clustering is highly congruent with the population structure as previously established by other molecular approaches including whole genome sequencing and correlates with geographic origin, time of isolation and virulence. For convenience, we divided the VNTR loci in two panels. Panel 1 assay, using six loci, recognizes 23 different haplotypes, clustered into ten complexes with highest congruence with previous classifications. Panel 2, with seven VNTR loci, provides discriminatory power. Using the total set of 13 VNTR loci, 58 haplotypes can be distinguished. The recent hypervirulent type shows very limited diversity and includes, beside the strains from Europe, New Zealand and Chile, a few strains from Shaanxi, China. A broad genetic variability is observed in China, but different types are also retrievable in Japan and Korea. The low virulent strains cluster together and are very different from the other MLVA genotypes. Data were used to generate a public database in MLVAbank. MLVA represents a very promising first-line assay for large-scale routine genotyping, prior to whole genome sequencing of only the most relevant samples.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Young, Jm" uniqKey="Young J">JM Young</name>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, CA USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">26262683</article-id>
<article-id pub-id-type="pmc">4532359</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0135310</article-id>
<article-id pub-id-type="publisher-id">PONE-D-15-15646</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Development of a Multiple Loci Variable Number of Tandem Repeats Analysis (MLVA) to Unravel the Intra-Pathovar Structure of <italic>Pseudomonas syringae</italic>
pv. <italic>actinidiae</italic>
Populations Worldwide</article-title>
<alt-title alt-title-type="running-head">MLVA Assay to Discern <italic>Pseudomonas syringae</italic>
pv. <italic>actinidiae</italic>
Populations</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Ciarroni</surname>
<given-names>Serena</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gallipoli</surname>
<given-names>Lorenzo</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Taratufolo</surname>
<given-names>Maria C.</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Butler</surname>
<given-names>Margi I.</given-names>
</name>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Poulter</surname>
<given-names>Russell T. M.</given-names>
</name>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pourcel</surname>
<given-names>Christine</given-names>
</name>
<xref ref-type="aff" rid="aff003"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Vergnaud</surname>
<given-names>Gilles</given-names>
</name>
<xref ref-type="aff" rid="aff003"><sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff004"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Balestra</surname>
<given-names>Giorgio M.</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mazzaglia</surname>
<given-names>Angelo</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref rid="cor001" ref-type="corresp">*</xref>
</contrib>
</contrib-group>
<aff id="aff001"><label>1</label>
<addr-line>Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy</addr-line>
</aff>
<aff id="aff002"><label>2</label>
<addr-line>Department of Biochemistry, University of Otago, Dunedin, New Zealand</addr-line>
</aff>
<aff id="aff003"><label>3</label>
<addr-line>Institute for Integrative Biology of the Cell, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France</addr-line>
</aff>
<aff id="aff004"><label>4</label>
<addr-line>ENSTA ParisTech, Université Paris-Saclay, Palaiseau, France</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Cloeckaert</surname>
<given-names>Axel</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>Institut National de la Recherche Agronomique, FRANCE</addr-line>
</aff>
<author-notes><fn fn-type="conflict" id="coi001"><p><bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: AM SC GMB GV. Performed the experiments: SC LG MCT. Analyzed the data: AM GV. Contributed reagents/materials/analysis tools: GMB MB RP. Wrote the paper: AM GMB RP MB CP GV.</p>
</fn>
<corresp id="cor001">* E-mail: <email>angmazza@unitus.it</email>
</corresp>
</author-notes>
<pub-date pub-type="epub"><day>11</day>
<month>8</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="collection"><year>2015</year>
</pub-date>
<volume>10</volume>
<issue>8</issue>
<elocation-id>e0135310</elocation-id>
<history><date date-type="received"><day>10</day>
<month>4</month>
<year>2015</year>
</date>
<date date-type="accepted"><day>20</day>
<month>7</month>
<year>2015</year>
</date>
</history>
<permissions><copyright-year>2015</copyright-year>
<copyright-holder>Ciarroni et al</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>
, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited</license-p>
</license>
</permissions>
<self-uri content-type="pdf" xlink:type="simple" xlink:href="pone.0135310.pdf"></self-uri>
<abstract><p>The bacterial canker of kiwifruit by <italic>Pseudomonas syringae</italic>
pv. <italic>actinidiae</italic>
is an emblematic example of a catastrophic disease of fruit crops. In 2008 a new, extremely virulent form of the pathogen emerged and rapidly devastated many <italic>Actinidia</italic>
spp. orchards all over the world. In order to understand differences in populations within this pathovar and to elucidate their diffusion and movements on world scale, it is necessary to be able to quickly and on a routine basis compare new isolates with previous records. In this report a worldwide collection of 142 strains was analyzed by MLVA, chosen as investigative technique for its efficacy, reproducibility, simplicity and low cost. A panel of 13 Variable Number of Tandem Repeats (VNTR) loci was identified and used to describe the pathogen population. The MLVA clustering is highly congruent with the population structure as previously established by other molecular approaches including whole genome sequencing and correlates with geographic origin, time of isolation and virulence. For convenience, we divided the VNTR loci in two panels. Panel 1 assay, using six loci, recognizes 23 different haplotypes, clustered into ten complexes with highest congruence with previous classifications. Panel 2, with seven VNTR loci, provides discriminatory power. Using the total set of 13 VNTR loci, 58 haplotypes can be distinguished. The recent hypervirulent type shows very limited diversity and includes, beside the strains from Europe, New Zealand and Chile, a few strains from Shaanxi, China. A broad genetic variability is observed in China, but different types are also retrievable in Japan and Korea. The low virulent strains cluster together and are very different from the other MLVA genotypes. Data were used to generate a public database in MLVAbank. MLVA represents a very promising first-line assay for large-scale routine genotyping, prior to whole genome sequencing of only the most relevant samples.</p>
</abstract>
<funding-group><funding-statement>This work was supported by Italian Minister of Agriculture and Food Polices, <ext-link ext-link-type="uri" xlink:href="http://www.politicheagricole.it">www.politicheagricole.it</ext-link>
, grant OIGA n. 247, GMB, AM; Direction Générale de l’Armement (DGA), <ext-link ext-link-type="uri" xlink:href="http://www.defense.gouv.fr/dga">http://www.defense.gouv.fr/dga</ext-link>
, grant Microtype 14- ASMA-0002-02, GV, CP; and Agence Nationale de la Recherche, <ext-link ext-link-type="uri" xlink:href="http://www.agence-nationale-recherche.fr">www.agence-nationale-recherche.fr</ext-link>
, grant program ASTRID Maturation, GV, CP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
<counts><fig-count count="6"></fig-count>
<table-count count="5"></table-count>
<page-count count="24"></page-count>
</counts>
<custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name>
<meta-value>All relevant data are within the paper and its Supporting Information files.</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
<notes><title>Data Availability</title>
<p>All relevant data are within the paper and its Supporting Information files.</p>
</notes>
</front>
</pmc>
</record>
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