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Rapid identification of quarantine bacterial plant pathogens by sequence comparisons within single housekeeping genes

Inman, Alan; Elphinstone, John; Lopéz, Maria Milagros; Horky, Jaroslav; Müller, Petra; Manceau, Charles; Maes, Martine; Loreti, Stefania; Gottsberger, Richard; Reisenzein, Helga; de Neergaard, Eigil; Stoyanova, Maria; Dreo, Tanja; Ravnikar, Maja; Bergsma-Vlami, Maria; Janse, Jaap; Cruz, Leonor


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{
  "inLanguage": {
    "alternateName": "eng", 
    "@type": "Language", 
    "name": "English"
  }, 
  "description": "<p>Monitoring and surveillance of bacterial plant pathogens is vital in efforts to control disease and maintain freedom from alien and newly emerging diseases. Rapid and reliable identification of species and pathovars provides the primary means of evaluating the disease threat from isolated pathogens. With the development and reduced cost of DNA sequencing technologies, phylogenetic-based identification based on comparative sequence analysis of protein coding genes has been shown to be rapid, reliable, reproducible and cost-effective. Multilocus sequence typing (MLST), multilocus sequence analysis (MLSA) and DNA barcoding methods are all now commonly used procedures for identification of bacteria to genus, species and subspecific levels. These methods enable discrimination of species, strains and pathovars that could not previously be reproducibly resolved using traditional phenotype profiling methods, representing a significant advance in pathogen identification.&nbsp;Full taxonomic identification using MLST, MLSA or multiple barcoding markers from a series of housekeeping genes can be time consuming and expensive and is not always required for routine identification purposes in the diagnostic laboratory. This work was therefore undertaken to validate a number of protocols, each based on partial sequence analysis of a single gene previously used in more comprehensive phylogenetic analyses, for the routine identification of specific plant pathogenic bacteria of quarantine importance.&nbsp;The aim of the project was to collate, evaluate and format data from published phylogenetic studies and ongoing sequencing studies in European diagnostic laboratories to provide standardised protocols for routine use in diagnostic laboratories for rapid identification of bacterial plant pathogens of statutory importance (including certain Xanthomonas spp., pathovars of the Pseudomonas syringae complex, Erwinia amylovora and Dickeya spp).</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "The Food and Environment Research Agency (Fera), Sand Hutton, United Kingdom", 
      "@type": "Person", 
      "name": "Inman, Alan"
    }, 
    {
      "affiliation": "The Food and Environment Research Agency (Fera), Sand Hutton, United Kingdom", 
      "@type": "Person", 
      "name": "Elphinstone, John"
    }, 
    {
      "affiliation": "Institute of Agricultural Research (INIA), Madrid, Spain", 
      "@type": "Person", 
      "name": "Lop\u00e9z, Maria Milagros"
    }, 
    {
      "affiliation": "Ministry of Agriculture (NAAR), Prague, Czech Republic", 
      "@type": "Person", 
      "name": "Horky, Jaroslav"
    }, 
    {
      "affiliation": "Julius Kuhn Institute (JKI), Braunschweig, Germany", 
      "@type": "Person", 
      "name": "M\u00fcller, Petra"
    }, 
    {
      "affiliation": "National Research Institute for Agriculture (INRA), Paris, France", 
      "@type": "Person", 
      "name": "Manceau, Charles"
    }, 
    {
      "affiliation": "The Agriculture Research Centre (ILVO), Merelbeke, Belgium", 
      "@type": "Person", 
      "name": "Maes, Martine"
    }, 
    {
      "affiliation": "The Agricultural Research Council (CRA), Rome, Italy", 
      "@type": "Person", 
      "name": "Loreti, Stefania"
    }, 
    {
      "affiliation": "The Austrian Agency for Health and Food Safety (AGES), Vienna, Austria", 
      "@type": "Person", 
      "name": "Gottsberger, Richard"
    }, 
    {
      "affiliation": "The Austrian Agency for Health and Food Safety (AGES), Vienna, Austria", 
      "@type": "Person", 
      "name": "Reisenzein, Helga"
    }, 
    {
      "affiliation": "Ministry of Food, Agriculture and Fisheries Danish Food Industry Agency (DFIA), Copenhagen, Denmark", 
      "@type": "Person", 
      "name": "de Neergaard, Eigil"
    }, 
    {
      "affiliation": "The National Service for Plant Protection (NSPP), Sofia, Bulgaria", 
      "@type": "Person", 
      "name": "Stoyanova, Maria"
    }, 
    {
      "affiliation": "The Ministry of Agriculture, Forestry and Food (MAFF), Ljubljana, Slovenia", 
      "@type": "Person", 
      "name": "Dreo, Tanja"
    }, 
    {
      "affiliation": "The Ministry of Agriculture, Forestry and Food (MAFF), Ljubljana, Slovenia", 
      "@type": "Person", 
      "name": "Ravnikar, Maja"
    }, 
    {
      "affiliation": "National Plant Protection Organization (NVWA), Wageningen, The Netherlands", 
      "@type": "Person", 
      "name": "Bergsma-Vlami, Maria"
    }, 
    {
      "affiliation": "National Plant Protection Organization (NVWA), Wageningen, The Netherlands", 
      "@type": "Person", 
      "name": "Janse, Jaap"
    }, 
    {
      "affiliation": "Direccao Geral de Porteccao das Culturas (DGPC), Lisbon, Portugal", 
      "@type": "Person", 
      "name": "Cruz, Leonor"
    }
  ], 
  "headline": "Rapid identification of quarantine bacterial plant pathogens by sequence comparisons within single housekeeping genes", 
  "image": "https://zenodo.org/static/img/logos/zenodo-gradient-round.svg", 
  "datePublished": "2011-06-30", 
  "url": "https://zenodo.org/record/1326346", 
  "keywords": [
    "Euphresco, plant health, diagnostics, single gene sequencing, quarantine bacteria"
  ], 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.5281/zenodo.1326346", 
  "@id": "https://doi.org/10.5281/zenodo.1326346", 
  "@type": "ScholarlyArticle", 
  "name": "Rapid identification of quarantine bacterial plant pathogens by sequence comparisons within single housekeeping genes"
}
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