title: An easy, simple inexpensive test for the specific detection of Pectobacterium carotovorum subsp. carotovorum based on sequence analysis of the pmrA gene.
abstract: BACKGROUND
  The species Pectobacterium carotovorum includes a diverse subspecies of bacteria that cause disease on a wide variety of plants. In Morocco, approximately 95% of the P. carotovorum isolates from potato plants with tuber soft rot are P. carotovorum subsp. carotovorum. However, identification of this pathogen is not always related to visual disease symptoms. This is especially true when different pathogen cause similar diseases on potato, citing as an example, P. carotovorum, P. atrosepticum and P. wasabiae. Numerous conventional methods were used to characterize Pectobacterium spp., including biochemical assays, specific PCR-based tests, and construction of phylogenetic trees by using gene sequences. In this study, an alternative method is presented using a gene linked to pathogenicity, in order to allow accuracy at subspecies level. The pmrA gene (response regulator) has been used for identification and analysis of the relationships among twenty nine Pectobacterium carotovorum subsp. carotovorum and other Pectobacterium subspecies.
  
  
  RESULTS
  Phylogenetic analyses of pmrA sequences compared to ERIC-PCR and 16S rDNA sequencing, demonstrated that there is considerable genetic diversity in P. carotovorum subsp. carotovorum strains, which can be divided into two distinct groups within the same clade.
  
  
  CONCLUSIONS
  pmrA sequence analysis is likely to be a reliable tool to identify the subspecies Pectobacterium carotovorum subsp. carotovorum and estimate their genetic diversity.
authors.affiliation: Laboratoire de Virologie, Microbiologie et Qualité /Eco Toxicologie et Biodiversité, Université Hassan II Mohammedia-Casablanca, Faculté des Sciences et Techniques-Mohammedia-FSTM, BP 146, Mohammedia 20650, Maroc. m.ennaji@yahoo.fr
authors.forename: Mohamed
authors.initials: M
authors.lastname: Kettani-Halabi
authors.forename: Meriam
authors.initials: M
authors.lastname: Terta
authors.forename: Mohamed
authors.initials: M
authors.lastname: Amdan
authors.forename: El Mostafa
authors.initials: el M
authors.lastname: El Fahime
authors.forename: François
authors.initials: F
authors.lastname: Bouteau
authors.forename: Moulay Mustapha
authors.initials: MM
authors.lastname: Ennaji
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D015373:Bacterial Typing Techniques / Q000191:economics / Q000379:methods*; D008969:Molecular Sequence Data; D016973:Pectobacterium carotovorum / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology*; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods*; D011198:Solanum tuberosum / Q000382:microbiology*; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; C081902:pmrA protein, Bacteria
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