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CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri

Jeong Kwanho, Muñoz-Bodnar Alejandra, Arias Rojas Nathalia, Poulin Lucie, Rodríguez-R Luis Miguel, Gagnevin Lionel, Vernière Christian, Pruvost Olivier, Koebnik Ralf. 2019. CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri. BMC Genomics, 20:917, 19 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
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Url - éditeur : https://rdcu.be/b5NEc

Quartile : Q2, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q2, Sujet : GENETICS & HEREDITY

Abstract : Background: Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen's diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools. Results: We analyzed CRISPR loci of 56 Xanthomonas citri pv. citri strains of world-wide origin, a regulated pathogen causing Asiatic citrus canker in several regions of the world. With one exception, 23 unique sequences built up the repertoire of spacers, suggesting that this set of strains originated from a common ancestor that already harbored these 23 spacers. One isolate originating from Pakistan contained a string of 14 additional, probably more recently acquired spacers indicating that this genetic lineage has or had until recently the capacity to acquire new spacers. Comparison of CRISPR arrays with previously obtained molecular typing data, such as amplified fragment length polymorphisms (AFLP), variable-number of tandem-repeats (VNTR) and genome-wide single-nucleotide polymorphisms (SNP), demonstrated that these methods reveal similar evolutionary trajectories. Notably, genome analyses allowed to generate a model for CRISPR array evolution in X. citri pv. citri, which provides a new framework for the genealogy of the citrus canker pathogen. Conclusions: CRISPR-based typing will further improve the accuracy of the genetic identification of X. citri pv. citri outbreak strains in molecular epidemiology analyses, especially when used concomitantly with another genotyping method.

Mots-clés Agrovoc : Pathologie végétale, Agent pathogène, Variation génétique, Surveillance épidémiologique

Mots-clés complémentaires : CRISPR, Xanthomonas citri pv citri

Mots-clés libres : Molecular typing, Genetic diversity, Clustered regularly interspaced short palindromic repeats, Variable numbers of tandem repeats, Spoligotyping, Epidemiology, Phylogeny, Evolution, Xanthomonas citri pv. citri

Classification Agris : H20 - Plant diseases
F30 - Plant genetics and breeding

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

Auteurs et affiliations

  • Jeong Kwanho, IRD (FRA)
  • Muñoz-Bodnar Alejandra, IRD (FRA)
  • Arias Rojas Nathalia, IRD (FRA)
  • Poulin Lucie, IRD (FRA)
  • Rodríguez-R Luis Miguel, IRD (FRA)
  • Gagnevin Lionel, CIRAD-BIOS-UMR IPME (FRA)
  • Vernière Christian, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0002-2312-2073
  • Pruvost Olivier, CIRAD-BIOS-UMR PVBMT (REU)
  • Koebnik Ralf, IRD (FRA) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/596216/)

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