Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence

Remenant Benoit, Coupat-Goutaland Bénédicte, Guidot Alice, Cellier Gilles, Wicker Emmanuel, Allen Caitilyn, Fegan Mark, Pruvost Olivier, Elbaz Mounira, Calteau Alexandra, Salvignol Georges, Mornico Damien, Mangenot Sophie, Barbe Valérie, Medigue Claudine, Prior Philippe. 2010. Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence. BMC Genomics, 11 (379) : pp. 1-16.

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Abstract : Background: The #Ralstonia solanacearum# species complex includes thousands of strains pathogenic to an unusually wide range of plant species. These globally dispersed and heterogeneous strains cause bacterial wilt diseases, which have major socio-economic impacts. Pathogenicity is an ancestral trait in #R. solanacearum# and strains with high genetic variation can be subdivided into four phylotypes, correlating to isolates from Asia (phylotype I), the Americas (phylotype IIA and IIB), Africa (phylotype III) and Indonesia (phylotype IV). Comparison of genome sequences strains representative of this phylogenetic diversity can help determine which traits allow this bacterium to be such a pathogen of so many different plant species and how the bacteria survive in many different habitats. Results: The genomes of three tomato bacterial wilt pathogens, CFBP2957 (phy. IIA), CMR15 (phy. III) and PSI07 (phy. IV) were sequenced and manually annotated. These genomes were compared with those of three previously sequenced #R. solanacearum# strains: GMI1000 (tomato, phy. I), IPO1609 (potato, phy. IIB), and Molk2 (banana, phy. IIB). The major genomic features (size, G+C content, number of genes) were conserved across all of the six sequenced strains. Despite relatively high genetic distances (calculated from average nucleotide identity) and many genomic rearrangements, more than 60% of the genes of the megaplasmid and 70% of those on the chromosome are syntenic. The three new genomic sequences revealed the presence of several previously unknown traits, probably acquired by horizontal transfers, within the genomes of #R. solanacearum#, including a type IV secretion system, a rhi-type anti-mitotic toxin and two small plasmids. Genes involved in virulence appear to be evolving at a faster rate than the genome as a whole. Conclusions: Comparative analysis of genome sequences and gene content confirmed the differentiation of #R. solanacearum# species complex strains into four phylotypes. Genetic distances between strains, in conjunction with CGH analysis of a larger set of strains, revealed differences great enough to consider reclassification of the #R. solanacearum# species complex into three species. The data are still too fragmentary to link genomic classification and phenotypes, but these new genome sequences identify a pan-genome more representative of the diversity in the #R. solanancearum# species complex. (Résumé d'auteur)

Mots-clés Agrovoc : Solanum lycopersicum, Ralstonia solanacearum

Mots-clés géographiques Agrovoc : Cameroun, Antilles françaises, Indonésie, France

Mots-clés complémentaires : Flétrissement bactérien

Classification Agris : H20 - Plant diseases

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

  • Remenant Benoit, CIRAD-BIOS-UMR PVBMT (REU)
  • Coupat-Goutaland Bénédicte, CNRS (FRA)
  • Guidot Alice, INRA (FRA)
  • Cellier Gilles, CIRAD-BIOS-UMR PVBMT (REU)
  • Wicker Emmanuel, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0003-0927-7404
  • Allen Caitilyn, University of Wisconsin (USA)
  • Fegan Mark, QDPI (AUS)
  • Pruvost Olivier, CIRAD-BIOS-UMR PVBMT (REU)
  • Elbaz Mounira, INRA (FRA)
  • Calteau Alexandra, CNRS (FRA)
  • Salvignol Georges, CNRS (FRA)
  • Mornico Damien, CNRS (FRA)
  • Mangenot Sophie, Centre national de séquençage (FRA)
  • Barbe Valérie, Centre national de séquençage (FRA)
  • Medigue Claudine, CNRS (FRA)
  • Prior Philippe, CIRAD-BIOS-UMR PVBMT (REU)

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