Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence
- Equal contributors
1 CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint Pierre F-97410, La Réunion, France
2 Université de Lyon, Unité Mixte de Recherche, Centre National de la Recherche Scientifique, UMR CNRS 5557 Ecologie Microbienne, IFR41 Bio Environnement et Santé, Université Lyon I, Villeurbanne cedex F-69622, France
3 CNRS-INRA, Laboratoire Interactions Plantes-Microorganismes, UMR2594, BP52627, Castanet-Tolosan F-31326, France
4 AgroParisTech, ENGREF, 19 avenue du Maine, Paris F-75732, France
5 University of Wisconsin-Madison, Department of Plant Pathology, 1630 Linden Drive, Madison, WI 53706, USA
6 Biosciences Research Division, Department of Primary Industries, 475 Mickleham Rd, Attwood, VIC, 3049, Australia
7 CNRS-UMR 8030, Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, Evry cedex F-91006, France
8 Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, Evry cedex F-91006, France
9 INRA-CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint Pierre F-97410, La Réunion, France
BMC Genomics 2010, 11:379 doi:10.1186/1471-2164-11-379Published: 15 June 2010
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.
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.
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.