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

Abstract

BackgroundThe 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.ResultsThe 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.ConclusionsComparative 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.

Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA

“…Incongruence of the phylogenetic assignment of this strain was already reported: the first published egl-based classification placed it within phylotype I (Poussier et al, 2000a), whereas intergenic transcribed tracer-based classification (Fegan et al, 1998) and mutS-based classification considered it a single phylogenetic group . Comparative genomic hybridization results (Remenant et al, 2010) established that ACH732 contained an original gene content, although placed within phylotype IV (Supplementary Figure S6). To date, exact position of ACH732 thus remains unsolved.…”

“…R. solanacearum is regarded as a species complex (Gillings and Fahy, 1994), composed of four phylotypes of probable different geographical origins (I: Asian, II: American, III: African, and IV: Indonesian) as previously defined based on hrpB, egl and mutS sequence analysis (Poussier et al, 2000a, b;Fegan and Prior, 2005;Prior and Fegan, 2005), whereas previous classifications were based on host range variations (races; Buddenhagen et al, 1962) and metabolic properties (biovars; Hayward, 1964). The four phylotypes, subdivided into sequevars based on egl sequence similarities , were further validated with comparative genomic hybridization (Guidot et al, 2007) and complete genome comparisons (Remenant et al, 2010).…”

Structural and functional genomics of plasmid pSinA of Sinorhizobium sp. M14 encoding genes for the arsenite oxidation and arsenic resistance

“…In contrast to the arsenic resistance genes, almost all found and documented arsenite oxidase genes are located within chromosomes. To date, the aio-like loci have been found only within three plasmids: megaplasmid pSI07 of Ralstonia solanacearum (Remenant et al, 2010), plasmid pPB12 of Nitrobacter hamburgiensis (Starkenburg et al, 2008), and plasmid pTT27 of Thermus thermophilus HB8 (AP008227). Information concerning above-mentioned plasmids and their functionality in the context of arsenite oxidation, as well as horizontal transfer of arsenic metabolism genes, is rather residual.…”

Occurrence and diversity of Ralstonia solanacearum populations in Brazil

“…In Brazil, the most affected species are solanaceae such as potato, tomato, bell pepper, eggplant, tobacco, and gilo, but also include banana, heliconia, eucalypt, and castor beans, among others (MALAVOLTA JÚNIOR et al, 2008). Such wide geographical distribution and host range can be attributed to the species genetic heterogeneity, including divergent strains with more than 30% dissimilarity (REMENANT et al, 2010), which confers it the definition of a species complex PRIOR, 2005).…”

“…Plant breeding for resistant cultivars, considered as the best control strategy for the bacteriosis, is troublesome due to the lack of good resistance sources among the vegetable species and the genetic diversity of the pathogen REMENANT et al, 2010).…”