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.
Highlights
The Ralstonia solanacearum species complex includes thousands of strains pathogenic to an unusually wide range of plant species
It has long been known that R. solanacearum is a highly heterogeneous group of strains and no one genome sequence could represent the entire species complex
Initial genomic studies revealed that R. solanacearum strains have a substantial backbone of common housekeeping and virulence functions, and carry a divergent set of genomic modules that likely confer distinct ecological phenotypes and host specificity [19,24]
Summary
The Ralstonia solanacearum species complex includes thousands of strains pathogenic to an unusually wide range of plant species. R. solanacearum, formerly known as Pseudomonas solanacearum and Burkholderia solanacearum, is the causal agent of bacterial wilt [1] This soil-borne vascular pathogen is widely distributed in tropical and subtropical climates and affects an unusually broad range of crops, including both monocot and dicot plants [2,3,4]. In the 1990s, potato brown rot strains of R. solanacearum historically known as race 3/biovar 2 (r3b2) were introduced in Europe and North America [5,6]. Due to their adaptation to tropical highland climates, these strains, which are more virulent at cool temperatures (~20°C) than tropical strains [7], may pose major threats in temperate zones. R. solanacearum was listed as a quarantine organism in Europe and Canada and as a Bioterrorism Select Agent in the U.S [8]
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