Genomic Structure and Phylogeny of the Plant Pathogen Ralstonia solanacearum Inferred from Gene Distribution Analysis

Abstract

In the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic ␤-proteobacterium Ralstonia solanacearum, paying particular attention to the status of known or candidate pathogenicity genes. Based on the use of comparative genomic hybridization on a pangenomic microarray for the GMI1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representative of the biodiversity of the R. solanacearum species. This identified a list of 2,690 core genes present in all tested strains. As a corollary, a list of 2,338 variable genes within the R. solanacearum species has been defined. The hierarchical clustering based on the distribution of variable genes is fully consistent with the phylotype classification that was previously defined from the nucleotide sequence analysis of four genes. The presence of numerous pathogenicity-related genes in the core genome indicates that R. solanacearum is an ancestral pathogen. The results establish the long coevolution of the two replicons that constitute the bacterial genome. We also demonstrate the clustering of variable genes in genomic islands. Most genomic islands are included in regions with an alternative codon usage, suggesting that they originate from acquisition of foreign genes through lateral gene transfers. Other genomic islands correspond to genes that have the same base composition as core genes, suggesting that they either might be ancestral genes lost by deletion in certain strains or might originate from horizontal gene transfers.

The Ralstonia solanacearum pathogenicity regulator HrpB induces 3-hydroxy-oxindole synthesis

“…It is very likely that hdf expression is mediated directly by HrpB because the conserved hrp II box control element is located upstream of the first hdf gene in the operon. The observation that hdf genes are conserved in 17 R. solanacearum strains representative of the genetic diversity of the species (25) indicates that these genes belong to the ''core genome,'' which supports the hypothesis that these genes may be important for the fitness of the pathogen.…”

The awr Gene Family Encodes a Novel Class of Ralstonia solanacearum Type III Effectors Displaying Virulence and Avirulence Activities

“…Genomic analysis of the awr genes in R. solanacearum GMI1000 showed some interesting features: i) four of the awr genes (awr2 to awr5) are borne by the megaplasmid whereas awr1 is located on the chromosome; ii) awr3 and awr4 lie side by side and adjacent to the hrp gene cluster; iii) awr2 and awr5 are placed near alternative codon usage regions, often indicative of genes that have been acquired by lateral gene transfer (Arnold et al 2003;Guidot et al 2007); and iv) the chromosomal paralogue awr1 encodes the only protein whose translocation was not detected in previous studies, although the gene seems functional because it has not accumulated any missense mutations. Pairwise analysis of AWR protein sequences from GMI1000 revealed that they all shared high identity and similarity (19 to 53% and 27 to 62%, respectively).…”

“…Strain GMI1000 contains five awr genes (Rsc2139, Rsp0099, Rsp0846, Rsp0847, and Rsp1024) that we have called here awr1, awr2, awr3, awr4, and awr5, respectively. Except for awr1, these genes are present in all R. solanacearum phylotypes (Guidot et al 2007) and their transcriptional activation requires HrpB, a master regulator of the T3SS (Cunnac et al 2004a). AWR2 was one of only two T3E whose disruption in GMI1000 showed delayed disease symptom development on tomato, indicating an important role in bacterial pathogenesis (Cunnac et al 2004a).…”

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

“…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).…”