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e found in all strains except Molk2, the only banana wilt pathogen sequenced to date. All six strains appear able to metabolize inorganic nutrients such as sul fate and nitrate, consistent with experimental data, However, the denitrification pathway was complete only in strains GMI1000 and CMR15, because the nosZ gene encoding nitrous oxide reductase was absent from the four other strains. Fer-1 this heterogeneity was previously noted, Genes for periplasmic nitrate reductase, nitrate reductase, nitric oxide reductase and nitrite reductase were present on the megaplasmids of all six sequenced R. solanacearum strains. Finally, all six genomes contain genes involved in the detoxification of noxious compounds and in metal resis tance, which likely support colonization and survival in specific ecological niches.
An interesting example is arse nic resistance which in bacteria is mediated in part by ars genes. Among these, arsC encodes an arsenate reductase, arsA and arsB encode an arsenite efflux pump, and arsR encodes a transcriptional regulator, As is known to induce oxidative stress, to cause DNA damage, and to inhibit OAC1 the DNA repair system, It is generally further oxidized by the arsenite oxidase encoded by aoxAB genes. The arsC gene is the sole gene in this pathway present Siponimod in all six strains, with two tandem copies in PSI07. In addition, only PSI07 can oxidize arsenite. on the PSI07 megaplasmid is a clus ter containing two arsC genes, aoxAB, and arsR. The annotation of the arsC like gene is probably erroneous in the other Ralstonia species, Virulence factors Many traits contribute to virulence of R.
solanacearum strains. The best known are the type III secreted effec tors, well described in this bacterium and in other plant pathogens, However, other traits, such as production of EPS and cell wall degrading RNA polymerase enzymes, are also impor tant for wilt disease development. Based on the literature, we created an inventory of 128 genes involved in viru lence from the six sequenced R. solanacearum genomes, Some genes are involved in Siponimod swimming motility, twitching motility and chemotaxis. Table S5 gives a representative pair of genes for each of those functions. Virulence genes were subdi vided into 5 categories. type III effectors and puta tive effectors, the exopolysaccharide biosynthetic genes, the cell wall degrading enzyme genes, response to host defence genes and key virulence regula tors.
Scrutiny of the genomes shows that all six strains have all genes needed for functional type II and III secre tion systems. Similarity distances between each sequenced strain were computed on the basis of gene presence absence data for these Fer-1 128 virulence genes, Phylogenetic analysis constructed on the basis of. 1 all known or putative Type 3 effector genes in the pan genome, and 2 all known virulence factor genes of all kinds in the pan genome, resulted in trees that were significantly different from each other, and significantly different from trees based on well conserved genes like mutS and egl sequences, or on the entire genome sequences, This result suggests Siponimod that vir ulence factor genes have evolved or been lost or added at substantially different rates than R.
solanacearum genes as a whole. A more fine scale case by case analysis will likely be needed to trace the evolutionary history of indi vidual virulence traits. Analysis of strains Fer-1 hosted by plants phylogenetically distant from tomato may elu cidate roles Siponimod of individual virulence factors in determining host range. Type III secreted effectors are an important potential source of host range variability in R. solanacearum strains. these have mainly been described in GMI1000 and UW551 to date, Specific effectors that are important in CMR15, CFBP2957 and PSI07 are unknown. We attempted to detect new type III effectors with the Effective software, but this did not work well for R. solanacearum strains, giving about 50% false nega tive on previously annotated effectors, Plasmids in Ralstonia solanacearu