Ralstonia solanacearum species complex is a highly destructive bacterial plant pathogen recognized as a group of genotypically diverse strains with broad geographic distribution and wide host range. Strains are divided into four phylotypes (I, II, III and IV) relating to their geographical origins. Based on the polyphasic approach, phylotypes I and III have been reclassified as R. pseudosolanacearum, phylotype IV as R. syzygii species and phylotype II as R. solanacearum. The large data sets of whole genome sequences for the members of R. solanacearum allow us to discover novel molecular markers to evaluate the phylogenetic relationships within this species. In the phylogenetic tree based on concatenated amino acid sequences of 57 housekeeping proteins, members of R. solanacearum species complex formed strongly supported clades that clearly distinguished R. solanacearum, R. pseudosolanacearum and R. syzygii species. In this study, the conserved signature indels (CSIs) which are specifically present in protein sequences and can be used to differentiate various groups of Ralstonia species are reported. Comparative analysis of whole protein sequences from the three species has identified 7 CSIs that are specific to R. solanacearum (phylotype II), 6 CSIs specific to R. pseudosolanacearum strains (phylotype I and III) and 5 CSIs that are specifically shared by members of R. syzygii (phylotype IV). These CSIs are flanked by conserved sequence regions; providing highly specific tools for identification of previously known or novel strains of these species.
