Comparative analysis of whole bacterial genomes and derivation of RIF, a DNA identification marker for bacterial phytopathogens.
K. L. SCHNEIDER (1), G. Marrero (1), A. Alvarez (1), G. G. Presting (1) (1) University of Hawaii, Honolulu, HI, USA.
Phytopathology 99:S115.

Abstract: We have identified a region of the replication initiation factor gene (RIF) as a useful DNA marker for identification of phytopathogens below the species level. RIF, which is present as a single copy in all genomes examined (Clavibacter, Erwinia [Dickeya, Pectobacterium and Pantoea], Ralstonia, and Xanthomonas)-CERX, is unlikely to be laterally transferred and is amplifiable with genus-specific primers. The RIF marker was derived using comparative genomics of six complete genomes of Xanthomonas (3 species and 4 pathovars) and comprises 925 nucleotides of the dnaA replication initiation factor. In silico analysis revealed that RIF has equal or higher resolution than the ribosomal intergenic spacer (ITS) for differentiating strains of the same pathovar of Xanthomonas. Initial attempts to sequence the RIF and ITS markers of 360 CERX strains yielded a higher success rate (33%–97%) with RIF. Sequencing frameworks were constructed using the RIF marker with 111 C. michiganensis, 70 Erwinia, 220 R. solanacearum and 354 Xanthomonas strains. These frameworks have been used successfully to identify unknown bacterial strains associated with recent disease outbreaks, illustrating the value of RIF for the identification of plant pathogens.