DNA markers for identification of the bacterial phytopathogens Clavibacter, Erwinia, Ralstonia, and Xanthomonas. K. L. SCHNEIDER (1), A. M. Alvarez (2), G. G. Presting (1)
(1) Molecular Biosciences and Bioengineering, University of Hawaii Manoa, Honolulu, HI, USA; (2) Plant and Environmental Protection Sciences, University of Hawaii Manoa, Honolulu, HI, USA
Phytopathology 98:S141

Abstract: Genomes of Clavibacter, Erwinia, Ralstonia and Xanthomonas were examined to identify DNA markers suitable for species identification. Selection criteria for a DNA marker included 1) presence in the four genera as a single copy, 2) a low rate of horizontal gene transfer as assessed by phylogenomic orthologous protein analysis and 3) having greater variablity than the internal transcribed spacer (ITS), found between the 16S and 23S rDNA. Six Xanthomonas genomes were examined using a whole genome analysis program (MUMmer) to find conserved regions from which to design primers. A single region contained within the chromosomal replication initiator gene, dnaA, met all of the selection criteria. DNA sequences of the ITS and dnaA markers were obtained for 120 Ralstonia, 24 Xanthomonas, 24 Erwinia and 24 Clavibacter strains. The dnaA marker generally provided resolution equal to or greater than the ITS marker, as exemplified by its ability to separate Ralstonia solanacearum race 3 biovar 2 from other strains.