Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker
Figure 5
The RIF marker separates Clavibacter michiganensis strains into the three subspecies.
The rooted neighbor-joining cladogram was constructed from 114 characterized Clavibacter strains from the PBC (Table 2), two reference strains from GenBank (see Table 1 for strain names) and the outgroup Leifsonia xyli. Identical sequences are represented only once and the number of sequenced strains is indicated on each leaf. Bootstrap values >50% (shown at the node) are expressed as a percentage of 5,000 replicates. Red text indicates C. michiganensis strains with no previous subspecies designation. Cm† is a non-pathogenic strain isolated from tomato that is most similar to Cmi. Unknowns #1-10 were isolated from a recent bacterial canker outbreak of tomato (see text) and perfectly match two of the Cmm RIF reference sequences. Cmm: C. michiganensis subsp. michiganensis. Cmi: C. michiganensis subsp. insidiosus. Cms: C. michiganensis subsp. sepedonicus.