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| Genomic DNA from DSM-1707 and from the sequenced isolate of PAO1 were digested with SfoI, SwaI and PacI. The SfoI digests were analyzed on conventional agarose gels while the SwaI and PacI digests were analyzed by pulsed-field gel electrophoresis. The latter enzymes revealed the expected large-scale differences in the structures of the PAO1 and DSM-1707 genomes, while digestion with SfoI confirmed the expected swapping of the single-copy sequences that flank rrnA and rrnB. We also carried out detailed comparisons of SpeI digests of PAO1, the sequence-derived map of PAO1, and the map of DSM-1707 since the most detailed physical map for P. aeruginosa was constructed using this enzyme. While SpeI is uninformative with respect to the inversion because it cleaves within the rDNA repeats, the SpeI analysis provided additional support for the overall assembly and also revealed a 20-kbp deletion in PAO1-UW that eliminated the SpeI site separating fragments Z and AF in the DSM-1707 map of Römling and Tümmler. Like the inversion between rrnA and rrnB , this alteration must have occurred during laboratory propagation of these PAO1 sub-isolates. |
