Comparative restriction maps of the archaeal megaplasmid pHM300 in different Haloferax mediterranei strains

We have constructed the restriction maps of the circular megaplasmid pHM300 of five different Haloferax mediterranei strains (ATCC 33500, M2, M4, M6, M10), and a pigmentary mutant from one of them (M2a), using the endonucleases BamHI, SwaI, and BglII. Either one-dimensional pulsed-field gel electrophoresis (PFGE) or two-dimensional PFGE (2D-PFGE) were used to resolve the genomic fragments generate by these enzymes. For physical mapping, we combined hybridization with multiple digestion straegies. pHM300 maps were identical for strains ATCC 33500/M10 (315 kb), and M2 (M2b)/M4/M6 (330 kb), respectively, with some regions conserved in both map types. The main difference between them appeared to be an insertion that corresponds roughly to a 7 kb SwaI fragment containing an abnormal density of rare-cutter sires as well as repeated sequences. In M2a, pHM300 has only 145 kb, and most likely suffered a large deletion from its original template: pHM300 from M2b.