Boundaries of deleted regions in the genome of the P. luminescens TT01α variant match with the module boundaries defined in the P. luminescens TT01 (Pl) genome. A. Schematic diagram of the strategy used for multiplex PCR amplification. The yellow box indicates the deleted region. Blue boxes represent the flanking regions. Red horizontal arrows indicate the location of the primers. The primer mixture (P1, P2, P3 and P4) was designed to amplify two fragments from the Pl genome and only one fragment if the region is effectively deleted, as predicted for the P. luminescens TT01α variant genome. B. Agarose gel electrophoresis of the PCR products generated by amplifying the genomic DNA of Pl (lanes 2, 5, 9, 12), of the TT01α variant (lanes 3, 6, 10, 13) or of water (lanes 4, 7, 11, 14) with primers P1, P2, P3 and P4, designed as indicated in (A) for loci D (lanes 2-4), E (lanes 5-7), F (lanes 9-11) and I (lanes 12-14). Loci D, E, F and I are four regions of the Pl genome identified as missing in the TT01α variant genome (see text for details). [1-2], [3-4] and [1-4]. indicate bands of sizes compatible with amplification of the regions between the P1 and P2 primers, the P3 and P4 primers and the P1 and P4 primers, respectively. Lanes 1, 8, 15: molecular markers. The sizes of fragments are indicated in kb to the left of the gel.