Fig. 5

Schematic presentation showing an overview of ∆TZ-16::MAG-gusA (a) and ∆TZ-17::MAG (b) genotypes. Green circle shows the final genotype including unexpected insertions or deletions by resequencing of strains ∆TZ-16::MAG-gusA and ∆TZ-17::MAG. Grey: MAI; white: M13 or mamABop deletions; black arrows: parts of predicted prophage sets, integrase and excisionase genes; green: most active insertion element genes; purple: irrelevant gene cluster. Enlargements indicate unexpected duplication of vector remnants. In ∆TZ-16::MAG-gusA (a) remnants and duplications of up- and downstream regions of pORFM-GalK-M04 suicide vector are still located within msr1_03120 (encoding a putative secreted effector protein PipB) at the position (305,858 nt) targeted for deletion. As observed before, parts of up- and downstream homologous regions were found fragmented and duplicated. pMDJM3-gusA of strain ∆TZ-16::MAG-gusA has been inserted within the intergenic region between mamY (msr1_03880) and the adjacent transposon gene (msr1_03890) (red box). b pMDJM3 in strain ∆TZ-17::MAG is located at nt position 699,709 (red box) within the ruvB gene (msr1_07040) encoding a putative holliday junction ATP-dependent DNA helicase. Remnants and duplication of pORFM-GalK-pks suicide vector are located at nt position 1,646,447 (intergenic region upstream of msr1_15660) in strains ∆TZ-16::MAG-gusA and ∆TZ-17::MAG. Additionally, an unintended spontaneous 178 bp deletion in fhaB 2 gene (msr1_24320) encoding a filamentous hemagglutinin is present at nt position 2,599,005 (green circle, orange), and an insertion of a copy of ISMgr2 at nt position 3,961,873 into cph1 40 gene (msr1_37870) encoding a phytochrome-like protein was found in both strains (green circle, dark green)