Figure 2

Schematic of recombination events in comK prophage. The figure represents an alignment of the 1892 polymorphic sites in the comK prophage (including coding and non-coding regions) as well as 13 polymorphic sites immediately upstream the prophage and 41 polymorphic sites immediately downstream of the prophage. Sites representing nt residues found in F6854 and F6900 (1988 isolates) are shown in black and sites representing nt residues found in FSL J1-194 (a L. monocytogenes serotype 1/2b isolate with the comK prophage most closely related to the prophage found in the 2000 isolates) are shown in gray. The nt sites in J0161 and J2818 (2000 isolates) are shaded so that nt identical to the 1988 isolates are in black, nt identical to FSL J1-194 are in gray, and nt that match neither the 1988 isolates nor FSL J1-194 are in white. Apparent darker shades of gray in this figure represent adjacent sites with black and gray or white. R1, R2, and R3 (recombination 1 to 3) represent three main recombinant blocks that were likely introduced from a lineage I strain similar to FSL J1-194 into a descended of the 1988 isolates, yielding the 2000 isolate genotype. The two shorter mixed gray and white blocks at the 5' end, marked as ER1 and ER 2 (ER = external recombination) are likely to have been introduced from a L. monocytogenes genotype not included in this alignment ("external") into a descendent of the 1988 isolates.