Fig. 3

Pairwise genome alignments comparing the genomes of LR 6475 and strains with higher transformation efficiency. Whole genome comparison showing areas that are conserved across genomes in light gray color. The alignment evidences genomic modification sequences located inside or around two LR 6475 prophages (P1, phage 1, yellow; P2, phage 2, cyan). Green areas represent deleted regions in LJO3 that took place in two different locations inside the inverted region and are 34 kb and 48 kb in size. Pink areas represent an insertion (17 kb) in the prophage one present in LJO1 and LJO8, which contains a phage integrase protein among other genes. The dark gray area flanked by P1 and P2, represents the genomic inversion observed in LR 4659 and LJO3 that also flipped part of the prophage genomes. The alignment was done using the Mauve method from the MegAlign Pro application (DNASTAR, Madison, WI)