Fig. 2.—

Whole genome alignments for Acyrthosiphon pisum-associated strains of Hamiltonella defensa. (A) The A2C strain was set as the reference with the main chromosome shown to the left and extrachromosomal plasmids shown to the right. Long red vertical bars indicate the boundaries of the main chromosome or extrachromosomal plasmids. Alignments are divided into Locally Collinear Blocks (LCBs) that correspond to regions of the genome in each strain that are internally free of rearrangements. Black blocks correspond to LCBs in the 5′ end and light gray blocks correspond to LCBs in the 3′ end of the main chromosome and extrachromosomal plasmids. Colored bars indicate the position of different TEs. Vertical arrows indicate the position of the origin of replication (ori) for each strain. Below A2C are alignments of the other strains. A dashed line surrounding an LCB indicates its reversal relative to A2C. (B) Location of prophage islands in the genomes of each strain. Dark blue indicates the location of small prophage fragments of different origins, while other colors indicate the location of APSE and other larger prophage islands present in all or particular strains. (C) Extrachromosomal plasmids and plasmid islands. The lower part of the figure illustrates the extrachromosomal plasmids. Plasmids that share homology are grouped by color and classification type. Internal vertical bars and letters identify domains in each plasmid while external vertical bars indicate homologous domains between plasmids. Plasmids in reverse complement are tagged with a minus sign “−”. The upper part of the figure shows the location of plasmid islands in the main chromosome. Islands derived from integration of extrachromosomal plasmids are indicated by the same color with letters corresponding to the domain of the extrachromosomal plasmid that still persists. Islands with other colors and letters derive from integration and decay of plasmids of unknown origin.