Fig 1.

Architecture of the REIS genome. (A) General statistics for the REIS chromosome and four plasmids (pREIS1 to pREIS4). For split genes, total genes are shown with split ORFs in parentheses. (B) Characteristics of the REIS chromosome. The putative origin of replication, positioned at 12 o'clock, was selected based on limited synteny with other SFG genomes (see Fig. S1 in the supplemental material). The outer black circle is a scale with coordinates (in Mb) listed at 200-kb intervals. Six rings inside the scale are the following: plus (1)- and minus (2)-strand genes with core Rickettsia genes colored blue, REIS singletons (not present in other Rickettsiaceae genomes) colored red, and all other genes colored gray; (3) 232 putative pseudogenes colored green (see Table S1 in the supplemental material) and gaps (109 total; see Table S3 in the supplemental material) in the assembly colored black; (4) mobile genetic elements, including transposases, integrases, phage-related ORFs, and other genes typically encoded on plasmids colored turquoise; (5) RAGE genes colored pink, with the location of the seven complete or nearly complete RAGE clusters illustrated (C, Be, F, D, A, E, and B); (6) regions of large-scale duplication and recombination (joined by lines) and regions resulting from plasmid integration (boxed numbers 1 to 3). The ring's six-color scheme is the following (clockwise from the top): purple, duplication of five ORFs and the 6S RNA gene; brown, group II intron and associated genes; black, six-gene insert from pREIS4; burgundy, N-terminal region of rickA (N) joined to the duplicated C-terminal regions (C) (see Fig. S5 in the supplemental material); magenta, four-gene duplication associated with RAGE-A and RAGE-B. (C) Main features of the four REIS plasmids. Duplicated regions within pREIS2 and pREIS4 are depicted with pink shading. Multigene regions (described above) that have been transferred to the chromosome are within dashed boxes. The color scheme depicts genes present on both the chromosome and plasmids (above line) and unique genes of the plasmids discussed in the text.