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Fig. S1. Schematic of R. insecticola genome scaffolds. Five R. insecticola scaffolds were reconstructed from 24 partially and completely sequenced BACs. Consensus contig sequences are shown as black bars with lengths in kilobases. The BACs comprising each contig are shown below as grey bars and sequence gaps in the BAC sequences are shown as dotted grey lines. Sequence gaps closed by PCR are shown as solid black lines and extensions generated by pyrosequencing contigs are orange. Curved lines above the contigs indicate the number of pairs of BAC end sequences that are contained within (grey) or connect contigs (black).

Fig. S2. Schematic of annotated R. insecticola genome scaffolds from BAC sequences. The five annotated genome scaffolds represent 1.48 Mb of the R. insecticola genome. CDS on the forward strand are shown in grey above, reverse strand below also in grey. Several specific gene features are highlighted; ribosomal RNAs (red), pseudogenes (dark grey) and transposases (green) as well as phage (blue), plasmid (purple), flagellar (orange) and T3SS and virulence genes (pink). Vertical red lines show the locations of gaps in the scaffolds. The asterisk (*) denotes the origin of replication.

Fig. S3. Numbers of syntenic gene blocks for SICO genes of R. insecticola and H. defensa. Conservation of gene order (syteny) between BAC encoded R. insecticola SICO genes and their H. defensa orthologues was determined (n = 711). Genes were found as singletons (1) or in blocks of 2–28 genes. Numbers above bars indicate the number of blocks of a given length (black) and the number of genes in these blocks (grey).

Fig. S4. Correlated rates of protein divergence in pairs of conserved bacterial orthologues. Estimates of non-synonymous substitutions per non-synonymous site (dN) were measured between genome pairs for 199 genes shared by nine bacteria; R. insecticola (Ri), H. defensa (Hd), E. coli (Ec), S. typhimurium (St), Blochmannia floridanus (Bf), Bl. pennsylvanicus (Bp), Buchnera aphidicola APS (BapA), Bu. aphidicola SG (BapS) and Bu. aphidicola BP (BapB). These values for Ri-Hd orthologues when plotted against the orthologues from the four other genome pairs show a significant correlation in pairwise dN. Significance values were determined for Spearman's rho (ρ), a non-parametric test of association. Ri-Hd and Bf-Bp have the lowest divergence, while dN is slightly higher in BapA-BapB, lower in BapA-BapS and much lower in Ec-St.

Table S1. Identity of pyrosequencing contigs from R. insecticola str. LSR1.

Table S2. Comparison of R. insecticola and H. defensa genes sets underlying different metabolic capabilities.

Table S3. Genomic islands inserted into the R. insecticola str. LSR1 genome.

Table S4. Major classes of R. insecticola insertion sequences (IS) identified in BAC scaffolds.

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