Comparative analysis of regions containing group-specific putative outer-surface proteins. A) Two genomic regions containing duplicated genes for novel putative surface exposed proteins in “Firm-5” strains. Genes are shown as boxes, where blue and grey boxes represent the putative outer surface proteins, and white boxes represent other genes in the regions. Grey boxes correspond to genes identified at contig borders in the genome assemblies (partially assembled). The tree topology is as in Figure 1. B) Comparative analysis of the main genomic region containing tandemly duplicated genes for RCC1-repeat domain proteins in “Bifido” strains.” Genes are shown as arrows, where genes corresponding to each of the two protein clusters indicated by OrthoMCL and phylogeny (Additional file 8: Figure S6) are shown in light and dark blue respectively. Genes containing RCC1-repeats that are members of other protein familes, as predicted by OrthoMCL, are shown in purple. Genes not containing the RCC1-repeat domains are shown in white. The genomic position of the region is indicated in Figure 6. The tree topology is as in Figure 2. C) Genomic regions containing the putative cscAB genes in “Firm-4″ strains. Genes are shown as arrows, where light-blue arrows represent the putative cscA genes, and dark-blue arrows represent the putative cscB genes. The gene with homologues in other lactobacilli strains used for the OrthoMCL search is shown with a red border. In all comparisons, the similarity between genomes was inferred with tblastx and is shown with connecting grey lines, where darker lines indicate higher similarity.