Circular representation of the S. pneumoniae TIGR4 (A) and G54 (B) genomes and transcriptomes. The two outermost circles show the predicted coding regions on the plus (outermost) and minus (2nd circle) strands color-coded by functional categories as in Tettelin et al.. The third circle (light grey) shows genes that are shared by both TIGR4 and G54 genomes and the fourth circle (gold) shows strain-specific genes. Colored boxes depict genes in regions of diversity  as well as other strain-specific clusters (listed in Additional file 6). The red and green circles correspond to transcriptome results; fifth – genes up-regulated in adherent bacteria; sixth – genes down-regulated in adherent bacteria; seventh – genes up-regulated in non-adherent bacteria; eighth – genes down-regulated in non-adherent bacteria. The two innermost circles correspond to the genes selected for mutagenesis (asterisked loci in Table 1); blue – successfully knocked out (SP_0462-SP_0468, SP_0737, SP_1294-SP_1295, SP_1758, SP_1855 and SP_1922) and black – unsuccessful/not viable (SP_0423-SP_0427, SP_0783 and SP_1270).