Lack of conservation of antisense promoters and internal promoters between C. jejuni and H. pylori . A) Comparison of the σ70 recognition sequences of C. jejuni and H. pylori, demonstrating that there is little difference between σ70 recognition sequences in the two species, with the σ70 -10 sequence of both species being gnTAnaAT. B) Comparison of the number of genes with antisense TSS and internal TSS in C. jejuni and H. pylori. Both species share 46 orthologs displaying antisense transcription in both species, whereas 41 shared orthologs have an internal promoter in both species. The lower number of antisense and internal promoters in C. jejuni is due to the lower coverage of 454 sequencing-based dRNA-seq. C) Examples of conservation and lack of conservation of antisense transcription in C. jejuni and H. pylori. Of the 46 genes with an antisense TSS shared between C. jejuni and H. pylori, only 2 out of 46 have the antisense TSS in the same position. This is shown for the clpB (cj0509c / hp0264) gene. The other 44 genes have the antisense promoters in different locations in the gene, as is shown for the gyrB (cj0003 / hp0501) gene. The boxes below the genes show the protein motifs encoded opposite to the antisense promoters, while the boxes below the protein sequence compare the antisense promoters. Asterisks indicate conserved residues, black and bold typeface indicates the antisense RNA sequence, the underlined residue is the transcript start site (TSS, +1), while red and bold typeface indicates the -10 sequence of the σ70 promoter. Complete information on antisense and internal promoters can be found in Additional file 19: Figure S9 and Additional file 18: Table S10 and Additional file 20: Table S11.