The lack of genome synteny between C. jejuni and H. pylori at the level of gene order is reflected at the level of TSS/promoter location and non-coding RNAs. A) A scatter plot of annotated gene numbers shows the lack of genome synteny and gene order between C. jejuni NCTC 11168 (Cje) and H. pylori 26695 (Hpy). The red and blue circles represent the two regions compared below the graph, with arrows representing conserved genes (green), genes only found in either C. jejuni or H. pylori (white). Orange bars indicate homologous genes. Line arrows above the gene representations indicate TSS and associated promoters. B) Alternative visualisation of genomic location of orthologs between C. jejuni NCTC 11168 and H. pylori 26695, based on pairwise BLASTP comparisons of annotated features, using the Artemis Comparison Tool (ACT) . Red lines indicate the presence of an ortholog between C. jejuni and H. pylori in the same transcriptional orientation, whereas blue lines indicate inverted transcriptional orientation. The spoT genomic region [57, 58] is used as example of a region with gene order conserved between the species, but a lack of conservation of transcriptional features. The dRNA-seq profiles of the C. jejuni cj1274c-1271c region and the H. pylori hp0777-hp0774 region (+TEX = enriched for TSS, -TEX = not enriched) are shown above and below, respectively. Promoters associated with TSS are indicated in black (primary TSS), blue (internal TSS for C. jejuni) and green (internal TSS for H. pylori). C) Non-coding RNAs of C. jejuni and H. pylori are not conserved between these two species with the exception of the 6S RNA (right), and are associated with a lack of conservation of flanking genes. One example of each category (C. jejuni-specific ncRNA, H. pylori-specific ncRNA and a conserved stable RNA) is shown. Orange bars connect orthologous genes.