Analysis of the primary transcriptome of C. jejuni NCTC 11168 by differential RNA-seq (dRNA-seq) analysis of transcription start sites (TSS). (A) Genome map of C. jejuni strain NCTC 11168 with the outer three rings showing the annotated features of the plus and minus strand and annotated pseudogenes [19, 20]. The inner rings show TSS associated with annotated features (green), antisense to annotated features (red), and non-coding RNAs (blue). The top inset shows the TSS and promoter of the porA gene and a putative non-coding RNA (NC3, CJnc140). The lower inset shows an operon with a primary TSS of a leaderless mRNA, an internal TSS and an antisense TSS. Red histograms (+TEX) show the cDNA read distribution in the cDNA library enriched for primary transcripts, dark blue histograms show cDNA read distribution in the non-enriched library (-TEX). B) WebLogo representations of the recognition sequences of σ28, σ54 and σ70, based on the sequences upstream of 26, 18 and 948 TSS, respectively (Additional file 5: Table S3). C) Identification of leaderless mRNAs of C. jejuni NCTC 11168. The graph shows the length distribution of 5′ untranslated regions (5′ UTRs) of 471 C. jejuni genes located downstream of a primary TSS. Red bars indicate proposed leaderless mRNAs, blue bars indicate a 5′ UTR with ribosome binding site (RBS). The insets show the motifs detected by MEME  upstream of the translational start codon of the C. jejuni genes with an RBS (right) and leaderless mRNAs (left). On the right side examples of 5′ UTRs are shown, with 3 proposed leaderless mRNAs, and 4 short 5′ UTRs containing a proposed RBS. The TSS (green, underlined), the σ70 -10 sequence (red) and the proposed RBS (blue) are highlighted. The full list of leaderless mRNAs is given in Additional file 13: Table S6.