A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus <em>Salmonella</em> Typhi

<div><p>High-density, strand-specific cDNA sequencing (ssRNA–seq) was used to analyze the transcriptome of <em>Salmonella enterica</em> serovar Typhi (<em>S</em>. Typhi). By mapping sequence data to the entire <em>S</em>. Typhi genome, we analyzed the transcriptome in a strand-specific manner and further defined transcribed regions encoded within prophages, pseudogenes, previously un-annotated, and 3′- or 5′-untranslated regions (UTR). An additional 40 novel candidate non-coding RNAs were identified beyond those previously annotated. Proteomic analysis was combined with transcriptome data to confirm and refine the annotation of a number of hpothetical genes. ssRNA–seq was also combined with microarray and proteome analysis to further define the <em>S</em>. Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA–seq provides a novel and powerful approach to the characterization of the bacterial transcriptome.</p></div>