Abstract

High-density, strand-specific cDNA sequencing (ssRNA-seq) was used to analyze the transcriptome of Salmonella enterica serovar Typhi (S. Typhi). By mapping sequence data to the entire S. 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 S. 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.

Keywords

BiologyTranscriptomeGeneticsComputational biologySalmonella typhiRNA-SeqRegulonGenomePseudogeneGeneRegulation of gene expressionGene expression

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Year
2009
Type
article
Volume
5
Issue
7
Pages
e1000569-e1000569
Citations
242
Access
Closed

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Timothy T. Perkins, Robert A. Kingsley, María Fookes et al. (2009). A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi. PLoS Genetics , 5 (7) , e1000569-e1000569. https://doi.org/10.1371/journal.pgen.1000569

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DOI
10.1371/journal.pgen.1000569