A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi

PLoS Genet. 2009 Jul;5(7):e1000569. doi: 10.1371/journal.pgen.1000569. Epub 2009 Jul 17.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / analysis
  • DNA, Complementary
  • Gene Expression Profiling
  • Proteomics
  • RNA, Bacterial / analysis
  • RNA, Bacterial / genetics
  • Salmonella typhi / genetics*
  • Sequence Analysis, RNA


  • Bacterial Proteins
  • DNA, Complementary
  • RNA, Bacterial