Open AccessA Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi
Author(s) -
Timothy T. Perkins,
Robert A. Kingsley,
María Fookes,
Paul P. Gardner,
Keith James,
Lu-Lu Yu,
Samuel Assefa,
Miaoxia He,
Nicholas J. Croucher,
Derek Pickard,
Duncan J. Maskell,
Julian Parkhill,
Jyoti S. Choudhary,
Nicholas R. Thomson,
Gordon Dougan
Publication year - 2009
Publication title -
plos genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.587
H-Index - 233
eISSN - 1553-7404
pISSN - 1553-7390
DOI - 10.1371/journal.pgen.1000569
Subject(s) - biology , transcriptome , genetics , computational biology , salmonella typhi , rna seq , regulon , genome , pseudogene , gene , regulation of gene expression , gene expression , escherichia coli
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.