Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580
Fig 8
The pBT1 plasmid encodes the functional cysteinyl-tRNA synthetase in S. Typhimurium D23580.
(A) RNA-seq data for cysS in 4/74 and chromosomal and pBT1-plasmid-encoded cysS in D23580 from the online JBrowse resources provided in this study. The scale of the mapped reads was 1 to 500. (B) Transposon library results for the cysSchr and cysSpBT1 genes in D23580. Figures were obtained using the Dalliance genome viewer [60]. Black arrows at the top represent genes. Each sample is represented by three tracks. The first track contains blue and red lines that correspond to transposon-insertion sites; red = orientation of the transposon is the same as the direction of the gene, blue = opposite direction. The second track shows raw data for the Illumina sequencing reads. The third track highlights in red those genes that were considered “required” for growth in that condition based on an insertion index. The insertion index was calculated for each gene as explained in [59,61], and genes with insertion index values <0.05 were considered as “required” for growth in the Lennox rich medium. The scale on the right represents sequence read coverage. EEP, early exponential phase; ESP, early stationary phase; InSPI2, SPI-2-inducing; LEP, late exponential phase; LSP, late stationary phase; MEP, middle exponential phase; NonSPI2, SPI-2-noninducing; RNA-seq, RNA sequencing; SPI, Salmonella pathogenicity island; tRNA, transfer RNA; TSS, transcriptional start site.