Figure 1.

Essential genes in S. Typhi. (A) Frequency and distribution of transposon directed insertion-site sequence reads across the entire S. Typhi Ty2 genome for a pool of one million transposon mutants. The y-axis shows the number of mapped sequence reads within a window size of 3. ori and ter indicate the approximate positions of the replication origin and terminus, respectively. (B) Bimodal frequency distribution of insertion index (number of inserts per gene divided by gene length). Genes with insertion indices in the leftmost peak represent those that have none, or very few insertions (essential genes). (C–E) Detailed plots generated using Artemis (Rutherford et al. 2000) showing distribution of sequence reads across selected regions of the S. Typhi Ty2 genome. The y-axis shows the number of mapped sequence reads within a window size of three. The maximum number of sequence reads within each plot is shown (top right) and the position of annotated genes relative to the plotted sequence reads is indicated below the distribution plot; gray boxes represent genes, and white boxes pseudogenes. (C) The essential plsC gene and topoisomerase IV genes, parC and parE, showing the absence of transposon insertions. (D) Sequence reads mapping to regions between essential genes and the fabZ lpxA lpxB rnhB dnaE accA operon disrupted by insertions into rnhB (E) show that the Tn5-derived transposon is capable of generating many nonpolar mutations.