Fig. 1

Schematic representation of the S. leeuwenhoekii chromosome, circular plasmid pSLE1, and linear plasmid pSLE2 (incomplete sequence). The chromosome is represented as an open circle, covering only the published sequence without the duplication of the terminal inverted repeat (represented as a grey band starting at position 1). From outside to inside, the concentric circles represent: nucleotide position; Protein Coding Sequences (PCSs) on the forward strand; PCSs on the reverse strand; PCSs for putative biosynthetic genes for specialised metabolites (dark red indicates the forward strand, orange the reverse strand); the orange box shown in the fifth circle indicates the chaxamycin biosynthetic gene cluster; tRNA and rRNA genes are shown in the sixth and seventh lines, respectively, in dark blue; the eighth concentric circle shows the GC-plot (GC %, window size = 10000; base step size = 200) and the inner-most circle the GC-skew ([(G − C)/(G + C)] window size = 10000; base step size = 200), both calculated using the sequence with both TIRs, a window size of 10000 and a step size of 200 (purple and olive indicate below and above average, respectively). For pSLE1 and pSLE2, PCSs are coloured red for putative regulatory genes; green, for plasmid replication and partitioning genes; the fourth circle in shows the GC-plot and the inner-most circle the GC-skew, both calculated as for the chromosome. For pSLE1, phage-related genes are shown in orange, and the type III PKS (chalcone synthase) gene is shown in brown. For pSLE2, genes with known plasmid functions are in orange; genes annotated as mobile elements and involved in transposition are in pink; the lasso-peptide biosynthetic gene cluster is shown in dark orange. Not to scale