Figure 3. Repeat-induced point (RIP) mutation in ribosomal DNA of L. maculans shown as RIPCAL output.

(a) Schematic representation of the rDNA unit in L. maculans (ITS, internal transcribed spacers; IGS, intergenic spacer); (b) a schematic multiple alignment of the 7.8 kb 'complete' ribosomal DNA (rDNA) units occurring in SuperContigs 2 and 19. Polymorphic nucleotides are coloured as a function of the type of RIP mutation observed, with black, invariant nucleotide; red, CpA TpA or TpG TpA mutations; dark blue, CpC TpC or GpG GpA mutations; pale blue, CpT TpT or ApG ApA mutations; green, CpG TpG or CpG CpA mutations; (c) RIP mutation frequency plot over a rolling sequence window, corresponding to the multiple alignment directly above. Nucleotide polymorphisms (against the alignment consensus, which is also the highest GC-content sequence) mostly correspond to CpA TpA or TpG TpA (red curve) and CpG TpG or CpG CpA (green curve).