Alignment between <i>F. graminearum</i> and <i>F. pseudograminearum</i>.

<p><i>F. graminearum</i> chromosomes are ordered in decreasing size. (A) Dot-plot representing a whole genome alignment between <i>F. graminearum</i> isolate Ph1 and <i>F. pseudograminearum</i> isolate CS3096. The alignment was generated with NUCmer, part of the MUMmer 3 comparative sequence analysis package. Sequences were pre-masked for known repetitive elements and simple repeats using RepeatMasker. The dot plot represents the best 1∶1 alignment between the two genomes. Dots closest to the diagonal represent co-linearity between the two genomes. Red represents matches in the forward direction and blue is indicative of inversions in part of the mapped contig relative to the <i>F. graminearum</i> genome. (B) Distribution of gaps in the alignment between <i>F. pseudograminearum</i> and <i>F. graminearum</i>, relative to the <i>F. graminearum</i> genome. <i>F. graminearum</i> chromosomes were divided into 100 Kbp non-overlapping windows and the unaligned nucleotides in each window summed and expressed as a percentage.