Figure 3

Alignment comparison. Panel A is a histogram of sequence similarity of alignments for the Clearwater clonal line. Alignments were produced by either Megablast or Novoalign and for every 80 nucleotide window the alignments were binned into their respective similarity category based on the number of mismatches in the window. The second peak of alignments around 92.5% with Megablast likely represents a set of genes duplicated during a whole genome duplication. Novoalign does not show this pattern because Novoalign uses a more stringent alignment algorithm. Panel B was produced in the same way, but it represents the combination of two polyploid wheat lines for 125 UniGenes used in SNP validation. The second peak for this panel is around 98.75% indicating a much more recent whole genome duplication. Both alignment programs have similar results with wheat because the paralogs have high sequence similarity.