Figure 3

Distribution of percent identities of alignments of ‘Chinese Spring’ full-length cDNAs versus genome assemblies. (A) Frequency distribution of best percent identity of flcDNA alignments to IWGSC ‘Chinese Spring’ (blue bars) and W7984 WGS (red bars) assemblies. Results for both assemblies are superimposed; red and blue overlap is shown as purple. Included are all alignments longer than 50% of query flcDNA length. Note that while most ‘Chinese Spring’ cDNAs align at >99.75% identity to the IWGSC ‘Chinese Spring’ genome assembly, there is a long tail of lower identity best matches that could arise from errors in the genome assembly or in the flcDNA sequences. Matches to the W7984 assembly show most matches >99.50%, as expected given the intra-specific polymorphism between ‘Chinese Spring’ and W7984, but also show the long tail of lower identity. For W7984, these may arise from the absence in the genotype of the locus corresponding to the ‘Chinese Spring’ cDNA. (B) Frequency distribution of percent identity of flcDNA alignments longer than 50% of query flcDNA length, showing only those cDNAs with five or fewer such alignments. The secondary peak centered at approximately 97 to 97.5% corresponds to homeologous matches. As expected given the polymorphism between the two hexaploid wheat lines, the ‘Chinese Spring’ cDNAs align at slightly higher identity to their own genotype than to W7984.