Figure 4

Analysis of sequence identity between WGS trace files and the BES DX409547 from H53F21 in octaploid-like contig 9077. Sequence analysis showed the region was octaploid-like as inferred by fingerprints. Panel A: MegaBlast of "H53F21_Build4MTP8A23_gi89261445_4" against 7.3 million reads with repeat masking gave 7 identical matches among 24 homeologous sequences. Cluster 1 was composed of traces ending in 822,160,569,607,662,749 and 105 that shared A at position 172 (boxed). HSVs were evident among the 4 clusters inferred. Cluster 2 was composed of traces ending in 749, 850,601 and shared C at position 172. Cluster 3 was composed of traces ending in 100, 117 and 535 that shared G at position 172. Cluster 4 also had G at that position and was heterogeneous being composed of clones with different HSVs (traces ended in 813, 663, 772, 301 and 891). Panel B: Treecluster analysis showed the most similar homeologs clustered into 4 or more separate sets as expected for an octaploid-like region (circled). Panel C: The sequences found among eight BACs that overlapped H53F21 in contig 9077were re-sequenced. A set of SNHs separated the BACs into two of the four groups expected to be present in contig 9077 from the data shown in Panel A. The region shown corresponds to the 152–210 bp of the BES encompassing the 22 bp region in bold and underlined in Panel A that contained two HSV.