Figure 7

MegaBlast analysis showing sequence identity to WGS reads using the BES CG817343 from H77P02 in octaploid-like contig 9354. Sequence analysis strongly supported the inferred octaploid-like structure for the region coalesced by fingerprints. MegaBlast against 7.3 million reads with repeat masking gave 3 identical matches (trace files ending 440, 810 and 625) among 68 homeologous sequences. Homeolog cluster 1 was composed of traces ending in 688, 254 278, 421 and 994 that shared GT instead of AC at position 114–115 (circled). Cluster 2 was composed of clones ending in 790, 233, 613 and 714 shared C instead of T at position 64 but not the G of Cluster 3. Cluster 3 was composed of clones ending in 326, 934, 443, 682 and 172 that shared G instead of A at position 73. Clusters 4, 5 and 6 contained more than 4 reads suggesting this region may be over-represented in the WGS collection or contain repetitive DNA.