Figure 3

Analysis of the right hand BES CG825359 from B47P08 in diploid contig 321. Sequence analysis suggested the inferred diploid contig contained a short octaploid-like region not detected by fingerprints. Panel A: Analysis of the BAC end from B47P08 detected an octaploid-like region on the end of ctg321. MegaBlast of CG825359 against 7.3 million reads with repeat masking gave 3 nearly identical sequences and 42 homeologus sequences. Among the 3 nearly identical matches a SNP was evident at nucleotide position 123 (circled). From positions 141 to 177 a set of four SNH polymorphisms were evident (circled in red at 141, blue at 143, dotted 148 and black at 170) that separated the homeologs into 4 groups. Panel B: Tree cluster analysis at 90% sequence identity showed the most similar homeologs clustered into 4 sets as expected for octaploid-like region in an inbreeding species. Clusters sharing SNHs are circled in red at nucleotide 141 (3 reads), blue at 143 (five reads), black dotted 148 (13 reads) and black solid at 170 (21 reads).