Soybean Genomics: Developments through the Use of Cultivar “Forrest”
Figure 2
Comparison of MegaBlast analysis of an unduplicated region and a twice duplicated region as inferred by the
fingerprint physical map (a). Analysis of the BESs from H53F21 in quadruplicated contig 9077. These BESs contained a
very common repeat with 400 copies per haploid genome. Sequence analysis supported the inference of four copies of the region per haploid genome made from BAC fingerprint data (a). MegaBlast of H53F21 (Build4MTP8A23, gi89261445) against 7.3 million
reads with repeated masking gave 7 identical matches among 24 homoeologous sequences. Cluster 1 was composed of traces
ending in 822,160,569,607,662,749, and 105 that shared A at position 172 (circled). Homoeolog specific
variations (polymorphisms) were evident among the 4 clusters inferred. Cluster 2 was composed of clones ending
in 749, 850, and 601 that shared C at position 172. Cluster 3 was composed of clones ending in 100, 117, and 535 that shared G at
position 172. Cluster 4 also had G at that position. TreeCluster analysis showed the most similar homoeologs clustered
into 4 separate sets as expected for regions duplicated twice (circled) (b). Analysis of the BESs from B47P08 in contig
321 from an unduplicated region. Sequence analysis supported the inferrence of an unduplicated region made from fingerprints at 90% sequence identity (c). The sequences found among BACs resequenced from contig 9077 showing a set of SNHs (HSVs)
separated two groups of the four inferred to be present: the A cluster and
the G cluster (adapted from [29]).
