Figure 6

Mapping retroelement domains onto the graph. G. max clusters GmCL2 and GmCL35 representing the LTR-retrotransposon gmGYPSY10 were combined in one graph and visualized by SeqGrapheR. (A) Coloring of the nodes is based on the similarity search using blastx against our protein database, revealing the gag and pol coding domains, and the blastn search to detect primer binding sites (pbs). The scheme on the bottom left shows a simplified two-dimensional representation of the same graph. Different shades of red and green are used to distinguish between alternative sequences. To simplify the complicated structure of the layout, the graph has been modified for the purpose of better perceptible visualization by manually removing 214 nodes. (B) Correlation of the graph structure with genomic sequences. The coloring of the graphs is based on the similarity to elements identified in the genomic sequences AC235175 79155-70675 (red) and AC235457 19033-13657 (blue). A diagram of the alignment of these retroelements is shown below the graph in the same color. Vertical lines in the alignment show the regions with similarity.