Figure 3

Example alignments of MSLL BACs with maize genomic assemblies. (a) routine observation, with the genes shown by arrows and the areas between the genome primarily comprised of LTR retrotransposons and a few other repeats. (b) unusual alignment, where MSLL ends flank apparently methylated genes. Predicted genes are shown by arrows, with the size and orientation indicating the predicted size and transcriptional orientation of the candidate gene. Each vertical lines indicates a gap in the sequence assembly, while the triangles indicate sites for the restriction enzyme Sal I, which was used to generate the two BACs shown. The genomic sequence scaffolds depicted are from Bruggmann and coworkers [31].