Figure 8

K -mer frequencies across orthologous regions of three maize cultivars. The B73-based WGS index was used to annotate the Bronze-1 locus and surrounding regions in cultivars B73, McC and Mo17 (Genbank accession numbers AF448416, AF391808, and AY664416, respectively). Orthologous genes present in all three cultivars are connected with red lines. The Bronze-1 locus is shown with an asterisk. Helitrons HelA and HelB in McC, were previously described by [45]. Ty1/copia retrotransposons are shown in red while those of the Ty3/gypsy class are shown in yellow, as classified using MIPS REcat masking. Though the transposition histories vary across the three cultivars, the frequency index can successfully be used to annotate the repeat regions in McC and Mo17.