Figure 3

Graph based clustering analysis of repetitive elements in the three species. Graph layouts of the four largest clusters of repetitive elements detected in the graph based clustering analysis. Herrania balaensis is shown on the left, T. grandiflorum in the middle and T. cacao cv. Criollo on the right. Clusters are ordered by size, with largest at the top and fourth largest at the bottom. Below each graph layout is the class of the repetitive element, the genome percentage of each cluster and number of paired reads belonging to it in parentheses. Coloured regions in the some graphs represent conserved domains identified by RepeatExplorer. A total of 11,243,224 reads were used in the graph based clustering.