Fig. 8

The shared history of chromosomes in columbine, grape, and cacao. Gene order-based clustering results (left panel) are summarized here for the chromosomes harboring the “orange” and “green” homologous portions. The former corresponds to 5, 7, 14 in grape and 1, 4, 5 in cacao. The latter corresponds to 3, 4 + 7 (products of a fission), 18 in grape, and 1, 2, 8 in cacao. In columbine, the “orange” portions are on chromosomes 2 and 5 while the “green” portions are on chromosomes 6 and 5, each pair of which being denoted as colum A and colum B, respectively. Both grape- and cacao-columbine pairing distinguish tetraploidy-derived regions (blue and purple rectangles) from hybridization-derived ones (light blue rectangles), defining the orthologous sets of regions across the three eudicot genomes (right panel). The conservation of gene order exclusively between the putatively orthologous regions of grape and cacao (black arrows, Additional file 1: Figure S10) further strengthens our columbine-based inference of orthology