Fig. 5

Gene order-based clustering expected under ancient tetraploidy common to all eudicots. Represented here by blue and purple rectangles, each member of the paralogous chromosome pair experiences intra-chromosomal rearrangements as a part of the diploidization process. Deletions (denoted as “-”) will create the gene order “1, 3, 5” on the blue chromosome while both deletions and an inversion will create the gene order “2, 1, 4” on the purple chromosome. These differential paralogous gene orders will be inherited by both columbine and grape. If we compare the gene order on the homologous chromosomes of columbine and grape at this particular region, we should see “blue” chromosomes of columbine and grape forming one cluster while “purple” chromosomes of columbine and grape forming another cluster. Note that we show here only the “allohexaploidy” model, which predicts that the third grape paralog added via hybridization is an outgroup in this clustering analysis. See Additional file 1: Figure S11 for the expected gene orders under the “autohexaploidy” model