Fig. 2

Definition of homologous gene quartets and inference of conversion between duplicates. a Definition of homologous gene quartets. Homoeologous chromosomal regions of P. trichocarpa and S. brachista (P and S) are represented by rectangles with different colors. Arrows indicate genes, and the same color indicates homologous genes. A homologous gene quartet consists of paralogous P1 and P2 and their respective orthologous genes S1 and S2. b-e Inference of conversion. The red squares indicate the SCT, and the blue circles indicate the divergence of P. trichocarpa and S. brachista. Expected phylogenetic relationships if no paralogs are affected by conversion are shown in b, P2 converted by P1 is shown in c, S1 converted by S2 is shown in d, and both paralogs affected by conversion are shown in e. (PDF 606 kb)