Fig. 4

Gain and loss of TLP genes in seven grass species. A The reconciliation between the species tree and gene tree along with the confirmation of the gene loss/duplication scenario was performed using Notung. The species tree is shown in Fig. 2B. The gene tree is shown in Fig. 1. Red “D”s at branching points indicate predicted gene duplications. Grey branches indicate gene losses. B Schematic diagram of gain and loss of tubby-like protein (TLP) genes in seven grass species. The numbers in the rectangles and circles represent the number of TLP genes in ancestors and existing species. The + and − signs represent the gain and loss of genes, respectively. C Evolutionary patterns of TLP genes in seven grass species. Z-S-S-S-B-H-O indicates the common ancestor of all seven grass species; Z-S-–S-S indicates the common ancestor of maize, sorghum, foxtail millet, and green foxtail; Z-S indicates the common ancestor of maize and sorghum; S-S indicates the common ancestor of foxtail millet and green foxtail; B-H-O indicates the common ancestor of Brachypodium, barley, and rice; and B-H indicates the common ancestor of Brachypodium and barley