Fig. 3: Identification of the WGD shared by woody bamboos.

a Number of GDs (red numbers) shared by woody bamboos (WBs) (see also Supplementary Fig. 5). Number in square brackets represents the number of GDs matched by syntenic genes. See Supplementary Fig. 31 for the number of GDs (and GDs matched by syntenic genes) shared by individual species in distinct retention types. #8 in purple rhombus is as in Fig.1 and named here as Kappa. The branches of Bambuseae and Arundinarieae, respectively, are labeled with capital letters A and B, for description of retention type. b Dot-plots illustrating intraspecific collinear blocks (continuous points) of Phyllostachys edulis (left) and Dendrocalamus latiflorus (right) genomes ordered by chromosomes. In each dot-plot, red, blue, green, or orange dots in the top-left part show the GDs mapped at the MRCA of WBs in Supplementary Fig. 5, and the pink dots in the bottom-right part shows the GDs mapped at the MRCA of WBs in Supplementary Fig. 32; different colors represent different retention types as shown below the dot-plots. Gray blocks represent syntenic genes not included in gene trees due to the lack of sufficient species with the gene or low BS support or mapped to other positions. c Number of GDs (green numbers) mapped at Bambusoideae. The meaning of numbers in square brackets is as in Fig. 3a and also shown below. The number in round parentheses represents the number of GDs matched by syntenic genes anchored in the syntenic blocks with some other gene pairs mapped at the WB MRCA. Capital A, WBs; Capital B, herbaceous bamboos (HBs). See details of retention type in Supplementary Fig. 33. d A model of woody bamboo genome evolution. Red star, the Kappa event. Green circle, hybridization between WB ancestor and HBs. Pink squares, speciation events. Blue star, the WGD event shared by hexaploids in Bambuseae. The parental lineage of the third subgenome of paleotropical bamboos in Bambuseae is proposed to have originated in parallel to the two parental lineages of WB ancestor (see topologies in Supplementary Fig. 37). Source data are provided in a Source Data file.