Fig. 2

Phylogenetic and gene family analysis of M. bimucronata and other representative plant genomes. a Estimation of the divergence time between 8 species. The length of the blue bar represents the range of the divergence time. The numbers at internodes show the median divergence time (million years ago, Mya) with a 95% confidence interval [CI]. One recent WGD event occurred at 6.8 Mya in M. bimucronata and F. albida is indicated by the red color. b Upset diagram showing the distribution of shared gene families among M. bimucronata and the other four species. Gene family complements comparisons among M. bimucronata, F. albida, S. tora, D. odorifera, and M. truncatula. There were 11,546 common gene families and 70 M. bimucronata-specific gene families. c WGD analysis of the F. albida, S. tora, and M. bimucronata genomes. The distribution of synonymous substitution rates (Ks) was analyzed for paralogs within M. bimucronata, S. tora, and F. albida, as well as orthologs between M. bimucronata and the other two genomes. Peaks in the Ks distribution of orthologs imply the potential time of species divergence, while a peak for paralogs indicates a whole genome duplication (WGD) event. d S. tora and M. bimucronata synteny showing the span of their shared regions. The gray line connects matched gene pairs