Fig. 3

Phylogenetic tree of individual Flaveria samples based on m-CDS. To remove the effect of F. pri × F. ang on phylogenetic relationships among other species, the phylogenetic tree was constructed without F. pri × F. ang. The m-CDS of A. thaliana was used as mapping reference to construct consensus sequence (CS) matrix according to Fig. 1. A CS matrix with 343,590 sites from 2,190 genes was used to infer phylogenetic relationships based on both Bayesian inference (BI) and Maximum likelihood (ML) using GTR + GAMMA + I model of sequence substitution and variation. BI tree and ML tree showed consistent topology. The numbers besides each node were posterior probability inferred from 1000,000 generations (up) and bootstrap score (down) from 500 bootstrap sampling. (^#/shoot^#/root^#/: leaf/shoot/root sample from HHU, j/m: juvenile/mature leaf sample from 1KP. m-CDS: reference contains the longest gene for each paralog family)