Phylogenetic analysis and divergence time estimation

Multiple sequence alignments on all single‐copy genes were performed and then combined to construct a phylogenetic tree called a super alignment matrix. Here, we performed the construction of 13 species phylogenetic trees (ML TREE) by a maximum likelihood method using RAxML software (Stamatakis, 2014). This study used 519 single‐copy gene families to estimate divergence time using MCMCTree in the PAML software (Yang, 2007). The time correction points were as follows: C. sativum and M. truncatula (107–125 Mya), B. rapa and P. trichocarpa (107.0–109.0 Mya), B. rapa and M. truncatula (107–109 Mya), O. sativa and N. nucifera (140–200 Mya), and B. rapa and A. thaliana (20.4–30.9 Mya). The time correction points were from TimeTree website (Kumar et al., 2017). The operating parameters of MCMCTree were burn‐in = 5 000 000, sample number = 1 000 000 and sample frequency = 50.