Fig. 1

Phylogenetic relationships of CMTs across Embryophyta. a CMTs are separated into four monophyletic clades based on bootstrap support and the relationship of A. thaliana CMTs: (1) the gbM-dependent CMT superclade with subclades CMT1, CMT3, ZMET, and A. trichopoda; (2) CMT2; and (3) homologous (hCMT) α and β. CMT1 and CMT3 clades only contain eudicot species of plants suggesting a eudicot-specific duplication event that occurred after the divergence of eudicots from monocots and monocots/commelinids. Sister to CMT1 and CMT3 is the monophyletic group ZMET, which contains monocots, monocots/commelinids, and magnoliids. CMT2 is sister to CMT1 and CMT3. Lastly, the polyphyletic hCMT clades are sister to all previously mentioned clades. HCMTα is sister to CMT2 and the CMT superclade and contains gymnosperm and ferns. HCMTβ contains gymnosperms, ferns, and other early diverging land plants. b A collapsed CMT gene family tree showing the seven clades described in (a). Pie charts represent species diversity within each clade and are scaled to the number of species. Two duplication events shared by all angiosperms (ε) and eudicots (ϒ) gave rise to what is now referred to as CMT1, CMT2, and CMT3. These duplication events correspond to what was reported by Jiao et al. (2011). Values at nodes in (a) and (b) represent bootstrap support from 1000 replicates and (a) was rooted to the clade containing all liverwort species