Phylogenetic relationships in the vascular plants, moss, and algaes. Maximum likelihood analysis of 696 plant bHLHs show as cladogram, and was rooted with a node of red algae protein. The gray balloons delineate the 18 subfamilies of bHLH proteins. Colored dots symbolize the species to which the bHLH proteins in each group belong (yellow: Oryza sativa [monocot]; red: Solanum lycopersicum [eudicot]; green: Arabidopsis thaliana [eudicot]; light-blue: Selaginella moellendorffii [lycophyte]; purple: Physcomitrella patens [moss]; black: Volvox carteri, Chlamydomonas reinhardtii, and Cyanidioschyzon merolae [chlorophytes and red algae]). A full tree with protein names is given in Additional file 10.