Phylogenetic analysis for amino acid sequences of selected plant bHLH TFs (A) and Alignment analysis of the bHLH2 domain (B). The sequences of bHLH domain of 58 selected plant bHLH TFs were analyzed using PhyML v. 3.0. The polar tree cladogram presented in panel A was visualized using FigTree v.1.3.1. (see Methods). The lengths of branches are expressed in aLTR values corresponding to the scale. Alignment of the bHLH domains of hop HlbHLH2, petunia PhAN1 and A. thaliana AtbHLH042 (TT8) is shown in panel B. The bHLH domain of HlbHLH2 was identified by similarity to the TT8 domain as described by . Amino acids within the basic region crucial for G-box DNA binders  are indicated by squares. See additional file 3 for amino acid alignment, ID numbers and annotations of individual TFs.