Phylogenetic relationships of WOX family proteins. (a) Relationship of the WOX family to the other members of the HB transcription factor superfamily. Proteins matching the PFAM Homeodomain hidden Markov model (PF00046)  were retrieved from completely sequenced genomes of plants, animals, algae and non-photosynthetic protists and subjected to multiple sequence alignment using MAFFT . After manual removal of nonconserved regions, essentially resulting in an alignment of homeodomains, phylogenetic inference was conducted using quicktree_sd [51, 52]. Subsequent midpoint-rooting and visualization was performed using FigTree v1.2.2 . Branch width corresponds to bootstrap support. The WOX family is in red. Other HB protein families consisting exclusively of proteins from one of the three kingdoms are colored in green (plants), blue (animals) and cyan (fungi), respectively. Families specific to opisthokonts (animals and fungi) are colored in brown (these clusters contain occasional protist sequences, for example, from Mycetozoa and Amoebozoa). Families indicated in black consist of members from both plants and opisthokonts or contain significant amounts of protist (algal, protozoan) sequences. (b) The WOX protein family. Proteins from genomes of completely sequenced plant and algal species were used to generate this phylogeny, which is essentially a representation of the red clade from (a). After manual removal of regions of low alignment quality, phylogenetic inference was conducted using MrBayes . Branch width corresponds to support values; the A. thaliana proteins are shown in red. The three subclades are color-coded, WUS/WOX1-7 (WUS) in purple, WOX8, 9, 11, 12 (intermediate) in orange and WOX10, 13, 14 (ancient) in green.