In contrast to the uniform DBD occurrence in Bacteria, a shows more distinct expansion patterns among the three main eukaryotic kingdoms: Metazoa (animals), Fungi and Viridiplantae (plants). Indeed, a relatively small proportion (29%) of eukaryotic DBD families have Eukaryota as their taxonomic limit. These eukaryotic families include the zinc finger families, HLH (helix-loop-helix) and bZIPs (basic leucine zippers). In addition, the homeobox family, well known for its role in morphogenesis and animal body development 
, is found throughout eukaryotic organisms, including fungi and plants.
The most notable difference in the Metazoa is between vertebrates and invertebrates. Although the majority of DBDs found in animals are present in both groups, the expansion tends to be less pronounced in the invertebrates. The DBDs with particularly extensive expansion in vertebrates include STAT (signal transduction), T-box (body plan and organogenesis) and p53 (cell cycle arrest and apoptosis). DBDs such as IRF (interferon regulator factor) and Churchill (neural development) are absent from invertebrates, which might reflect the more elaborate immune and nervous systems in vertebrates. In contrast, the Runt and GCM families regulate fundamental developmental processes in both vertebrates and invertebrates, and are equally expanded in both groups.
Metazoa and Fungi are phylogenetically closer and share more DBD families with Viridiplantae (see the supplementary material online
). In accordance with earlier work 
, we observed a number of fungal-specific DBDs, including Zn2/Cys6 (Zn cluster), and Copper-fist (copper utilisation). Interestingly, HTH_AraC (arabinose operon regulatory) and FMN (flavin mononucleotide) binding domains are exceptional cases of bacterial DBDs broadly found across Fungi. These families have been shown experimentally to be involved in sugar uptake 
and sporulation regulation 
in Bacteria. Their functionality in Fungi has yet to be investigated. Plants possess a number of mainly plant-specific DBDs, such as AP2 (activation of defence genes) and SBP (flowering development).
Apart from the three major kingdoms, we observe an interesting DBD occurrence in the unicellular eukaryote Monosiga brevicollis,
a marine choanoflagellate that is thought to be the closest sequenced unicellular relative of animals 
. Earlier studies showed that the species contains a considerable amount of signalling components in common with animals 
. Besides the more elaborate signalling machineries, uni- to multicellular transitions also require a greater amount of components that contribute to the more complex genetic regulatory networks in functionally diverse cell types 
. One possible way to enhance the regulation capacity is by recruiting novel sets of TFs. We observed DBDs common to the fungi/animal group in M. brevicollis
, and many DBDs specific to animals (MB, a). Among these DBDs there are families that regulate animal-specific processes such as STAT (signal transduction), p53 (apoptosis) and Tub (nervous system development), as well as those involved in more general pathways like E2F/DP (cell cycle).
In addition, we observed several interesting DBD occurrences in rare protist genomes (a). For example, STAT and WRKY were detected in Dictyostelid
and are detected in our dataset. We note the occurrence of two DBDs thought to be plant-specific DBDs in protists. Apart from AP2, which was detected in apicomplexa 
, we discovered a rare presence of the zinc finger LSD1 in many euglenozoa for the first time. Our understanding of transcriptional regulation and the number of sequenced genomes in these protists are, however, still very limited.