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Published on March 2, 2007; 10.1104/pp.107.095760

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Received January 10, 2007
Accepted February 19, 2007

PlanTAPDB: A Phylogeny-based Resource of Plant Transcription Associated Proteins

Sandra Richardt , Daniel Lang , Ralf Reski , Wolfgang Frank , and Stefan A. Rensing *

Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, D-79104 Freiburg, Germany

* Corresponding author; email: stefan.rensing{at}biologie.uni-freiburg.de.

Diversification of transcription associated protein families during land plant evolution is a key process yielding increased complexity of plant life. Understanding the evolutionary relationships between these genes is crucial to the insight of plant evolution. We have determined a substantial set of transcription associated proteins which are focused on, but not limited to, land plants by using PSI-BLAST searches and subsequent filtering and clustering steps. Phylogenies were created in an automated way using a combination of distance and maximum likelihood methods. Comparison of the data to previously published work confirmed their accuracy and usefulness for the majority of gene families. Evidence is presented that the flowering plant apical stem cell regulator WUSCHEL evolved from an ancestral homeobox gene which was already present after the water to land transition. The presence of distinct expanded gene families, such as COP1 and HIT in moss, is discussed within the evolutionary backdrop. Comparative analyses revealed that almost all angiosperm transcription factor families were already present in the earliest land plants, while many are missing among unicellular algae. A global analysis not only of transcription factors but also of transcriptional regulators and novel putative families is presented. A wealth of data about plant transcription associated protein families and all data accrued throughout their automated detection and analysis is made available via the PlanTAPDB web interface. Evolutionary relationships of these genes are readily accessible to the non-expert at a mouse-click. Initial analyses of selected gene families revealed that PlanTAPDB can easily be exerted for knowledge discovery.




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