TreeTFDB hosted by the RIKEN Biomass Engineering Program and Plant Science Center is a public database that provides the complete transcription factor (TF) repertoires of 6 genome sequenced tree species: papaya (Carica papaya), jatoropha (Jatropha curcas), cassava (Manihot esculenta), poplar (Populus trichocarpa), castor bean (Ricinus communis) and grape vine (Vitis vinifera). from annotated genes on each genome. The current version (ver.1.0) of TreeTFDB contains 1,552 TF models of papaya, 1,481 TF models of jatoropha, 2,638 TF models of cassava, 3,110 TF models of poplar, 1,512 TF models of castor bean and 1,493 TF models of grape vine, respectively. TreeTFDB is aimed at integrating knowledge on the TFs of sequenced industrially important tree members, and providing public resource for transfactoromics and comparative genomics of TFs of tree species, model plants and other organisms.
The papaya, cassava, poplar, castor bean and grape vine sequence data were downloaded from the US Department of Energy Joint Genome Institute, Phytozome v.7.0 (http://www.phytozome.net/). The sequence data of jatoropha genome was downloaded from the web site of Kazusa DNA research institute, Jatropha Genome Database JAT_r3.0 (http://www.kazusa.or.jp/jatropha/).
TreeTFDB: An Integrative Database of the Transcription Factors from Six Economically Important Tree Crops for Functional Predictions and Comparative and Functional Genomics
Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS.
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