Romeuf et al. BMC Genomics 2010, 11:185 http://www.biomedcentral.com/1471-2164/11/185 OHIO-ATTFDB [4], RARTF http://rarge.gsc.riken.jp/ rartf/, TRANSFAC [5] and TrSDB [6]. Another Arabi- dopsis TF database (DATF, http://datf.cbi.pku.edu.cn/) was created that integrates information from multiple sources (expressed sequence tags (ESTs), transcription factor binding sites) and contains 1,922 known or pre- dicted TF sequences, classified in 64 families [7]. The same approach was taken for both O. sativa spp. japo- nica and spp. indica to create DRTF http://drtf.cbi.pku. edu.cn/, which contains 2,384 rice TF sequences classi- fied in 63 families [8]. The discrepancies in the total number of TFs included in databases and the classifica- tion into families for the same species depends on the methods used for predicting TFs. For example, the dif- ferences between the dataset in DRTF and the results of Xiong et al. [3] are mostly because of new annotation in the latest version (Release 4) of the TIGR database that uses a broader definition of TFs. The sensu stricto defi- nition of TFs is based on the DNA binding domain, but in the broader sense proteins having co-activator activity can also be considered as TFs. This broader definition explains why more TF families (63 versus 37) were found more recently. Wheat is the most important crop in world food pro- duction. Triticum aestivum and other cereal genomes are substantially larger than those of A. thaliana and O. sativa. The genome of hexaploid wheat is about 16,000 Mb which is 38 times larger than that of the monocotyle- don model O. sativa. It is an allohexaploid composed of three homoeologous subgenomes, AA, BB, and DD, thus generally each gene is represented by three homoeolo- gous copies. The large hexaploid nature of the genome is a drawback in determining the complete sequence which is not yet available. Nevertheless, many wheat cDNA libraries have been constructed generating a rich source of ESTs; more than one million wheat ESTs are currently available in dbEST [9]. These ESTs have been assembled into contigs such as Tentative consensus (TC) contigs ([10]; http://compbio.dfci.harvard.edu/cgi-bin/tgi/gimain. pl?gudb=Wheat) along with data collated from the NCBI GenBank nucleotide database (full length and partial cDNAs). ESTs directly represent the transcribed portions of the genome so while waiting for the full genome to be sequenced, the analysis of expressed sequences is a good starting point for gene discovery. Recently some T. aestivum TF families have been described such as MIKC-type MADS-box [11], NF-Y and Dr1 [12], Myb [13] and the plant-specific DOF (DNA-binding with One Finger) gene families [14,15]. The DNA-binding domain of DOF proteins contains 52 amino acids structured as a Cys2/Cys2 zinc finger [16]. This domain recognizes and binds a core motif 5’- AAAG-3’ on gene promoters [17]. In the Arabidopsis and rice genomes 36 and 30 Dof genes have been Page 2 of 15 identified, respectively, and phylogenetic relationships between the genes have been established such that four major orthologous clusters have been defined [1,15]. Recently, 26 different Dof genes were identified in barley by sequence analysis of clones isolated by screening genomic libraries and ESTs [18]. By analysing soybean ESTs, 39 putative unigenes that encode DOF proteins were identified [19], 27 of which were confirmed as hav- ing the highly conserved domain [20]. DOF TFs participate in the regulation of many pro- cesses exclusive to plants. For example in barley, DOF TFs are involved at several developmental stages in seeds, in the accumulation of storage proteins and in germination [21-23]. In wheat, two Dof genes have been reported: wheat prolamin-box binding factor (WPBF), shown to be an activator of T. aestivum L. storage pro- tein genes [24], and TaDof1 [25]. The three homoeolo- gous genes encoding WPBF were sequenced and shown to be specifically expressed in seeds between 3 and 39 days after anthesis [26]. The aim of this study was to identify all unique T. aestivum TFs (i.e. each homoeolog is considered inde- pendently) by using generally available wheat transcript sequences and the model plant rice genome. We con- structed a database compiling the wheat TF sequences identified, the corresponding in silico expression data and the predicted DNA-binding domains. The study of DOF family members illustrates the utility of wDBTF and the overall analytical approach. Construction and content Source data and database construction The 2,384 putative TF protein sequences of O. sativa japonica were downloaded from the DRTF database http://drtf.cbi.pku.edu.cn/. T. aestivum sequences were downloaded from the Gene Indices database (wheat lat- est release 11.0, http://compbio.dfci.harvard.edu/tgi/ plant.html) which represents 1,036,933 sequences either as TC contigs or singletons. The wheat sequences were translated to peptide sequences and compared using the BlastX program [27] with O. sativa japonica TF pro- teins. We used an e-value cut-off of 1e-05 with other parameters at the default setting, keeping only the best Blast hit. As TFs are composed of several conserved domains, some BlastX results gave a high Blast score against a rice TF protein because of particular conserved domains but were not really related to the query TF. To avoid such false associations, all Blast results were checked by eye and the database was edited to remove 2,296 sequences. The wheat TF sequences identified were compiled in the wDBTF database (Figure 1). The amino acid sequences from T. aestivum were deduced from BlastX alignment against O. sativa pro- teins using the method described by Sado et al. [28].