Romeuf et al. BMC Genomics 2010, 11:185 http://www.biomedcentral.com/1471-2164/11/185 48% 18% Page 10 of 15 10% 13% 2% 9% whole plant shoot root leaf crown spike Figure 5 Expression of Dof sequences in various organs of wheat. 226 libraries that represent 98% of the publicly available wheat sequences of this kind. The genomes of grasses are very different in terms of size, ploidy level and chromosome number. Despite these significant differences, the linear order of genes and protein coding sequences are very well conserved between genomes. Thus, the rice genome can serve as a good model for identifying genes in larger non sequenced genomes like the wheat genome. In addition, O. sativa TFs have been well defined [3,8] and informa- tion on these TFs has been organized into databases. Thus this species is ideally suited for comparative geno- mics like identifying wheat TFs. In the first step of our study, we used all TF protein sequences from rice DRTF as seed in Blast searches to better identify wheat TFs compared to using HMMER or core-consensus sequences. Significant similarity between known rice TF proteins and wheat accessions showed that 7,112 wheat accessions potentially belong to TF gene families. A minimum of 3,820 genes really corresponded to wheat TFs as they have a DNA-binding domain characteristic of a regulatory protein. Within the wheat data, we found members corresponding to every rice TF family suggesting that TF families are conserved between rice and wheat. Previous global approaches to studying plant TFs have already led to some TFs being identified from bread wheat ESTs [33]. PlantTFDB http://planttfdb.cbi. pku.edu.cn is a plant TF database for five model organ- isms, including Arabidopsis (DATF) and rice (DRTF), and 17 other plant species including wheat [33]. In October 2006 1,127 TFs were identified from wheat transcripts available in PlantGDB (v155a; http://www. plantgdb.org/) based on HMMER searches of the Pfam database (v20.0). These 1,127 TFs were classified into 57 families. For six families - GARP-ARR-B, HRT-like, LFY, NZZ, SRS, and ZF-HD - no TF was identified based on these criteria and no detail was given on whether allowance was made for the polyploidy of wheat. Two reasons could explain the differences between the results of this previous study and the work we report here. First, the results depend on the methods and cut-offs used, more or less stringent, to predict TFs. Depending on how the data is to be used, either high sensitivity or high specificity may be more desirable. Generally, stringent filtering is used to avoid false posi- tives. To increase the chances of isolating TF genes from expressed sequences, especially for short or incom- plete sequences and divergent members of gene families, we used less stringent criteria. Second, progress in gen- erating DNA sequences in recent years has vastly increased the number of expressed sequences available in databanks to be searched. As the full genome sequence of wheat is not yet available, using all these sequences to update the catalogue of TF genes is useful.