Romeuf et al. BMC Genomics 2010, 11:185 http://www.biomedcentral.com/1471-2164/11/185 18 16 14 s 12 e c n e u q s e 10 d e s s e r exp 8 f o r e b um 6 N 4 2 0 Page 11 of 15 whole plant shoot root leaf crown spike TC2774T1C42774T3C82775T7C32840T9C82854T8C12855T9C02859T3C02899T1C62939T6C62982T1C62984T7C93067T8C13109T5C53142T7C93154T7C93158T1C33161T5C53212T3C23327T8C73352T3C53398T4C53441T6C33558T1C23561T5C2361262 Figure 6 Tissue specific in silico expression of wheat Dof as represented by EST contigs. To evaluate the accuracy and reliability of TFs identi- fied in this way, we compared our results to other recent studies of wheat TF families. Using rice TF pro- teins from PlnTFDB v2.0 as seed in Tblastn searches, Shaw et al. [34] identified wheat Dof. Sequences con- taining the Dof domain were re-assembled with the cri- terion of 98% nucleotide identity thus defining 31 Dof genes. Similarly, we identified 28 Dof-domain genes using a different strategy based on another source of rice protein sequences. The differences observed may come from the way ESTs are assembled and from the discovery of a previously unpublished Dof member. Another TF family has been studied in detail by Ste- phenson et al. [12] who identified 37 CCAAT binding factors based in a Tblastn search of several EST sources (available in October 2006) with an e-value cutoff of 1e- 08 using the core-conserved sequences of O. sativa and A. thaliana. With recent data and less stringent criteria we detected 81 CCAAT binding factors including those TFs previously detected. The results obtained with Dof and CCAAT TFs suggest that our approach performs well and with acceptable accuracy. In plants, 5% to 7% of all the protein-encoding genes are for TFs [1,35]. Because many of the grass genomes are not yet completely sequenced or annotated, the total number of TFs expected is hard to predict. Based on the information available for four sequenced genomes, i. e. from Arabidopsis, rice, poplar (Populus trichocarpa), and Chlamydomonas (Chlamydomonas reinhardtii), lin- ear regression was used to predict the number of TFs in non sequenced genomes from the total number of genes [36]. Studies based on the annotation of BAC sequences suggest that the hexaploid wheat genome could contain 108,000 genes [37] or between 164,000 and 334,000 pro- tein-encoding genes including pseudogenes [38]. Thus, applying the linear regression to wheat would give 9,676 TFs. We have found a minimum of 3,820 sequences coding for TFs in data currently available, i.e. almost 40% of the expected number. However, 7,112 (about 73% of the expected number) wheat accessions have