Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana.

Basic helix-loop-helix (bHLH) transcription factors represent a family of proteins that contain a bHLH domain, a motif involved in binding DNA. Recently, two groups independently analyzed the BHLH gene family of Arabidopsis thaliana (Heim et al., 2003; Toledo-Ortiz et al., 2003). These analyses revealed that this family is one of the largest transcription factor gene families in Arabidopsis thaliana . Although both analyses intended to give complete overviews of AtBHLH genes, some discrepancies were detected when the data sets were compared. After careful re-examination, we have resolved these discrepancies. In Table 1, we provide a uniform nomenclature for all of the genes that are mentioned in our two articles, and we encourage the use of this nomenclature in future reports concerning bHLH domain transcription factors (e.g., AtBHLH042 / TT8 ). Cross-referencing between the two data sets and further analysis have extended the total number of detected AtBHLH genes to 162 (Table 1). We assume that this count is very close to the final number of AtBHLH genes present in the Arabidopsis thaliana genome, but clearly, corrections or additions to the “complete” Arabidopsis thaliana genome sequence in the future still may cause this number to change. During examination and comparison of the data sets, we observed some common problems that contributed to the discrepancies. These problems arise commonly during the handling of large data sets and are discussed here to aid future attempts at gene family annotation. The main reasons for discrepancies were as follows.