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Published on March 12, 2008; 10.1104/pp.107.114041

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Received November 27, 2007
Accepted March 4, 2008

Tobacco Transcription Factors: Novel Insights into Transcriptional Regulation in the Solanaceae

Paul J. Rushton , Marta T. Bokowiec , Shengcheng Han , Hongbo Zhang , Jennifer F. Brannock , Xianfeng Chen , Thomas W. Laudeman , and Michael P. Timko *

Department of Biology, University of Virginia, Charlottesville, Virginia 22904 USA Department of Microbiology, University of Virginia Health Systems, Charlottesville, Virginia 22908 USA Academic Computing Health Science, Information Technology & Communication, University of Virginia, Charlottesville, Virginia 22908, USA

* Corresponding author; email: mpt9g{at}virginia.edu.

Tobacco (Nicotiana tabacum L.) is a member of the Solanaceae, one of the agronomically most important groups of flowering plants. We have performed an in silico analysis of 1.15 million gene space sequence reads from the tobacco nuclear genome and report the detailed analysis of over 2,500 tobacco transcription factors (TFs). The tobacco genome contains at least one member of each of the 64 well-characterized TF families identified in sequenced vascular plant genomes, indicating that evolution of the Solanaceae was not associated with the gain or loss of TF families. However, we found notable differences between tobacco and non-Solanaceae species in TF family size and evidence for both tobacco- and Solanaceae-specific subfamily expansions. Compared to TF families from sequenced plant genomes, tobacco has a higher proportion of ERF/AP2, C2H2 zinc finger, homeodomain, GRF, TCP, zinc finger homeodomain, BES and SAP genes and novel subfamilies of BES, C2H2 zinc finger, SAP and NAC genes. The novel NAC subfamily, termed TNACS, appears restricted to the Solanaceae as they are absent from currently sequenced plant genomes but present in tomato, pepper and potato. They comprise about 25% of NAC genes in tobacco. Based on our phylogenetic studies we predict that many of the over 50 tobacco Group IX ERF genes are involved in jasmonate responses. Consistent with this, over two thirds of Group IX ERF genes tested showed increased mRNA levels following jasmonate treatment. Our data is a major resource for the Solanaceae and fills a void in studies of TF families across the plant kingdom.






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