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First published online January 11, 2006; 10.1104/pp.105.073783

Plant Physiology 140:411-432 (2006)
© 2006 American Society of Plant Biologists

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GENOME ANALYSIS

Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice[W]

Toshitsugu Nakano1, Kaoru Suzuki1, Tatsuhito Fujimura and Hideaki Shinshi*

Molecular and Cellular Breeding Research Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305–8566, Japan (T.N., K.S., H.S.); and Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305–8672, Japan (T.N., T.F.)

Genes in the ERF family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. In this study, a comprehensive computational analysis identified 122 and 139 ERF family genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L. subsp. japonica), respectively. A complete overview of this gene family in Arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. As a result of these analyses, the ERF families in Arabidopsis and rice were divided into 12 and 15 groups, respectively, and several of these groups were further divided into subgroups. Based on the observation that 11 of these groups were present in both Arabidopsis and rice, it was concluded that the major functional diversification within the ERF family predated the monocot/dicot divergence. In contrast, some groups/subgroups are species specific. We discuss the relationship between the structure and function of the ERF family proteins based on these results and published information. It was further concluded that the expansion of the ERF family in plants might have been due to chromosomal/segmental duplication and tandem duplication, as well as more ancient transposition and homing. These results will be useful for future functional analyses of the ERF family genes.

1 These authors contributed equally to the paper.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Hideaki Shinshi (h.shinshi{at}aist.go.jp).

[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.073783.

* Corresponding author; e-mail h.shinshi{at}aist.go.jp; fax 81–29–861–6090.

Received November 7, 2005; returned for revision December 5, 2005; accepted December 14, 2005.




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