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First published online July 9, 2004; 10.1104/pp.104.039669

Plant Physiology 135:1738-1752 (2004)
© 2004 American Society of Plant Biologists

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GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

Contrasting Modes of Diversification in the Aux/IAA and ARF Gene Families1,[w]

David L. Remington*, Todd J. Vision, Thomas J. Guilfoyle and Jason W. Reed

Department of Biology, University of North Carolina, Greensboro, North Carolina 27402–6170 (D.L.R.); Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599–3280 (T.J.V., J.W.R.); and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211 (T.J.G.)

The complete genomic sequence for Arabidopsis provides the opportunity to combine phylogenetic and genomic approaches to study the evolution of gene families in plants. The Aux/IAA and ARF gene families, consisting of 29 and 23 loci in Arabidopsis, respectively, encode proteins that interact to mediate auxin responses and regulate various aspects of plant morphological development. We developed scenarios for the genomic proliferation of the Aux/IAA and ARF families by combining phylogenetic analysis with information on the relationship between each locus and the previously identified duplicated genomic segments in Arabidopsis. This analysis shows that both gene families date back at least to the origin of land plants and that the major Aux/IAA and ARF lineages originated before the monocot-eudicot divergence. We found that the extant Aux/IAA loci arose primarily through segmental duplication events, in sharp contrast to the ARF family and to the general pattern of gene family proliferation in Arabidopsis. Possible explanations for the unusual mode of Aux/IAA duplication include evolutionary constraints imposed by complex interactions among proteins and pathways, or the presence of long-distance cis-regulatory sequences. The antiquity of the two gene families and the unusual mode of Aux/IAA diversification have a number of potential implications for understanding both the functional and evolutionary roles of these genes.

1 This work was supported in part by the National Institutes of Health (Individual Postdoctoral Fellowship 5–F32–GM29554 to D.L.R. and grant no. R01–GM52456 to J.W.R.) and by the National Science Foundation (grant no. IBN–0116106 to J.W.R. and T.J.G., grant no. MCB–0080096 to T.J.G., and grant no. DBI–0227314 to T.J.V.).

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

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.104.039669.

* Corresponding author; e-mail dlreming{at}uncg.edu; fax 336–334–5839.

Received January 23, 2004; returned for revision April 22, 2004; accepted April 26, 2004.




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