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MBE Advance Access published online on March 31, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msk016
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted March 29, 2006

Research Article

Promoter Analysis of MADS-Box Genes in Eudicots Through Phylogenetic Footprinting

Stefanie De Bodt 1, Guenter Theissen 2, and Yves Van de Peer 1 *

1 Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
2 Friedrich-Schiller-University, Genetics Chair, Philosophenweg 12, D-07743 Jena, Germany

* To whom correspondence should be addressed.
Yves Van de Peer, E-mail: yves.vandepeer{at}psb.ugent.be


  Abstract

The MIKC MADS-box gene family has been shaped by extensive gene duplications giving rise to subfamilies of genes with distinct functions and expression patterns. However, within these subfamilies the functional assignment is not that clear-cut and considerable functional redundancy exists. One way to investigate the diversity in regulation present in these subfamilies is promoter sequence analysis. With the advent of genome sequencing projects, we are now able to exert a comparative analysis of Arabidopsis and poplar promoters of MADS-box genes belonging to the same subfamily. Based on the principle of phylogenetic footprinting, sequences conserved between the promoters of homologous genes are thought to be functional. Here, we have investigated the evolution of MADS-box genes at the promoter level and show that many genes have diverged in their regulatory sequences after duplication and/or speciation. Furthermore, using phylogenetic footprinting, a distinction can be made between redundancy, neo/nonfunctionalisation and subfunctionalisation.

Keywords: phylogenetic footprinting; MADS-box genes; eudicots; evolution; promoter.
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