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MBE Advance Access published online on August 22, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl095
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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 August 16, 2006

Research Article

Molecular and Phylogenetic Analyses of the MADS-box Gene Family in Tomato

Lena C. Hileman 1, Jens F. Sundstrom 2, Amy Litt 3, Meiqin Chen 4, Takudzwa Shumba 5, and Vivian F. Irish 6 *

1 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8104; Current Address: University of Kansas, Dept of Ecology and Evolutionary Biology, Lawrence KS 66045, USA
2 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8104; Current address: Dept of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
3 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8104; Current address: New York Botanic Garden, 200th St. and Kazimiroff, Bronx, NY 10458-5126, USA
4 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8104; Current Address: Department of Plant Developmental and Molecular Biology, College of Life Sciences, Peking University. Beijing 100871, P.R. China
5 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8104
6 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8104; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8104

* To whom correspondence should be addressed.
Vivian F. Irish, E-mail: Vivian.irish{at}yale.edu


  Abstract

MIKCc-type MADS-box genes encode key transcriptional regulators of a variety of developmental processes in Arabidopsis thaliana. However, there has been relatively little effort to systematically carry out comparative genomic or functional analyses of these genes across flowering plants. Here we describe a strategy to identify members of the MIKCc-type MADS-box gene family from any angiosperm species of interest. Using this approach, we have identified 24 MIKCc-type MADS-box genes in tomato, including 17 that have not previously been characterized. Using these sequences, we have performed phylogenetic analyses that indicate that there have been a number of gene duplication and loss events in tomato relative to Arabidopsis. We also describe the expression domains of these genes and compare these results to their cognates in Arabidopsis. These analyses demonstrate the utility of this approach for characterizing a large number of MIKCc-type MADS-box genes from any flowering plant species of interest, and provide a framework for evolutionary comparisons of this important gene family across angiosperms.

Keywords: tomato; Solanaceae; homeotic gene; MADS box gene; gene duplication.
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