Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.
Identifieur interne : 003E37 ( Main/Corpus ); précédent : 003E36; suivant : 003E38Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.
Auteurs : Stefanie De Bodt ; Guenter Theissen ; Yves Van De PeerSource :
- Molecular biology and evolution [ 0737-4038 ] ; 2006.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : MADS Domain Proteins.
- classification : Populus.
- genetics : Arabidopsis, Populus, Promoter Regions, Genetic.
- Conserved Sequence, Gene Duplication, Genetic Speciation, Genome, Plant, Phylogeny.
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/nonfunctionalization, and subfunctionalization.
DOI: 10.1093/molbev/msk016
PubMed: 16581940
Links to Exploration step
pubmed:16581940Le document en format XML
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<author><name sortKey="De Bodt, Stefanie" sort="De Bodt, Stefanie" uniqKey="De Bodt S" first="Stefanie" last="De Bodt">Stefanie De Bodt</name>
<affiliation><nlm:affiliation>Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Ghent, Belgium.</nlm:affiliation>
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<author><name sortKey="Theissen, Guenter" sort="Theissen, Guenter" uniqKey="Theissen G" first="Guenter" last="Theissen">Guenter Theissen</name>
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<author><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name>
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<author><name sortKey="Theissen, Guenter" sort="Theissen, Guenter" uniqKey="Theissen G" first="Guenter" last="Theissen">Guenter Theissen</name>
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<series><title level="j">Molecular biology and evolution</title>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term>
<term>Conserved Sequence (MeSH)</term>
<term>Gene Duplication (MeSH)</term>
<term>Genetic Speciation (MeSH)</term>
<term>Genome, Plant (MeSH)</term>
<term>MADS Domain Proteins (genetics)</term>
<term>Phylogeny (MeSH)</term>
<term>Populus (classification)</term>
<term>Populus (genetics)</term>
<term>Promoter Regions, Genetic (genetics)</term>
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<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MADS Domain Proteins</term>
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<term>Populus</term>
<term>Promoter Regions, Genetic</term>
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<keywords scheme="MESH" xml:lang="en"><term>Conserved Sequence</term>
<term>Gene Duplication</term>
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<front><div type="abstract" xml:lang="en">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/nonfunctionalization, and subfunctionalization.</div>
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<Title>Molecular biology and evolution</Title>
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<ArticleTitle>Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.</ArticleTitle>
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<Abstract><AbstractText>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/nonfunctionalization, and subfunctionalization.</AbstractText>
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