Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.
Identifieur interne : 003885 ( Main/Corpus ); précédent : 003884; suivant : 003886Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.
Auteurs : An-Yuan Guo ; Qi-Hui Zhu ; Xiaocheng Gu ; Song Ge ; Ji Yang ; Jingchu LuoSource :
- Gene [ 0378-1119 ] ; 2008.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : MicroRNAs.
- Binding Sites, Conserved Sequence, Evolution, Molecular, Genes, Plant, Genome, Plant, Multigene Family, Phylogeny, Transcription Factors, Zinc Fingers.
Abstract
We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land-plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land-plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.
DOI: 10.1016/j.gene.2008.03.016
PubMed: 18495384
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pubmed:18495384Le document en format XML
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<author><name sortKey="Guo, An Yuan" sort="Guo, An Yuan" uniqKey="Guo A" first="An-Yuan" last="Guo">An-Yuan Guo</name>
<affiliation><nlm:affiliation>College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing, 100871, China.</nlm:affiliation>
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<author><name sortKey="Zhu, Qi Hui" sort="Zhu, Qi Hui" uniqKey="Zhu Q" first="Qi-Hui" last="Zhu">Qi-Hui Zhu</name>
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<author><name sortKey="Gu, Xiaocheng" sort="Gu, Xiaocheng" uniqKey="Gu X" first="Xiaocheng" last="Gu">Xiaocheng Gu</name>
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<author><name sortKey="Ge, Song" sort="Ge, Song" uniqKey="Ge S" first="Song" last="Ge">Song Ge</name>
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<author><name sortKey="Yang, Ji" sort="Yang, Ji" uniqKey="Yang J" first="Ji" last="Yang">Ji Yang</name>
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<author><name sortKey="Luo, Jingchu" sort="Luo, Jingchu" uniqKey="Luo J" first="Jingchu" last="Luo">Jingchu Luo</name>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites (MeSH)</term>
<term>Conserved Sequence (MeSH)</term>
<term>Evolution, Molecular (MeSH)</term>
<term>Genes, Plant (MeSH)</term>
<term>Genome, Plant (MeSH)</term>
<term>MicroRNAs (analysis)</term>
<term>Multigene Family (MeSH)</term>
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<term>Transcription Factors (MeSH)</term>
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<term>Evolution, Molecular</term>
<term>Genes, Plant</term>
<term>Genome, Plant</term>
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<front><div type="abstract" xml:lang="en">We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land-plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land-plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.</div>
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<Abstract><AbstractText>We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land-plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land-plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.</AbstractText>
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