Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family
Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family
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DOI：
10.1016/j.gene.2008.03.016
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发表时间：
2008-07-15
期刊：
影响因子：
3.5
通讯作者：
Luo, Jingchu
中科院分区：
文献类型：
--
作者：
Guo, An-Yuan;Zhu, Qi-Hui;Luo, Jingchu
我们进行了全基因组分析，以探索 SBP-box 基因家族的进化过程。我们从代表主要绿色植物谱系的九个物种中鉴定出了 120 个 SBP-box 基因：绿藻、苔藓、石松植物、裸子植物和被子植物。使用SBP-box基因的DNA结合域（SBP域）的蛋白质序列构建了最大似然系统发育树。我们的结果表明，绿藻的所有 SBP-box 基因都聚集到一个进化枝（CR 组）中，而来自陆地植物的所有基因则分为两个不同的组。除杨树外，第一组在每个物种中都有一个副本，而第二组在每个物种中都有多个成员，并且可以分为几个亚组。所有 SBP-box 基因编码的 SBP 结构域都具有两个锌指。 I组和II组的C端锌指具有相同的C2HC基序，而它们的N端锌指显示出不同的特征，I组为C4，II组为C3H。拟南芥和水稻SBP-box基因的外显子-内含子结构模式与系统发育结果一致。 microRNA miR156 的靶位点在陆地植物 SBP-box 基因中高度保守。我们的结果表明，SBP-box 基因家族可能起源于绿色植物的共同祖先，随后在每个谱系中出现复制和分歧，包括外显子-内含子丢失过程。 (C) 2008 Elsevier B.V. 保留所有权利。
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. (C) 2008 Elsevier B.V. All rights reserved.