Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics.
Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics.
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Dof 转录因子基因家族的全基因组分析揭示了大豆特异性的复制和功能特征
DOI：
10.1371/journal.pone.0076809
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Qiu LJ
中科院分区：
文献类型：
--
作者：
Guo Y;Qiu LJ
Dof结构域蛋白家族是一个典型的植物特异性锌指转录因子家族，参与多种生物过程。不同植物的Dof基因数量差异很大。然而，关于大豆中Dof转录因子（Glycine max）的表征报道非常有限。本研究从大豆全基因组序列中鉴定出78个Dof基因。预测的GmDof基因非随机分布在20条染色体中的19条内或跨19条，97.4%（38对）是位于基因组重复区域的优先保留的重复旁系基因。大豆特异性片段重复对大豆Dof基因家族的扩展起着重要作用。这些Dof蛋白在系统发育上聚为9个不同的亚群，其中基因结构和基序组成相当保守。比较系统发育分析显示，这些Dof蛋白有4个主要类群，与拟南芥和水稻相似。基于RNA-seq数据分析，大多数gmdof显示出特定的表达模式。一些重复基因的表达模式是部分冗余的，而另一些则表现出功能多样性，表明在随后的进化中发生了亚功能化。综合表达谱分析也提供了Dof基因家族成员之间大豆特异性功能差异的见解。这些GmDof基因的顺式调控元件分析表明，这些基因在不同的过程中具有不同的功能。综上所述，我们的研究结果将系统发育分析与全球基因表达谱相结合，为大豆Dof基因的功能表征提供了有用的信息。
The Dof domain protein family is a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes. There is great diversity in the number of Dof genes in different plants. However, there are only very limited reports on the characterization of Dof transcription factors in soybean (Glycine max). In the present study, 78 putative Dof genes were identified from the whole-genome sequence of soybean. The predicted GmDof genes were non-randomly distributed within and across 19 out of 20 chromosomes and 97.4% (38 pairs) were preferentially retained duplicate paralogous genes located in duplicated regions of the genome. Soybean-specific segmental duplications contributed significantly to the expansion of the soybean Dof gene family. These Dof proteins were phylogenetically clustered into nine distinct subgroups among which the gene structure and motif compositions were considerably conserved. Comparative phylogenetic analysis of these Dof proteins revealed four major groups, similar to those reported for Arabidopsis and rice. Most of the GmDofs showed specific expression patterns based on RNA-seq data analyses. The expression patterns of some duplicate genes were partially redundant while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. Comprehensive expression profile analysis also provided insights into the soybean-specific functional divergence among members of the Dof gene family. Cis-regulatory element analysis of these GmDof genes suggested diverse functions associated with different processes. Taken together, our results provide useful information for the functional characterization of soybean Dof genes by combining phylogenetic analysis with global gene-expression profiling.
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Pfam：氏族、网络工具和服务。
影响因子：
14.9
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