PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins
PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins
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DOI：
10.1104/pp.107.095760
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发表时间：
2007-04-01
期刊：
影响因子：
7.4
通讯作者：
Rensing, Stefan A.
中科院分区：
文献类型：
--
作者：
Richardt, Sandra;Lang, Daniel;Rensing, Stefan A.
陆地植物进化过程中转录相关蛋白(TAP)家族的多样化是导致植物生命复杂性增加的关键过程。了解这些基因之间的进化关系对于深入了解植物进化至关重要。我们使用PSI-BLAST搜索以及随后的过滤和聚类步骤确定了一组专注于(但不限于)陆地植物的TAP。利用距离和最大似然法的组合，以自动的方式创建了系统发育图。将这些数据与以前发表的工作进行比较，证实了它们对大多数基因家族的准确性和实用性。有证据表明，开花植物顶端干细胞调节基因WUSCHEL是从一个祖先的同源框基因进化而来的，该基因在水陆过渡后就已经存在了。在进化的背景下讨论了不同的扩展基因家族的存在，如苔藓中的COP1和HIT。比较分析表明，几乎所有被子植物转录因子家族都已经存在于最早的陆地植物中，而许多转录因子家族在单细胞藻类中缺失。不仅对转录因子，而且对转录调控因子和新的假定家族进行了全球分析。通过PlanTAPDB Web界面可获得有关植物水龙头家族的大量数据以及在其自动化检测和分析过程中积累的所有数据。非专家只需点击鼠标即可访问这些基因的进化关系。对选定的基因家族的初步分析表明，PlanTAPDB可以很容易地用于知识发现。
Diversification of transcription-associated protein (TAP) families during land plant evolution is a key process yielding increased complexity of plant life. Understanding the evolutionary relationships between these genes is crucial to gain insight into plant evolution. We have determined a substantial set of TAPs that are focused on, but not limited to, land plants using PSI-BLAST searches and subsequent filtering and clustering steps. Phylogenies were created in an automated way using a combination of distance and maximum likelihood methods. Comparison of the data to previously published work confirmed their accuracy and usefulness for the majority of gene families. Evidence is presented that the flowering plant apical stem cell regulator WUSCHEL evolved from an ancestral homeobox gene that was already present after the water-to-land transition. The presence of distinct expanded gene families, such as COP1 and HIT in moss, is discussed within the evolutionary backdrop. Comparative analyses revealed that almost all angiosperm transcription factor families were already present in the earliest land plants, whereas many are missing among unicellular algae. A global analysis not only of transcription factors but also of transcriptional regulators and novel putative families is presented. A wealth of data about plant TAP families and all data accrued throughout their automated detection and analysis are made available via the PlanTAPDB Web interface. Evolutionary relationships of these genes are readily accessible to the nonexpert at a mouse-click. Initial analyses of selected gene families revealed that PlanTAPDB can easily be exerted for knowledge discovery.