Modeling gene and genome duplications in eukaryotes
Modeling gene and genome duplications in eukaryotes
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DOI：
10.1073/pnas.0501102102
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发表时间：
2005-04-12
影响因子：
11.1
通讯作者：
Van de Peer, Y
中科院分区：
文献类型：
--
作者：
Maere, S;De Bodt, S;Van de Peer, Y
对完整真核基因组序列的最新分析表明，基因重复猖ramp。此外，除了连续的基因重复模式之外，在许多真核生物中，完整的基因组在其进化的过去都被复制了。这种大规模的基因重复事件与重要的进化过渡或物种的自适应辐射有关。在这里，我们提出了一个进化模型，该模型模拟了基因的重复动力学，考虑了全基因组复制事件和基因重复的连续模式。建模基因不同功能类别的演变评估了不同重复事件对参与特定功能或过程的基因家族的重要性。通过将我们的模型应用于拟南芥基因组，为此，有令人信服的证据证明了三个全基因组重复，我们表明，对于大规模和小规模的重复事件而言，基因丧失有很大的不同，并且对某些功能类别有很大偏见。我们提供的证据表明，某些类别的基因几乎完全通过大规模的基因重复事件扩展。特别是，我们表明拟南芥中的三个全基因组重复直接导致了过去3.5亿年中转录因子，信号传感器和发育基因增加的90％。我们的进化模型广泛适用，可用于评估真核基因组中有关小型或大型基因复制事件的不同假设。
Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has been rampant. Moreover, next to a continuous mode of gene duplication, in many eukaryotic organisms the complete genome has been duplicated in their evolutionary past. Such large-scale gene duplication events have been associated with important evolutionary transitions or major leaps in development and adaptive radiations of species. Here, we present an evolutionary model that simulates the duplication dynamics of genes, considering genome-wide duplication events and a continuous mode of gene duplication. Modeling the evolution of the different functional categories of genes assesses the importance of different duplication events for gene families involved in specific functions or processes. By applying our model to the Arabidopsis genome, for which there is compelling evidence for three whole-genome duplications, we show that gene loss is strikingly different for large-scale and small-scale duplication events and highly biased toward certain functional classes. We provide evidence that some categories of genes were almost exclusively expanded through large-scale gene duplication events. In particular, we show that the three whole-genome duplications in Arabidopsis have been directly responsible for >90% of the increase in transcription factors, signal transducers, and developmental genes in the last 350 million years. Our evolutionary model is widely applicable and can be used to evaluate different assumptions regarding small- or large-scale gene duplication events in eukaryotic genomes.