Reconstruction of highly heterogeneous gene-content evolution across the three domains of life
Reconstruction of highly heterogeneous gene-content evolution across the three domains of life
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DOI：
10.1093/bioinformatics/btm165
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发表时间：
2007-07-01
期刊：
影响因子：
5.8
通讯作者：
Takagi, Toshihisa
中科院分区：
文献类型：
--
作者：
Iwasaki, Wataru;Takagi, Toshihisa
动机：重建基因内容的进化历史是研究基因组和生物系统进化的基础。为了重建合理的进化历史，应该通过考虑高度的异质性来估计基因获得/丢失的速率：G.基因组复制和寄生分别导致基因获得和丢失的高比率。考虑这种异质性的基因内容进化重建方法，这是既有效地估计基因的增益和损失率和足够有效地分析丰富的基因组data.Results：一个有效的和高效的方法重建异质性基因内容进化开发。该方法包括基因内容进化的分析可积模型，期望最大化的分析公式和使用内部仿射算法的边缘似然的有效计算。在数百个基因组规模上的模拟测试表明，在几天的计算时间内，基因的获得/丢失率和进化历史都得到了有效的估计。随后，将该算法应用于近200个基因组的实际数据集，以重建跨越生命三个领域的异质基因内容进化。重建的历史包含了与生物学观察相一致的几个特征，表明基因内容进化的趋势不仅在原核生物和真核生物之间有着巨大的差异，而且在每种生命形式中都有很大的差异。这些结果表明，在研究基因内容、基因组和生物系统的进化时，应考虑异质性。
Motivation: Reconstruction of gene-content evolutionary history is fundamental in studying the evolution of genomes and biological systems. To reconstruct plausible evolutionary history, rates of gene gain/loss should be estimated by considering the high level of heterogeneity: e. g. genome duplication and parasitization, respectively, result in high rates of gene gain and loss. Gene-content evolution reconstruction methods that consider this heterogeneity and that are both effective in estimating the rates of gene gain and loss and sufficiently efficient to analyze abundant genomic data had not been developed.Results: An effective and efficient method for reconstructing heterogeneous gene-content evolution was developed. This method comprises analytically integrable modeling of gene-content evolution, analytical formulation of expectation-maximization and efficient calculation of marginal likelihood using an inside-outsidelike algorithm. Simulation tests on the scale of hundreds of genomes showed that both the gene gain/ loss rates and evolutionary history were effectively estimated within a few days of computational time. Subsequently, this algorithm was applied to an actual data set of nearly 200 genomes to reconstruct the heterogeneous gene-content evolution across the three domains of life. The reconstructed history, which contained several features consistent with biological observations, showed that the trends of gene-content evolution were not only drastically different between prokaryotes and eukaryotes, but were highly variable within each form of life. The results suggest that heterogeneity should be considered in studies of the evolution of gene content, genomes and biological systems.