Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention
Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention
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DOI：
10.1016/j.cels.2016.01.013
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发表时间：
2016-02-24
期刊：
影响因子：
9.3
通讯作者：
Williams, Ben P.
中科院分区：
文献类型：
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作者：
Johnston, Iain G.;Williams, Ben P.
由于它们的内共生起源，线粒体已经失去了大部分基因。虽然已经提出了许多线粒体基因组进化的选择机制，但缺乏对这些假设的数据驱动探索，并且仍然缺乏定量支持的共识。我们开发了HyperTraPS，这是一种将随机建模与贝叶斯推理相结合的方法，用于识别进化事件的顺序并提出其原因。使用2015年完整的线粒体基因组，我们推断了真核生物生命树中mtDNA基因丢失的进化轨迹。我们发现，包括电子传递链的结构核心的蛋白质优先编码的线粒体基因组在真核生物。高GC含量和高蛋白质疏水性的组合需要解释mtDNA基因保留的模式;解释这些选择压力的模型也可以预测人工基因转移实验在体内的成功。这项工作提供了一种通用的方法，用于数据驱动的进化和进步事件的顺序推断，在这里确定塑造当今物种线粒体基因组的独特特征。
Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species.