Supertrees disentangle the chimerical origin of eukaryotic Genomes
Supertrees disentangle the chimerical origin of eukaryotic Genomes
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DOI：
10.1093/molbev/msm095
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发表时间：
2007-08-01
影响因子：
10.7
通讯作者：
McInerney, James O.
中科院分区：
文献类型：
--
作者：
Pisani, Davide;Cotton, James A.;McInerney, James O.
真核生物传统上被认为是生命之树的三个自然分支之一，是古细菌的姐妹群。然而，真核生物的基因组充满了真核细菌祖先的基因，并且提出了20多种互不相容的假设来解释真核生物的起源。在这里，我们使用一种新的基于超树的系统发育信号剥离方法来测试这些假设的预测，并基于分布在185个基因组中的多达5,741个单基因家族的系统发育恢复了生命超树。利用我们的信号剥离方法，我们发现真核生物基因组中有三种不同的系统发育信号。按照强度的顺序，它们将真核生物与蓝藻、变形菌和热原菌（古细菌群）联系起来。这些信号对应于真核生物进化中不同的共生伙伴：质体、线粒体和难以捉摸的宿主谱系。根据我们的全基因组数据，真核生物几乎不是古细菌的姐妹群，因为高达83%的真核基因与原核同源物来自真核细菌，而不是古细菌。这些结果否定了目前关于真核生物起源的所有假说，只有两种假说除外：假设线粒体的起源是硫依赖或氢依赖的syntrophy。
Eukaryotes are traditionally considered to be one of the three natural divisions of the tree of life and the sister group of the Archaebacteria. However, eukaryotic genomes are replete with genes of eubacterial ancestry, and more than 20 mutually incompatible hypotheses have been proposed to account for eukaryote origins. Here we test the predictions of these hypotheses using a novel supertree-based phylogenetic signal-stripping method, and recover supertrees of life based on phylogenies for up to 5,741 single gene families distributed across 185 genomes. Using our signal-stripping method, we show that there are three distinct phylogenetic signals in eukaryotic genomes. In order of strength, these link eukaryotes with the Cyanobacteria, the Proteobacteria, and the Thermoplasmatales, an archaebacterial (euryarchaeotes) group. These signals correspond to distinct symbiotic partners involved in eukaryote evolution: plastids, mitochondria, and the elusive host lineage. According to our whole-genome data, eukaryotes are hardly the sister group of the Archaebacteria, because up to 83% of eukaryotic genes with a prokaryotic homolog have eubacterial, not archaebacterial, origins. The results reject all but two of the current hypotheses for the origin of eukaryotes: those assuming a sulfur-dependent or hydrogen-dependent syntrophy for the origin of mitochondria.