Data from: Gene similarity networks provide new tools for understanding eukaryote origins and evolution

The complexity and depth of the relationships between the three domains of life challenge the reliability of phylogenetic methods, encouraging the use of alternative analytical tools. We reconstructed a gene similarity network comprising the proteomes of 14 eukaryotes, 104 prokaryotes, 2,389 viruses and 1,044 plasmids. This network contains multiple signatures of the chimerical origin of Eukaryotes as a fusion of an archaebacterium and a eubacterium that could not have been observed using phylogenetic trees. A number of connected components (gene sets with stronger similarities than expected by chance) contain pairs of eukaryotic sequences exhibiting no direct detectable similarity. Instead, many eukaryotic sequences were indirectly connected through a “eukaryote–archaebacterium–eubacterium–eukaryote” similarity path. Furthermore, eukaryotic genes highly connected to prokaryotic genes from one domain tend not to be connected to genes from the other prokaryotic domain. Genes of archaebacterial and eubacterial ancestry tend to perform different functions and to act at different subcellular compartments, but in such an intertwined way that suggests an early rather than late integration of both gene repertoires. The archaebacterial repertoire has a similar size in all eukaryotic genomes whereas the number of eubacterium-derived genes is much more variable, suggesting a higher plasticity of this gene repertoire. Consequently, highly reduced eukaryotic genomes contain more genes of archaebacterial than eubacterial affinity. Connected components with prokaryotic and eukaryotic genes tend to include viral and plasmid genes, compatible with a role of gene mobility in the origin of Eukaryotes. Our analyses highlight the power of network approaches to study deep evolutionary events.

生命三域（three domains of life）之间的关系兼具复杂性与深度，这对系统发育方法（phylogenetic methods）的可靠性提出了挑战，也推动了替代性分析工具的研发与应用。本研究构建了一套基因相似性网络（gene similarity network），涵盖14种真核生物（eukaryote）、104种原核生物（prokaryote）、2389条病毒（virus）以及1044个质粒（plasmid）的蛋白质组（proteome）。该网络蕴含多项真核生物嵌合起源（chimerical origin）的特征——真核生物由古细菌（archaebacterium）与真细菌（eubacterium）融合而来，这类特征无法通过系统发育树（phylogenetic tree）观测得到。部分连通分量（connected component，即相似度显著高于随机预期的基因集合）中存在多对无直接可检测相似度的真核生物序列，但实际上，多数真核序列可通过"真核生物-古细菌-真细菌-真核生物"的相似性路径实现间接连接。此外，与某一类原核生物基因存在高度连接的真核基因，通常不会与另一类原核生物基因产生连接。古细菌起源与真细菌起源的真核基因往往执行不同功能，且定位在不同的亚细胞区室（subcellular compartment），但二者的整合方式却紧密交织，这表明两类基因库（gene repertoire）的整合发生在演化早期，而非晚期。所有真核基因组中古细菌起源的基因库规模较为相近，而真细菌起源的基因数量则差异显著，这说明后者的基因库具有更高的可塑性（plasticity）。因此，高度简化的真核基因组（highly reduced eukaryotic genome）中，古细菌起源基因的占比高于真细菌起源基因。包含原核与真核生物基因的连通分量往往同时包含病毒与质粒基因，这与基因流动性（gene mobility）在真核生物起源中发挥的作用相符。本研究的分析结果凸显了网络分析方法在研究深层演化事件中的优势。