Eukaryogenesis is one of the most enigmatic evolutionary transitions, during which simple prokaryotic cells gave rise to complex eukaryotic cells. While evolutionary intermediates are lacking, gene duplications provide information on the order of events by which eukaryotes originated. Here we use a phylogenomics approach to reconstruct successive steps during eukaryogenesis. We find that gene duplications roughly doubled the proto-eukaryotic gene repertoire, with families inherited from the Asgard archaea-related host being duplicated most. By relatively timing events using phylogenetic distances, we inferred that duplications in cytoskeletal and membrane-trafficking families were among the earliest events, whereas most other families expanded predominantly after mitochondrial endosymbiosis. Altogether, we infer that the host that engulfed the proto-mitochondrion had some eukaryote-like complexity, which drastically increased upon mitochondrial acquisition. This scenario bridges the signs of complexity observed in Asgard archaeal genomes to the proposed role of mitochondria in triggering eukaryogenesis.

真核发生是最神秘的进化转变之一，在此期间，简单的原核细胞产生了复杂的真核细胞。虽然缺乏进化中间体，但基因重复提供了有关真核生物起源事件顺序的信息。在这里，我们使用系统基因组学方法来重建真核发生过程中的连续步骤。我们发现基因重复使原真核基因库大致翻了一番，其中从 Asgard 古细菌相关宿主继承的家族被复制得最多。通过使用系统发育距离对事件进行相对计时，我们推断细胞骨架和膜运输家族中的重复是最早的事件之一，而大多数其他家族主要在线粒体内共生之后扩展。共，我们推断吞噬原线粒体的宿主具有一些类似于真核生物的复杂性，在获得线粒体后急剧增加。这种情况将在 Asgard 古细菌基因组中观察到的复杂性迹象与线粒体在触发真核发生中的拟议作用联系起来。