Asgard is a recently discovered superphylum of archaea that appears to include the closest archaeal relatives of eukaryotes^1,2,3,4,5. Debate continues as to whether the archaeal ancestor of eukaryotes belongs within the Asgard superphylum or whether this ancestor is a sister group to all other archaea (that is, a two-domain versus a three-domain tree of life)^6,7,8. Here we present a comparative analysis of 162 complete or nearly complete genomes of Asgard archaea, including 75 metagenome-assembled genomes that—to our knowledge—have not previously been reported. Our results substantially expand the phylogenetic diversity of Asgard and lead us to propose six additional phyla that include a deep branch that we have provisionally named Wukongarchaeota. Our phylogenomic analysis does not resolve unequivocally the evolutionary relationship between eukaryotes and Asgard archaea, but instead—depending on the choice of species and conserved genes used to build the phylogeny—supports either the origin of eukaryotes from within Asgard (as a sister group to the expanded Heimdallarchaeota–Wukongarchaeota branch) or a deeper branch for the eukaryote ancestor within archaea. Our comprehensive protein domain analysis using the 162 Asgard genomes results in a major expansion of the set of eukaryotic signature proteins. The Asgard eukaryotic signature proteins show variable phyletic distributions and domain architectures, which is suggestive of dynamic evolution through horizontal gene transfer, gene loss, gene duplication and domain shuffling. The phylogenomics of the Asgard archaea points to the accumulation of the components of the mobile archaeal ‘eukaryome’ in the archaeal ancestor of eukaryotes (within or outside Asgard) through extensive horizontal gene transfer.

Asgard 是最近发现的古细菌超门，似乎包括真核生物^1,2,3,4,5最接近的古细菌亲属。关于真核生物的古生菌祖先是否属于 Asgard 超门或该祖先是否是所有其他古生菌的姐妹群（即两域与三域生命树）的争论仍在继续^6,7,8. 在这里，我们对 162 个完整或接近完整的 Asgard 古细菌基因组进行了比较分析，其中包括 75 个宏基因组组装的基因组，据我们所知，这些基因组以前从未被报道过。我们的结果大大扩展了 Asgard 的系统发育多样性，并引导我们提出了另外六个门，其中包括一个我们暂时命名为 Wukongarchaeota 的深分支。我们的系统基因组分析并没有明确地解决真核生物和 Asgard 古生菌之间的进化关系，而是——取决于物种的选择和用于构建系统发育的保守基因——支持真核生物起源于 Asgard 内部（作为 Asgard 的姐妹群）。扩展的 Heimdallarchaeota-Wukongarchaeota 分支）或更深的分支，用于古细菌内的真核生物祖先。我们使用 162 个 Asgard 基因组进行的全面蛋白质结构域分析导致真核特征蛋白集的重大扩展。Asgard 真核生物特征蛋白显示出可变的种系分布和结构域结构，这表明通过水平基因转移、基因丢失、基因复制和结构域改组的动态进化。Asgard 古菌的系统基因组学表明，通过广泛的水平基因转移，在真核生物的古菌祖先（在 Asgard 内部或外部）中积累了移动古菌“真核组”的成分。这暗示了通过水平基因转移、基因丢失、基因复制和域改组的动态进化。Asgard 古菌的系统基因组学表明，通过广泛的水平基因转移，在真核生物的古菌祖先（在 Asgard 内部或外部）中积累了移动古菌“真核组”的成分。这暗示了通过水平基因转移、基因丢失、基因复制和域改组的动态进化。Asgard 古菌的系统基因组学表明，通过广泛的水平基因转移，在真核生物的古菌祖先（在 Asgard 内部或外部）中积累了移动古菌“真核组”的成分。