Data from: Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteobacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal ‘dark matter’, is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.真核生物的起源堪称一道难解的谜题，至今仍缺失诸多核心环节。尽管目前学界普遍认为，真核发生（eukaryogenesis）过程涉及宿主细胞与α-变形菌门（Alphaproteobacteria）内共生体的相互作用，但我们目前仍缺乏关于这两类参与者的具体身份与本质特征的详细信息。多项研究愈发支持：真核宿主细胞起源于古菌域，并与古菌TACK超门（TACK superphylum）存在特定的系统发育亲缘关系。近期研究表明，对尚未获得纯培养的古菌——即所谓的古菌“暗物质”——进行基因组探索，能够为真核发生过程提供前所未有的研究视角。本文概述了当前最先进的非培养依赖型（cultivation-independent）基因组学方法，并展示了如何利用这些方法获取TACK超门多个新类群的草图基因组序列，包括洛基古菌（Lokiarchaeum）、奇古菌门杂类群（Miscellaneous Crenarchaeotal Group，即深海古菌门（Bathyarchaeota））的两个代表类群，以及一类与古球菌属（Korarchaeum）近缘的谱系。非培养依赖型基因组学方法的成熟，以及下一代测序（next-generation sequencing）技术的未来发展，将彻底革新我们对微生物演化与多样性的现有认知，并为生命早期演化——包括真核细胞的神秘起源——提供全新的深刻见解。