Abstract
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.
Highlights
Eukaryogenesis represents a fundamental evolutionary transition in the history of life on Earth, and a better understanding of the underlying events is highly relevant
While it is widely accepted that mitochondria derived from a bacterium related to Alphaproteobacteria, the identity of the host cell remains the subject of debate
Single-cell genomics (SCG) represents a powerful tool to complement metagenomics as it facilitates the genomic exploration of DNA from individual uncultured cells rather than from communities obtained by metagenomics
Summary
Eukaryogenesis represents a fundamental evolutionary transition in the history of life on Earth, and a better understanding of the underlying events is highly relevant. Signature proteins (ESPs) previously identified solely in eukaryotes including proteins involved in the ubiquitination pathway, ESCRT machinery components, cytoskeletal proteins such as actins, and a large number of small GTPases [16] These findings lend further support to the emergence of eukaryotes from within the archaeal domain of life (consistent with a two domain topology [12]), and illuminate some of the early steps leading to the evolution of important eukaryotic characteristics, such as those involved in the origin of the endomembrane system, cytoskeleton and phagocytosis. The discovery of Lokiarchaeota exemplifies that the generation of novel sequence data derived from yet-uncultivated archaeal lineages affiliating with the TACK superphylum will reveal a more detailed picture of the process of eukaryogenesis, and that it will help to obtain a better resolution of deep, domainlevel evolutionary relationships [3,16]. We provide several examples of how these approaches were used to obtain genomic data of new TACK members, thereby revealing new insights into the dark ages of eukaryogenesis
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