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

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. In conclusion, 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.

Authors:
 [1];  [1];  [1];  [1];  [2];  [3];  [4];  [4];  [5];  [1];  [1]
  1. Uppsala Univ., Uppsala (Sweden)
  2. Univ. of Nevada, Las Vegas, NV (United States); California State Univ. (CalState), San Bernardino, CA (United States)
  3. Univ. of Nevada, Las Vegas, NV (United States)
  4. Univ. of New Mexico, Albuquerque, NM (United States)
  5. Univ. of Nevada, Las Vegas, NV (United States). School of Life Sciences
Publication Date:
Research Org.:
Univ. of Nevada, Las Vegas, NV (United States)
Sponsoring Org.:
USDOE; National Aeronautic and Space Administration (NASA); National Science Foundation (NSF); EU; ERC; Swedish Research Council (SRC); Marie Curie
OSTI Identifier:
1343570
Grant/Contract Number:  
SC0006771; EE-0000716; EXO-NNX11AR78G; 621-2009-4813
Resource Type:
Accepted Manuscript
Journal Name:
Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences
Additional Journal Information:
Journal Volume: 370; Journal Issue: 1678; Journal ID: ISSN 0962-8436
Publisher:
The Royal Society Publishing
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Archaea; eukaryogenesis; metagenomics; microbial diversity; single-cell genomics; tree of life

Citation Formats

Saw, Jimmy H., Spang, Anja, Zaremba-Niedzwiedzka, Katarzyna, Juzokaite, Lina, Dodsworth, Jeremy A., Murugapiran, Senthil K., Colman, Dan R., Takacs-Vesbach, Cristina, Hedlund, Brian P., Guy, Lionel, and Ettema, Thijs J. G. Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes. United States: N. p., 2015. Web. doi:10.1098/rstb.2014.0328.
Saw, Jimmy H., Spang, Anja, Zaremba-Niedzwiedzka, Katarzyna, Juzokaite, Lina, Dodsworth, Jeremy A., Murugapiran, Senthil K., Colman, Dan R., Takacs-Vesbach, Cristina, Hedlund, Brian P., Guy, Lionel, & Ettema, Thijs J. G. Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes. United States. doi:10.1098/rstb.2014.0328.
Saw, Jimmy H., Spang, Anja, Zaremba-Niedzwiedzka, Katarzyna, Juzokaite, Lina, Dodsworth, Jeremy A., Murugapiran, Senthil K., Colman, Dan R., Takacs-Vesbach, Cristina, Hedlund, Brian P., Guy, Lionel, and Ettema, Thijs J. G. Mon . "Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes". United States. doi:10.1098/rstb.2014.0328. https://www.osti.gov/servlets/purl/1343570.
@article{osti_1343570,
title = {Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes},
author = {Saw, Jimmy H. and Spang, Anja and Zaremba-Niedzwiedzka, Katarzyna and Juzokaite, Lina and Dodsworth, Jeremy A. and Murugapiran, Senthil K. and Colman, Dan R. and Takacs-Vesbach, Cristina and Hedlund, Brian P. and Guy, Lionel and Ettema, Thijs J. G.},
abstractNote = {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. In conclusion, 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.},
doi = {10.1098/rstb.2014.0328},
journal = {Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences},
number = 1678,
volume = 370,
place = {United States},
year = {2015},
month = {8}
}

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Cited by: 14 works
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Figures / Tables:

Figure 1 Figure 1: Phylogenetic diversity of the TACK superphylum based on known 16S rRNA gene sequences. Maximum-likelihood phylogeny of archaeal lineages withinthe TACK superphylum was constructed based on a total of 343 16S rRNA gene sequences. Five members of Euryarchaeota were used as outgroup to root the tree.Acronyms used for somemore » of the archaeal clades are MHVG, marine hydrothermal vent group; AAG, ancient archaeal group. The TACK clades AK8, Fhm5A01 and pMC2A209 are derived from clone names. See figure S1 for a full, uncollapsed version of this tree.« less

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      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.