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

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Jimmy H SawThijs J G Ettema

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,...Continue Reading

Associated Datasets

References

Aug 1, 1972·Journal of Bacteriology·C B Fliermans, T D Brock
Mar 1, 1994·Proceedings of the National Academy of Sciences of the United States of America·S M BarnsN R Pace
Aug 20, 1996·Proceedings of the National Academy of Sciences of the United States of America·S M BarnsN R Pace
May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·M C RiveraJ A Lake
Jun 26, 2001·Genome Biology·M W GrayB F Lang
Apr 5, 2002·International Journal of Systematic and Evolutionary Microbiology·T Cavalier-Smith
May 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·B CanbackC G Kurland
Apr 16, 2003·Molecular Microbiology·John N Reeve
Sep 1, 2004·Trends in Biochemical Sciences·Juli PeretóDavid Moreira
Dec 14, 2004·Microbiology and Molecular Biology Reviews : MMBR·Jo Handelsman
Jan 5, 2005·Nature Reviews. Genetics·Thorsten Allers, Moshe Mevarech
Jan 27, 2005·Proceedings of the National Academy of Sciences of the United States of America·John R SpearNorman R Pace
Oct 26, 2005·Current Opinion in Microbiology·William Martin
Mar 31, 2006·Nature·T Martin Embley, William Martin
Dec 21, 2006·Nature Methods·Alice Carolyn McHardyIsidore Rigoutsos
Jan 27, 2007·Genome Research·Daniel H HusonStephan C Schuster
May 17, 2007·Molecular Biology and Evolution·Davide PisaniJames O McInerney
Jul 11, 2007·Proceedings of the National Academy of Sciences of the United States of America·Yann MarcyStephen R Quake
Sep 22, 2007·Trends in Microbiology·Christian Esser, William Martin
Feb 21, 2008·Nucleic Acids Research·Lutz KrauseJens Stoye
Nov 7, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ann-Christin LindåsRolf Bernander
Nov 15, 2008·Science·Rachel Y SamsonStephen D Bell
Feb 28, 2009·Biology Direct·Natalya YutinEugene V Koonin
Apr 25, 2009·PloS One·Tanja WoykeRamunas Stepanauskas
Aug 25, 2009·Genome Biology·Gregory J DickJillian F Banfield
Aug 26, 2009·Communicative & Integrative Biology·Thijs Jg Ettema, Rolf Bernander
Apr 7, 2010·Proceedings of the National Academy of Sciences of the United States of America·Peter J TurnbaughJeffrey I Gordon
Sep 17, 2010·Nature Reviews. Microbiology·Simonetta GribaldoCéline Brochier-Armanet
Dec 2, 2010·Nature Communications·Rolf B PedersenSteffen L Jorgensen
Mar 19, 2011·Molecular Microbiology·Thijs J G EttemaRolf Bernander
Apr 30, 2011·Nature Methods·Arthur Brady, Steven Salzberg
May 4, 2011·Genome Research·Yun KangTung T Hoang
Sep 29, 2011·Annual Review of Genetics·Tomer KaliskyStephen R Quake
Oct 25, 2011·Trends in Microbiology·Lionel Guy, Thijs J G Ettema
Dec 20, 2011·Standards in Genomic Sciences·Amrita PatiNatalia Ivanova
Feb 4, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yi WangFrancis Y L Chin
Mar 27, 2012·Communicative & Integrative Biology·Rolf BernanderThijs J G Ettema
Mar 31, 2012·Biology Direct·Natalya Yutin, Eugene V Koonin

❮ Previous
Next ❯

Citations

Aug 31, 2016·Nature Microbiology·Brett J BakerThijs J G Ettema
Dec 25, 2015·Proceedings of the National Academy of Sciences of the United States of America·Eugene V Koonin
Feb 20, 2016·Molecular Biology and Evolution·Christen M KlingerThijs J G Ettema
Sep 2, 2015·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Tom A Williams, T Martin Embley
May 5, 2017·Annual Review of Biochemistry·Michael P Rout, Mark C Field
Nov 11, 2017·Nature Reviews. Microbiology·Laura EmeThijs J G Ettema
Jun 16, 2017·Microbiology and Molecular Biology Reviews : MMBR·William F MartinSven B Gould
May 11, 2017·MBio·Takahito MukaiDieter Söll
Jan 11, 2019·FEMS Microbiology Letters·Nina DombrowskiAnja Spang
Aug 20, 2019·Applied Microbiology and Biotechnology·Annerys Carabeo-PérezJanet Jiménez-Hernández
Sep 25, 2018·Evolutionary Bioinformatics Online·Laurynas KalesinskasCatherine Putonti
May 24, 2017·Proceedings of the National Academy of Sciences of the United States of America·Tom A WilliamsT Martin Embley
Jun 14, 2019·BMC Biology·Andrew Maltez Thomas, Nicola Segata
Jan 13, 2017·Nature·Katarzyna Zaremba-NiedzwiedzkaThijs J G Ettema
May 16, 2017·Frontiers in Microbiology·Marion H StagarsKatrin Knittel
Jan 28, 2021·FEMS Microbiology Ecology·Rebecca C MuellerBrent M Peyton
Sep 18, 2020·Microbiome·Hon Lun WongBrendan P Burns

❮ Previous
Next ❯

Methods Mentioned

BETA
ubiquitination
activated
fluorescence-activated cell sorting
MDA
GTPase
GTPases

Software Mentioned

PhyloPythia
CARMA
PhymmBL
read aligner
ClaMS
GroopM
BLAST
MEGAN
S +
CONCOCT

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.

Related Papers

Cold Spring Harbor Perspectives in Biology
Lionel GuyThijs J G Ettema
Archaea : an International Microbiological Journal
Gustavo Caetano-Anollés, Kyung Mo Kim
© 2021 Meta ULC. All rights reserved