Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism

Demystifying Eukaryote Lateral Gene Transfer (Response to Martin 2017 DOI: 10.1002/bies.201700115)

(2018) Michelle M. Leger et al.   BIOESSAYS

Structure of an Ancient Respiratory System

(2018) Hongjun Yu et al.   CELL

Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota

(2018) Yang Liu et al.   ISME Journal

Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

(2018) Panagiotis S. Adam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ConvertingEscherichia coliinto an archaebacterium with a hybrid heterochiral membrane

(2018) Antonella Caforio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Farming the mitochondrial ancestor as a model of endosymbiotic establishment by natural selection

(2018) István Zachar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Asgard archaea are the closest prokaryotic relatives of eukaryotes

(2018) Anja Spang et al.   PLoS Genetics

Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis

(2018) Courtney W Stairs et al.   eLife

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

(2018) Benjamin J. Tully et al.   Scientific Data

Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids

(2018) Adrienne B Narrowe et al.   Genome Biology and Evolution

Deep mitochondrial origin outside the sampled alphaproteobacteria

(2018) Joran Martijn et al.   NATURE

The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

(2017) Panagiotis S Adam et al.   ISME Journal

Symbiosis in eukaryotic evolution

(2017) Purificación López-García et al.   JOURNAL OF THEORETICAL BIOLOGY

The Physiology of Phagocytosis in the Context of Mitochondrial Origin

(2017) William F. Martin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Asgard archaea illuminate the origin of eukaryotic cellular complexity

(2017) Katarzyna Zaremba-Niedzwiedzka et al.   NATURE

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Archaea and the origin of eukaryotes

(2017) Laura Eme et al.   NATURE REVIEWS MICROBIOLOGY

Mechanisms of gene flow in archaea

(2017) Alexander Wagner et al.   NATURE REVIEWS MICROBIOLOGY

Integrative modeling of gene and genome evolution roots the archaeal tree of life

(2017) Tom A. Williams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life

(2017) Anja Spang et al.   SCIENCE

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

(2017) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

(2017) Takunari Kono et al.   Nature Communications

Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes

(2017) Violette Da Cunha et al.   PLoS Genetics

Energetics and Application of Heterotrophy in Acetogenic Bacteria

(2016) Kai Schuchmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

(2016) Kelly C Wrighton et al.   ISME Journal

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

(2016) Kiley W Seitz et al.   ISME Journal

Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks

(2016) Christen M. Klinger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Thermophilic archaea activate butane via alkyl-coenzyme M formation

(2016) Rafael Laso-Pérez et al.   NATURE

Mitochondria in the second act

(2016) Thijs J. G. Ettema   NATURE

Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry

(2016) Alexandros A. Pittis et al.   NATURE

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Lokiarchaeon is hydrogen dependent

(2016) Filipa L. Sousa et al.   Nature Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

(2015) Chris Greening et al.   ISME Journal

Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria

(2015) Gunter Wegener et al.   NATURE

Single cell activity reveals direct electron transfer in methanotrophic consortia

(2015) Shawn E. McGlynn et al.   NATURE

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

(2015) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Endosymbiotic theories for eukaryote origin

(2015) William F. Martin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?

(2015) Eugene V. Koonin   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Reductive Dehalogenases Come of Age in Biological Destruction of Organohalides

(2015) Bat-Erdene Jugder et al.   TRENDS IN BIOTECHNOLOGY

Open Questions on the Origin of Eukaryotes

(2015) Purificación López-García et al.   TRENDS IN ECOLOGY & EVOLUTION

A Metagenomics-Based Metabolic Model of Nitrate-Dependent Anaerobic Oxidation of Methane by Methanoperedens-Like Archaea

(2015) Arslan Arshad et al.   Frontiers in Microbiology

Phylogenomic reconstruction of archaeal fatty acid metabolism

(2014) Daria V. Dibrova et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogenomic Test of the Hypotheses for the Evolutionary Origin of Eukaryotes

(2014) Nicolas C. Rochette et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria

(2014) Kai Schuchmann et al.   NATURE REVIEWS MICROBIOLOGY

The Archaeal Legacy of Eukaryotes: A Phylogenomic Perspective

(2014) L. Guy et al.   Cold Spring Harbor Perspectives in Biology

Electron uptake by iron-oxidizing phototrophic bacteria

(2014) A. Bose et al.   Nature Communications

Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes

(2013) Ryoma Kamikawa et al.   BMC EVOLUTIONARY BIOLOGY

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

An archaeal origin of eukaryotes supports only two primary domains of life

(2013) Tom A. Williams et al.   NATURE

Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases

(2013) L. A. Hug et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation

(2012) Wolfgang Buckel et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions

(2012) Nicolas Lenfant et al.   NUCLEIC ACIDS RESEARCH

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation

(2010) Jessica R. Sieber et al.   Annual Review of Microbiology

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Anaerobic Oxidation of Methane: Progress with an Unknown Process

(2009) Katrin Knittel et al.   Annual Review of Microbiology

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Microbial Architecture of Environmental Sulfur Processes: A Novel Syntrophic Sulfur-Metabolizing Consortia

(2009) Kelsey L.I. Norlund et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Acyl-CoA Dehydrogenases: Dynamic History of Protein Family Evolution

(2009) Zuzana Swigoňová et al.   JOURNAL OF MOLECULAR EVOLUTION

Electron transfer in syntrophic communities of anaerobic bacteria and archaea

(2009) Alfons J. M. Stams et al.   NATURE REVIEWS MICROBIOLOGY

Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation

(2008) Stephen W. Ragsdale et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS