Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes

“Sifarchaeota” a novel Asgard phylum from Costa Rica sediment capable of polysaccharide degradation and anaerobic methylotrophy

(2021) Ibrahim F. Farag et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Expanded diversity of Asgard archaea and their relationships with eukaryotes

(2021) Yang Liu et al.   NATURE

A standardized archaeal taxonomy for the Genome Taxonomy Database

(2021) Christian Rinke et al.   Nature Microbiology

Bacterial genes outnumber archaeal genes in eukaryotic genomes

(2020) Julia Brueckner<sup1> et al.   Genome Biology and Evolution

Giant virus diversity and host interactions through global metagenomics

(2020) Frederik Schulz et al.   NATURE

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

Isolation of an archaeon at the prokaryote–eukaryote interface

(2020) Hiroyuki Imachi et al.   NATURE

A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index

(2020) R. A. Barco et al.   mBio

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation

(2020) Mingwei Cai et al.   Science China-Life Sciences

The Syntrophy hypothesis for the origin of eukaryotes revisited

(2020) Purificación López-García et al.   Nature Microbiology

CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci

(2020) Jakob Russel et al.   CRISPR Journal

Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism

(2019) Disa Bäckström et al.   mBio

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Asgard archaea capable of anaerobic hydrocarbon cycling

(2019) Kiley W. Seitz et al.   Nature Communications

Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche

(2019) Paul-Adrian Bulzu et al.   Nature Microbiology

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

(2019) Anja Spang et al.   Nature Microbiology

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

(2019) Benjamin J Callahan et al.   NUCLEIC ACIDS RESEARCH

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

(2019) Charlotte D. Vavourakis et al.   BMC BIOLOGY

Microbial community composition and functional potential in Bothnian Sea sediments is linked to Fe and S dynamics and the quality of organic matter

(2019) Olivia Rasigraf et al.   LIMNOLOGY AND OCEANOGRAPHY

Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire

(2019) Eugene V. Koonin et al.   NATURE REVIEWS GENETICS

CDD/SPARCLE: the conserved domain database in 2020

(2019) Shennan Lu et al.   NUCLEIC ACIDS RESEARCH

Phylogenomics provides robust support for a two-domains tree of life

(2019) Tom A. Williams et al.   Nature Ecology & Evolution

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes

(2018) Hon Lun Wong et al.   ISME Journal

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

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

Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment

(2018) Mohammad Bahram et al.   Environmental Microbiology Reports

Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin

(2018) Holly C. Betts et al.   Nature Ecology & Evolution

Discovery of Hydrothermal Vent Fields on Alarcón Rise and in Southern Pescadero Basin, Gulf of California

(2018) Jennifer B. Paduan et al.   GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments

(2018) Nina Dombrowski et al.   Nature Communications

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Asgard archaea illuminate the origin of eukaryotic cellular complexity

(2017) Katarzyna Zaremba-Niedzwiedzka et al.   NATURE

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Dynamics of genome size evolution in birds and mammals

(2017) Aurélie Kapusta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

(2017) Sergey A. Shmakov et al.   mBio

Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions

(2017) Jordan C. Angle et al.   Nature Communications

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

Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction

(2016) S. Scheller et al.   SCIENCE

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

(2016) Benjamin R. K. Roller et al.   Nature Microbiology

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

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA

(2015) Olivia U. Mason et al.   MICROBIAL ECOLOGY

Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated

(2015) Mathieu Groussin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

Bacterial gene import and mesophilic adaptation in archaea

(2015) Purificación López-García et al.   NATURE REVIEWS MICROBIOLOGY

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes

(2015) Chuan Ku et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

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

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

Origins of major archaeal clades correspond to gene acquisitions from bacteria

(2014) Shijulal Nelson-Sathi et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Gene similarity networks provide tools for understanding eukaryote origins and evolution

(2013) D. Alvarez-Ponce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phosphatidic acid synthesis in bacteria

(2012) Jiangwei Yao et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS