Expanding archaeal diversity and phylogeny: past, present, and future
G Tahon, P Geesink, TJG Ettema - Annual Review of …, 2021 - annualreviews.org
The discovery of the Archaea is a major scientific hallmark of the twentieth century. Since
then, important features of their cell biology, physiology, ecology, and diversity have been …
then, important features of their cell biology, physiology, ecology, and diversity have been …
Evolution of microbial genomics: conceptual shifts over a quarter century
EV Koonin, KS Makarova, YI Wolf - Trends in microbiology, 2021 - cell.com
Prokaryote genomics started in earnest in 1995, with the complete sequences of two small
bacterial genomes, those of Haemophilus influenzae and Mycoplasma genitalium. During …
bacterial genomes, those of Haemophilus influenzae and Mycoplasma genitalium. During …
A standardized archaeal taxonomy for the Genome Taxonomy Database
The accrual of genomic data from both cultured and uncultured microorganisms provides
new opportunities to develop systematic taxonomies based on evolutionary relationships …
new opportunities to develop systematic taxonomies based on evolutionary relationships …
A rooted phylogeny resolves early bacterial evolution
INTRODUCTION Bacteria are the most diverse and abundant cellular organisms on Earth,
and in recent years environmental genomics has revealed the existence of an enormous …
and in recent years environmental genomics has revealed the existence of an enormous …
ATP synthase evolution on a cross-braced dated tree of life
The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the
origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have …
origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have …
Genome-centric metagenomics insights into functional divergence and horizontal gene transfer of denitrifying bacteria in anammox consortia
Denitrifying bacteria with high abundances in anammox communities play crucial roles in
achieving stable anammox-based systems. Despite the relative constant composition of …
achieving stable anammox-based systems. Despite the relative constant composition of …
An estimate of the deepest branches of the tree of life from ancient vertically evolving genes
Core gene phylogenies provide a window into early evolution, but different gene sets and
analytical methods have yielded substantially different views of the tree of life. Trees inferred …
analytical methods have yielded substantially different views of the tree of life. Trees inferred …
Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota
The archaeal phylum Woesearchaeota, within the DPANN superphylum, includes
phylogenetically diverse microorganisms that inhabit various environments. Their biology is …
phylogenetically diverse microorganisms that inhabit various environments. Their biology is …
Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota
Abstract Background Candidatus Nanohaloarchaeota, an archaeal phylum within the
DPANN superphylum, is characterized by limited metabolic capabilities and limited …
DPANN superphylum, is characterized by limited metabolic capabilities and limited …
Parameter estimation and species tree rooting using ALE and GeneRax
ALE and GeneRax are tools for probabilistic gene tree–species tree reconciliation. Based on
a common underlying statistical model of how gene trees evolve along species trees, these …
a common underlying statistical model of how gene trees evolve along species trees, these …