ArticleNature microbiology2021
A standardized archaeal taxonomy for the Genome Taxonomy Database.
Article in Nature microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 253 papers, 1 of them a synthesis that pooled it.
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253 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Abiotic sources of fixed nitrogen sustained early ecosystems for several hundred million years after the origin of life.Science advances · 2026Article
- Large-scale comparative genomics of chitin metabolism in extremely halophilic archaea from the Halobacteria class.Extremophiles : life under extreme conditions · 2026Article
- Evolutionary analysis of transcription elongation factors reveals conserved and lineage-specific regulatory domains.PLoS biology · 2026Article
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- ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics.bioRxiv : the preprint server for biology · 2026Article
- Molecular Evolution of the Archaeal DNA-Dependent RNA Polymerase: Cooperative Changes in Subunit Composition and Specific Domains of Small Subunits.International journal of molecular sciences · 2026Article
- Genomic and evolutionary factors influencing the prediction accuracy of optimal growth temperature in prokaryotes.mSystems · 2026Article
- Resistance of the Archaeal Community to a Severe Disturbance in an Extreme Alkaline Saline Soil.Current microbiology · 2026Article
- Article
193 more citing papers are in PubMed but not listed here.
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9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The accrual of genomic data from both cultured and uncultured microorganisms provides new opportunities to develop systematic taxonomies based on evolutionary relationships. Previously, we established a bacterial taxonomy through the Genome Taxonomy Database. Here, we propose a standardized archaeal taxonomy that is derived from a 122-concatenated-protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. The resulting archaeal taxonomy, which forms part of the Genome Taxonomy Database, is stable for a range of phylogenetic variables including marker gene selection, inference methods, corrections for rate heterogeneity and compositional bias, tree rooting scenarios and expansion of the genome database. Rank normalization is shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes while taking into account proposals to formally recognize the rank of phylum and to use genome sequences as type material. This taxonomy is based on 2,392 archaeal genomes, 93.3% of which required one or more changes to their existing taxonomy, mainly owing to incomplete classification. We identify 16 archaeal phyla and reclassify 3 major monophyletic units from the former Euryarchaeota and one phylum that unites the Thaumarchaeota-Aigarchaeota-Crenarchaeota-Korarchaeota (TACK) superphylum into a single phylum.
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