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A standardized archaeal taxonomy for the Genome Taxonomy Database
Christian Rinke1, Maria Chuvochina2, Aaron J Mussig2
1Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia. c.rinke@uq.edu.au.
Nature Microbiology
|June 22, 2021
Summary
A new archaeal taxonomy based on genomic data and evolutionary relationships has been developed. This standardized system, part of the Genome Taxonomy Database, reclassifies most existing archaeal classifications.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Genomic data accrual from microorganisms enables systematic taxonomies based on evolutionary relationships.
- A bacterial taxonomy was previously established using the Genome Taxonomy Database.
Purpose of the Study:
- To propose a standardized archaeal taxonomy using a 122-concatenated-protein phylogeny.
- To resolve polyphyletic groups and normalize taxonomic ranks based on evolutionary divergence.
Main Methods:
- Phylogenetic analysis of 2,392 archaeal genomes using 122 concatenated proteins.
- Rank normalization to correct for varying substitution rates.
- Taxonomic curation adhering to the International Code of Nomenclature of Prokaryotes.
Main Results:
- A stable archaeal taxonomy was developed, forming part of the Genome Taxonomy Database.
- Rank normalization robustly corrected for substitution rates up to 30-fold.
- 16 archaeal phyla were identified, with significant reclassification of existing groups.
Conclusions:
- The proposed taxonomy is stable across various phylogenetic variables.
- Most (93.3%) of the 2,392 archaeal genomes required taxonomic changes.
- Three major monophyletic units from Euryarchaeota and the TACK superphylum were reclassified into single phyla.
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