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A rank-normalized archaeal taxonomy based on genome phylogeny resolves widespread incomplete and uneven classifications

By Christian Rinke, Maria Chuvochina, Aaron J. Mussig, Pierre-Alain Chaumeil, David W. Waite, William B. Whitman, Donovan H. Parks, Philip Hugenholtz

Posted 03 Mar 2020
bioRxiv DOI: 10.1101/2020.03.01.972265

The increasing wealth of genomic data from cultured and uncultured microorganisms provides the opportunity to develop a systematic taxonomy based on evolutionary relationships. Here we propose a standardized archaeal taxonomy, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. The resulting archaeal taxonomy is stable under a range of phylogenetic variables, including marker genes, inference methods, and tree rooting scenarios. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes (ICNP) while taking into account proposals to formally recognise the rank of phylum and to use genome sequences as type material. The taxonomy is based on 2,392 quality screened archaeal genomes, the great majority of which (93.3%) required one or more changes to their existing taxonomy, mostly as a result of incomplete classification. In total, 16 archaeal phyla are described, including reclassification of three major monophyletic units from the Euryarchaeota and one phylum resulting from uniting the TACK superphylum into a single phylum. The taxonomy is publicly available at the GTDB website (https://gtdb.ecogenomic.org).

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