Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy

Abstract

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).

Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes

“…Notably, the topology of our complete phylogenetic tree (Fig. 2a) within the archaeal clade is mostly consistent with the tree obtained in a preliminary analysis of a larger set of archaeal genomes and a larger marker gene set ( 26 ). Taking into account these observations and the fact that we used the largest set of Asgard archaea and other archaea compared to all previous phylogenetic analyses, the appearance of the 3D topology in our tree indicates that the origin of eukaryotes from within Asgard cannot be considered a settled issue.…”

A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny

“…Briefly, the NCBI taxonomy associated with every fungal genome was obtained from the NCBI Taxonomy FTP site on January 17, 2020. PhyloRank linearly interpolates the RED values of every internal node according to lineage-specific rates of evolution under the constraints of the root being defined as zero and the RED of all present taxa being defined as one 57,79 .…”

RESCRIPt: Reproducible sequence taxonomy reference database management for the masses

“…Our results have shown that formatting and correcting taxonomy and other metadata are critical components of reference database generation and management prior to applications for sequence classification, e.g., to standardize taxonomic ranks across entries [87]. We have already implemented functions in RESCRIPt to format the popular SILVA rRNA gene and NCBI GenBank databases, and are planning future support for parsing and editing other taxonomy formats, as well as mapping between these formats [71].…”

“…These curational efforts result in a well integrated suite of biological information that can be interrogated through a variety of means and data types [25,88]. The GTDB extracts and curates data from both NCBI-RefSeq and NCBI-GenBank to generate a phylogeny of archaea and bacteria from roughly 120 ubiquitous single-copy proteins [23,87]. This phylogeny is used to inform microbial taxonomy, especially in cases where a given taxonomy is observed to be polyphyletic.…”

“…In this case, a conservative approach is used to remove polyphyletic groups and normalize taxonomic ranks according to their relative evolutionary divergence. Any remaining polyphyletic groups are then flagged as a "regions of instability" in the hopes that future in-depth analyses will result in a stable set of classifiable taxa [23,87]. The efforts by NCBI and GTDB enables researchers to not only more accurately classify uncultured microbes, but also place them into ecological and evolutionary context based on their nearest phylogenetic and taxonomic neighbors.…”