RT Journal Article
SR Electronic
T1 Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 771964
DO 10.1101/771964
A1 Donovan H. Parks
A1 Maria Chuvochina
A1 Pierre-Alain Chaumeil
A1 Christian Rinke
A1 Aaron J. Mussig
A1 Philip Hugenholtz
YR 2019
UL http://biorxiv.org/content/early/2019/09/18/771964.abstract
AB We recently introduced the Genome Taxonomy Database (GTDB), a phylogenetically consistent, genome-based taxonomy providing rank normalized classifications for nearly 150,000 genomes from domain to genus. However, nearly 40% of the genomes used to infer the GTDB reference tree lack a species name, reflecting the large number of genomes in public repositories without complete taxonomic assignments. Here we address this limitation by proposing 24,706 species clusters which encompass all publicly available bacterial and archaeal genomes when using commonly accepted average nucleotide identity (ANI) criteria for circumscribing species. In contrast to previous ANI studies, we selected a single representative genome to serve as the nomenclatural type for circumscribing each species with type strains used where available. We complemented the 8,792 species clusters with validly or effectively published names with 15,914 de novo species clusters in order to assign placeholder names to the growing number of genomes from uncultivated species. This provides the first complete domain to species taxonomic framework which will improve communication of scientific results.