Journal
NUCLEIC ACIDS RESEARCH
Volume 50, Issue D1, Pages D785-D794Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkab776
Keywords
-
Categories
Funding
- AustralianResearch Council Laureate Fellowship [FL150100038, FT170100213]
- University of Queensland
- Australian Research Council Laureate Fellowship [FL150100038]
- Australian Research Council [FT170100213] Funding Source: Australian Research Council
Ask authors/readers for more resources
The Genome Taxonomy Database (GTDB) provides a phylogenetically consistent taxonomy for prokaryotic genomes sourced from the NCBI database. It includes a large number of bacterial and archaeal genomes, highlights the importance of metagenome-assembled genomes, and discusses improvements to the GTDB website and the procedure for updating species clusters.
The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic genomes sourced from the NCBI Assembly database. GTDB R06-RS202 spans 254 090 bacterial and 4316 archaeal genomes, a 270% increase since the introduction of the GTDB in November, 2017. These genomes are organized into 45 555 bacterial and 2339 archaeal species clusters which is a 200% increase since the integration of species clusters into the GTDB in June, 2019. Here, we explore prokaryotic diversity from the perspective of the GTDB and highlight the importance of metagenome-assembled genomes in expanding available genomic representation. We also discuss improvements to the GTDB website which allow tracking of taxonomic changes, easy assessment of genome assembly quality, and identification of genomes assembled from type material or used as species representatives. Methodological updates and policy changes made since the inception of the GTDB are then described along with the procedure used to update species clusters in the GTDB. We conclude with a discussion on the use of average nucleotide identities as a pragmatic approach for delineating prokaryotic species.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available