Release 89 Statistics

Taxon Overview

GTDB r89 spans 145,904 genomes organized into 24,706 species clusters.

Bacteria Archaea Total
Phylum 112 16 128
Class 296 36 332
Order 816 96 912
Family 1,969 238 2,207
Genus 7,372 534 7,906
Species 23,458 1,248 24,706
Genome Categories

GTDB taxa are comprised of isolate genomes, metagenome-assembled genomes (MAGs), and single-amplified genomes (SAGs). The following plot indicates the proportion of taxa at each taxonomic rank comprised exclusively of isolate genomes, exclusively of environmental genomes (i.e. MAGs/SAGs), or both isolate and environmental genomes.

genome_category_per_rank
GTDB Species Representatives

Each GTDB species cluster is represented by a single genome. Genomes assembled from the type strain of the species were selected where possible, though the majority of species clusters are currently assigned only placeholder names. The proportion of species clusters comprised of isolates or environmental genomes is given for each species category.

sp_rep_type
Quality of GTDB Representative Genomes

The quality of the genomes selected as GTDB species representatives is given below. Genome completeness and contamination were estimated using CheckM and are colored based on the MIMAG genome standards. In general, representative genomes were restricted to having a quality satisfying completeness - 5*contamination >50. A few exceptions exist in order to retain well-known species with abnormal CheckM quality estimates.

genome_quality_species
Taxa with the largest number of species

Taxa encompassing the largest number of GTDB species clusters is given for each taxonomic rank.

Taxa with largest number of sequenced genomes

Taxa encompassing the largest number of genomes in the GTDB is given for each taxonomic ranks.

Relative Evolutionary Divergence

The following graphs show the relative evolutionary divergence (RED) of taxa at each taxonomic rank from phylum to genus. RED values provide an operational approximation of relative time with extant taxa existing in the present (RED=1), the last common ancestor occurring at a fixed time in the past (RED=0), and internal nodes being linearly interpolated between these values according to lineage-specific rates of evolution. RED intervals for normalizing taxa at taxonomic ranks was operationally defined as the median RED value (indicated by a blue bar) at each rank ±0.1 (indicated by grey bars).

Bacteria

Archaea

Comparison of GTDB and NCBI taxa

Comparison of GTDB and NCBI taxonomic assignments across GTDB species representative genomes and all GTDB genomes which have an assigned NCBI taxonomy. For each taxonomic rank, a taxon was classified as being unchanged if its name was identical in both taxonomies, passively changed if the GTDB taxonomy provided name information absent in the NCBI taxonomy, or actively changed if the name was different between the two taxonomies.

ncbi_compare_species ncbi_compare_genomes
Genomic Statistics

Key genomic statistics for the GTDB species representative genomes and all genomes in the GTDB.

genomic_stats_species genomic_stats_genomes