Taxonomy

We provide both NCBI and GTDB taxonomy, original and curated, for the 10,575 genomes in the phylogenetic trees.

General files

ranks: Name or IDs at the seven standard taxonomic ranks:

  • kingdom, phylum, class, order, family, genus, species

The use of kingdom is to comply with the Greengenes standard. In this work, it may be “Archaea” or “Bacteria”. These two taxonomic groups are defined as superkingdom in NCBI, or domain in many modern literatures.

lineages: Greengenes-style lineage strings. They can be used in many applications such as QIIME.

Metadata

Properties and metrics of each taxonomic unit with at least two taxa represented. Columns:

  • rank, name: Taxonomic rank and name
  • taxid: NCBI taxonomic ID (TaxID).
  • count: Number of genomes assigned to this taxon.
  • mono_strict, mono_relaxed: Whether this taxonomic unit is monophyletic in the tree, considering all tips, or only tips classified at this rank.
  • consistency: Consistency score computed using tax2tree (larger is better, 1.0 is equivalent to strict monophyly).
  • quartet: Quartet score computed using ASTRAL (larger is better, 1.0 is equivalent to strict monophyly).
  • markers: Average number of marker genes (out of 400) found in each member genome.

Curation

Phylogeny-based annotation and curation were performed using tax2tree (McDonald et al., 2012). (The same tool was used to curate Greengenes and GTDB.)

The reference phylogeny is astral.e5p50 (built using ASTRAL, with low-support branches collapsed). The curated lineage strings and rank tables cover both tips (genomes) and internal nodes of the tree. We also provide curations using alternative trees.

Note that tax2tree does NOT create new taxonomic units. Instead, it modifies the assignments of genomes to existing taxonomic units. If a taxonomic unit is strongly polyphyletic, the program will append a numeric suffix to it for each clade, sorted by size from large to small (e.g., Firmicutes_1, Firmicutes_2…). We also provide curation results without this suffix (thus taxon names strictly match the original) in the noidx directories.