Get a reference phylogenetic tree of known taxa from GTDB
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12 months ago
Gio • 0

Hello,

I have a set of genomes I downloaded from NCBI. I would like to make a reference phylogenetic tree where only they appear.

Instead of aligning them or using mash distance to make my own tree, is there a way I can simply provide the genomes or taxa to GTDB and get a tree back from it?

phylogenetic-tree bacteria gtdb • 1.7k views
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12 months ago
Mensur Dlakic ★ 28k

To the best of my knowledge, there is no way to do this using GTDB website. However, it can be done locally using the GTDB-toolkit. You select a group of genomic sequences and run it through the program. It will do gene predictions, single-copy marker identification, and a taxonomic assignment that will include a global GTDB tree with your organisms (too big for most applications) plus a tree with just your organisms.

https://github.com/Ecogenomics/GTDBTk

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11 months ago
fredjaya ▴ 20

If I understand correctly, given a list of the NCBI genome IDs, you can prune a .tree (e.g. the GTDB tree) with Biopython. Note that the NCBI IDs must match the taxa labels in the tree.

Example script here.

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Nicely done. Yet pruning the tree will not suffice for the user-specific entries that may not already be in the tree.

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Good point. I think it's possible to "place" tips via IQ-TREE2's contrained tree search option.

iqtree -s user_sequences.fa -g pruned_gtdb.tree

Here the starting tree is fixed to the pruned tree, and will infer the whole tree to include the "new" user-specific sequences.

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I think it is highly likely that most (or all) user-specified NCBI genomes can be found in GTDB. The reference GTDB tree encompasses approximately 80,000 bacterial species, each represented by a single genome (representative genome for species). However, the complete GTDB database comprises around 400,000 genomes, including both representative and non-representative genomes. To access the full genome list, including NCBI identifiers, the user can download the metadata file from GTDB at https://data.gtdb.ecogenomic.org/releases/latest/. This file provides details for all 400,000 genomes present in the GTDB database.

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