Eukaryotes classified as new phyla or divergent prokaryotes

[Puri_Lopez-Garcia]

Hello,
Due to the lack of reference eukaryotic genomes, GTDB-tk tends to classify eukaryotic sequences as new prokaryotic phyla or as divergent high-rank taxa within archaea or bacteria. Several publications have this problem and can spread this type of misinformation. Can GTDB consider including a few reference eukaryotic genomes to avoid this?
Thank you!

[Phil_Hugenholtz]

Hi Puri

This is concerning. Do you have some examples of eukaryotic genomes that have been classified as bacteria or archaea by Tk? We’ll begin investigating and increase marker stringency and/or include euk refs as you suggest.

Bw, Phil

[jolespin]

This might be helpful:

How does GTDB-Tk handle protists like single-cell algae and diatoms?

I’m going to run a GTDB-Tk on a dataset that has a lot of protists in it in addition to a few bacteria. I was wondering how GTDB-Tk handles bins/MAGs that are eukaryotic such as single-celled algae and diatoms. Would it force a classification into something like a basal archaea or come back as something like NA? I asked a similar question a while back and you mentioned PhyloRank would be a useful tool in this endeavor. Would you suggest running PhyloRank to get domain level classification, t…

[Puri_Lopez-Garcia]

Hi Phil,

I realize my message below never got out.

Yes, we do have several examples. The last concerned fungal sequences from soil, which were classified as a new clade of Korarchaeia.

We also have diatom sequences classified as new cyanobacterial taxa.

Plus a few other examples which propose new bacterial phyla for protist sequences.

Cheers

[Phil_Hugenholtz]

Hi Puri

Please email me (p.hugenholtz@uq.edu.au) the examples and that will help us to build an extra euk filter into Tk.

Thx, Phil