What would it take to adapt GTDB-Tk for protista and single-celled fungi?

I’ve been trying to dive into the abyss of microeukaryotic organisms but there’s no tool that can classify them at the same quality as GTDB-Tk. I understand gene modeling for microeukaryotes can’t be done via Prodigal which is running in the back end of GTDB-Tk I believe.

Give we had precomputed gene models and quality filtered genomes:

  1. What would it take to adapt GTDB-Tk to handle microeukaryotes?
  2. What type of database structure would we need to use for the taxonomy?
  3. Are there any caveats where this methodology wouldn’t work for microeukaryotes?

I know this isn’t in the current scope of GTDB-Tk but I’m just wondering how these methods can be adapted.