Hi @colinbrislawn,
Following up on this question, I have used the pre-trained classifier unite_ver10_dynamic_all_19.02.2025-Q2-2024.10.qza for AMF sequences targeting D2 of the LSU and I have actually obtained good results. Would it be safe to assume that my results are correct?
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I have no idea 
(I don't make the UNITE database, just the classifier for the q2-feature-classifier plugin.)
Here's a list of Primers referenced by Unite. AMF is mentioned so I would start investigating here:
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Hi @Pablo_V ,
I would urge against this. UNITE is specific to the ITS domain. The fact that you get any results with LSU D2 domain data is probably either noise or just that fragments of LSU data might be in some of the UNITE sequences (as ITS primers are always embedded in the flanking SSU/5.8S/LSU rRNA genes), but taxonomic coverage is probably very inconsistent in this case. So I would suggest instead using an LSU-specific dataset: e.g., SILVA has an LSU database as well (which you can also retrieve with RESCRIPt). Or check out this database:
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