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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