I am going to use D1-D2 domain for barcoding sponge-associated fungi. My primer choice is LR0R&LR3, generating 600bp products. But I didn't see any articles talking about the cutoff for 28S rRNA OTU determination. If you know the answer, please tell me.
I'm not sure this ansers your question, but here is some relevant reading:
Porter, T.M. and Golding, G.B. (2012) Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error. PLoS ONE, 7(4): e35749.
I should also have said: depending on the number of sequences you have, you may find V-XtractorLSU (http://www.microbiome.ch/web/Tools.html) to be of assistance in your pursuit. But if you have fewer than a couple of thousand, then you could do the same thing by hand using, say, MAFFT and SeaView.
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