From my one experience I can tell you that it depends on the basidiomycete in question. I have done karyotyping (by protoplast formation and PFGE runs) of Phaffia rhodozyma, Saccharomyces cerevisiae and Squizosaccharomyces pombe and the same protocol works well to S. cerevisiae and P. rhodozyma but not at all for S. pombe (the part for the formation of protoplasts). So I really encourage you to do a good bibliographic search about PFGE, Karyotyping and your particular basidiomycete. If no one ever did it for your organism try to see other that are phylogenetically close.