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Many fungi undergo a reproductive phase in which more than one genetically distinct nuclei (from 2 separate mating types) is present within the same cytoplasm. In the Ascomycota and Basidiomycota, this phase is termed "dikaryotic", whereas in other fungal phyla the phase is "heterokaryotic." What is the difference here? Is it purely number of nuclei per cell, or does the difference depend on how many genetically distinct nuclei are present (2 or >2)?

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A heterokaryon is a fungal cell which has two or more genetically-distinct but allelically-compatible nuclei, as suggested by this resource, as well as this Wikipedia article.

A dikaryon is a fungal cell which has precisely two genetically-distinct but allelically-compatible nuclei, as shown here and here.

In this sense, a heterokaryon is a general term, whereas a dikaryon is a specific term. A dikaryon and a trikaryon (although not often seen in literature) are both heterokaryons.

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So heterokaryon is the general case, and dikaryon is a specific case? –  Daniel Standage Apr 6 '12 at 20:18
Good answer, thanks - one other thing I found is that a dikaryon may then divide, with each nucleus being replicated once per division, to form dikaryotic hyphae. In Basidiomycota, the entire basidiocarp (mushroom) is formed from these dikaryotic hyphae. –  gremau Apr 18 '12 at 20:30

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