The basis of symbiotic partnership are the molecular signals that are exchanged between partners leading to recognition and interactions between phototroph and the fungus. The natures of the molecules involved in cross-talk allowing the partners to live in total harmony with mutual beneficial adjustments are not known. Also not known is how existence in symbiosis causes a massive efflux of particular molecules from the autotroph. The identification of common genes with roles in mycorrhizal and lichen symbioses, the molecular forms and mechanisms by which nitrogen, phosphate and carbon move across the membranes, and the mechanisms by which the fungus forms a carbohydrate sink are among questions that require study. One hypothesis is that the heterotroph directly affects membrane transport systems in the autotroph, generating a strong carbohydrate sink. The possibility of gene transfer between photobiont and mycobiont in lichens needs to be explored. How genetically divergent nuclei arise in arbuscular mycorrhizal fungi in the absence of sexual reproduction is an enigma.
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