For centuries, fungal identification has been based on morphological, physiological, and chemical characteristics of specimens. For the most part, these systems still work extremely well. They provide accurate species identification inexpensively, are not labor-intensive, and require little equipment beyond a microscope and chemical reagents. Since phenotype is the result of the expression of hundreds of genes, the higher level classifications based on morphology/ physiology are generally sound. A major drawback of the traditional identification methods is that they require some technical training in order to acquire the skills necessary to identify fungi or characterize strains. This training has become increasingly difficult to acquire, whereas molecular biology techniques are now taught widely in secondary schools and can be applied to a multitude of fields. Another drawback of the traditional methods is that they can take a week or more for fungal colonies to grow and develop the characters necessary for identification. In some cases, the necessary characters never develop. Several of the molecular methods provide identifications more quickly and do not rely on the presence of reproductive structures.
Molecular biology has brought many powerful new tools to fungal taxonomists including the potential for rapid identification of isolates, methods for rapid determination of virulence or toxicity of strains, and the means to elucidate the relationships among fungal species. DNA sequence data provide large numbers of data points that can be compared among fungi and analyzed to determine sequence relatedness, which can be assumed to reflect phylogenetic relatedness among species. If "phylogenetic trees" from different molecular sites concur with one another and with "trees" based on morphological and physiological data, one has fairly strong evidence that the phylogeny is accurate. Some fungi do not grow or do not sporulate in culture. Molecular methodologies allow identification of these isolates by comparison of DNA sequence data from the unknown isolate with sequences from known species. Molecular methods have also been used to distinguish between closely related species with few morphological differences and to distinguish strains (or even specific isolates) within a species. In studies of fungal metabolites, especially mycotoxins, there has been no way of knowing whether a nonproducing strain is truly (genetically) incapable of producing the metabolite or if it could possibly produce it under different environmental conditions. Once the genes of a metabolic pathway have been cloned, they can be used to determine whether or not a strain possesses the genes for production of the metabolite, providing a better indication of the potential of a given strain to produce a metabolite.
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