The suitability and resolution of individual markers will depend very much on the fungus being considered, and a marker that is useful for differentiating species in one group of fungi, may be considerably more conserved or variable in other fungal groups. One example of this is the use of presumptive mtDNA RFLPs (AT rich DNA). The mtDNA RFLPs have been found useful for determining species and subspecific populations in some species of Aspergillus, whereas in the species Metarhizium anisopliae and Verti-cillium lecanii the same approach identifies numerous subspecific groupings (Kouvelis and Typas 1997; Typas et al. 1998; Varga et al. 1994). In the plant pathogen F. oxysporum sp. f. cubense mtDNA RFLPs have been used to distinguish between different races and supported the theory that the recently determined race 4 was not derived from the existing race 1 or 2 (Thomas et al. 1994). In the basidiomycete Ganoderma boninense mtDNA RFLPs have been found useful for defining individuals (Miller et al. 1999), and in some Phytophthora species they have been used for determining parental lines (Whittaker et al. 1994).
Differences in the level of variability seen with the same marker from different taxa is not restricted to mtDNA, and appears to be a feature of most markers investigated for population and species level investigations. One example of this is the degree of ITS sequence difference seen between isolates of a single species, or between closely related species. As an example there is generally up to around 5% ITS sequence variation within individual species of Colleto-trichum, and a maximum of about 23% variation between species (Sreenivasaprasad et al. 1996). In Rhizoctonia solani, up to 30% variation in the ITS sequences has been reported between isolates of the same anastomosis group (Kuninaga et al. 1997).
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