The mitochondrial (mt) genome has been used extensively in the investigation of population structures in the plant pathogenic fungi. In fungi the mitochondrial genome is a circular structure of between 17 and 121 Kb [see Zimmer et al.
(1984); Curole and Kocher (1999); Grossman and Hudspeth
(1985); Lu (1996)]. The fungal mitochondrial genome makes up between 1 -20% of the DNA occurring in fungal cells, and generally contains a high proportion of sequences that lack a coding function. In addition it may contain many repeat sequences and introns, and these features can allow for considerable variation in mitochondrial sequences between closely related organisms [see Clark-Walker (1992); Clark-Walker et al. (1987); see chapter numbers 11 and 12 in this book]. As it is present in multiple copies, mtDNA can be a good target for molecular methods. In most cases mito-chondrial DNA is inherited unilinearly during meiosis but recombination may occur in some fungi (Wolf 1996). In addition, mtDNA can be transferred independently of the nuclear genome during unstable vegetative fusion (Collins and Saville 1990). The mtDNA can contain GC rich palindromic repeats, but overall, simple GC sequences are relatively rare in fungal mitochondria, and this has been used in differential DNA restriction protocols to generate presumptive mitochon-drial RFLPs [e.g., Kouvelis and Typas (1997); Lacourt et al. (1994)]. The mitochondrial genome contains both variable and conserved regions and so sequence information may be used at a variety of taxonomic levels [see Zhou and Stanosz (2001)]. In some cases closely related species may have very different mitochondrial genomes, and one example of this is in the yeast Saccharomyces, where mtDNA varies from 24 to 78 Kb between different species [see Grossman and Hudspeth (1985)]. Analysis of mtDNA variation has been used at a variety of different population and systematic levels, and these have correlated with subspecies, vegetative incompatibility groups, different populations and individuals (Gordon and Okamoto 1992; Jacobson and Gordon 1990; Miller et al. 1999).
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