The choice of molecular target depends on the aim wished to be achieved. For panfungal detection, usually the conserved regions the rRNA gene cluster are targeted. Other targets could also be used, including genes of the ergosterol biosynthesis (Morace et al. 1997), translation elongation factor genes (Vaitilingom et al. 1998), and the chitin synthase gene (Jordan 1994). For specific detection of a single genus or species, more variable regions of the genome, e.g., spacer regions of the rRNA gene cluster, or sequence characterized amplified region (SCAR) markers should be targeted. For the detection of mycotoxin producing fungi, sequences of the mycotoxin biosynthetic genes are the best targets. In the following, the targets used for molecular detection of fungi are dealt with, with special emphasis on mycotoxin producing fungi.
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