Genome analysis of the fungal plant pathogen, Leptosphaeria maculans using pulsed field gel electrophoresis

Pulsed field gel electrophoresis (PFGE), or electrophoretic karyotyping, separates chromosomal-sized pieces of DNA in agarose gels where the orientation of the electric field is periodically altered. This technique has revealed that many fungi have a high degree of chromosomal length polymorphisms. Often the only isolates with identical karyotypes are derived from a single clone, thus PFGE provides a 'genetic fingerprint' for them. The size range and number of chromosomes within isolates of a particular species are usually constant, hence PFGE can distinguish between morphologically similar fungi. This technique can also be used to follow inheritance of chromosomal length polymorphisms and shows that in some fungi novel-sized chromosomes are produced during meiosis. As well as resolving the nuclear (A-type) chromosomes, it can also resolve dispensable (B-type) chromosomes and cytoplasmic genomes including mitochondrial DNA and linear plasmids. The application of this technique to Australian isolates of Leptosphaeria maculans, which causes blackleg disease of canola (Brassica napus), is discussed.