Rearrangements at a DNA-fingerprint locus in the rice blast fungus

Populations of the rice blast fungus, Magnaporthe grisea, can be sorted into clonal lineages based on restriction fragment length polymorphisms (RFLPs) detected with the repetitive DNA sequence MGR586. Mechanisms that produce DNA-fingerprint variation among lineages, are not known. In the process of analyzing the meiotic segregation of MGR586 RFLPs we identified a novel polymorphism, called MGR586-P2, in one member of a sister-spore pair from a complete tetrad. Molecular cloning revealed that P2 was generated by a nearby insertion of a novel, long-terminal-repeat (LTR)-containing retrotransposon. Genetic analysis showed that P2 and its progenitor polymorphism (P1) are alleles of a single polymorphic locus termed MGR586-PL (PL). Surprisingly, we found that a strain harboring PL recurrently produced clonal descendants harboring P1, P2 and possibly a third allele designated P3. PL is not located near a telomeric region. Our results show that some DNA-fingerprint loci may be hypervariable and undergo recurrent rearrangements. These findings have implications for interpreting DNA-fingerprint profiles from M. grisea populations.