The nuclear rDNA intergenic spacer (IGS) of the ectomycorrhizal basidiomycete was amplified and sequenced to identify the source of its intraspecific polymorphism. The IGS was amplified by PCR in several strains and shown to exhibit multiple bands and length polymorphism. The IGS loci were shown to segregate in a 1:1 ratio within haploid progenies in three dikaryotic strains, suggesting that divergent IGS haplotypes were present in the two nuclei of these strains. The two haplotypes of S238N were sequenced: the β-haplotype was 4160 bp in length, whereas the size of the α-haplotype was estimated to be about 4700 bp. These represent the largest published fungal IGS sequences to date. These sequences can be subdivided into three main regions, IGS, 5S rDNA and IGS. The IGS sequences are AT-rich and contain numerous occurrences of three types of subrepeats (e.g. TAC). The length polymorphism, observed between the IGS sequence of the α- and β-haplotypes, results from the insertion of various numbers of a 71 bp subrepeat, called B, occurring in IGS. This variation in subrepeat number suggests that the two haplotypes resulted from unequal cross-overs. The IGS was aligned with IGS sequences of two other Tricholomataceae (i.e. and No sequence similarity was observed between these IGSs, but homologous subrepeats were found in and Analysis of IGS length polymorphism is therefore an efficient tool for investigating genetic relationships between genets and within progenies in natural fungal populations.


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