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The nuclear rDNA intergenic spacer of the ectomycorrhizal basidiomycete Laccaria bicolor: structural analysis and allelic polymorphism

Equipe de Microbiologie Forestière, Centre de Recherche de Nancy, Institut National de la Recherche Agronomique, Champenoux F-54280, France

Author for correspondence: Francis Martin. Tel: -33 383 39 40 80. Fax: -33 383 39 40 69. e-mail: fmartin@nancy.inra.fr

ABSTRACT

The nuclear rDNA intergenic spacer (IGS) of the ectomycorrhizal basidiomycete Laccaria bicolor was amplified and sequenced to identify the source of its intraspecific polymorphism. The IGS was amplified by PCR in several L. bicolor 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 L. bicolor S238N were sequenced: the β-haplotype was 4160 bp in length, whereas the size of the -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, IGS₁, 5S rDNA and IGS₂. The IGS sequences are AT-rich and contain numerous occurrences of three types of subrepeats (e.g. T₂AC₃). The length polymorphism, observed between the IGS sequence of the - and β-haplotypes, results from the insertion of various numbers of a 71 bp subrepeat, called B, occurring in IGS₂. This variation in subrepeat number suggests that the two haplotypes resulted from unequal cross-overs. The L. bicolor IGS was aligned with IGS sequences of two other Tricholomataceae (i.e. Tricholoma matsutake and Collybia fusipes). No sequence similarity was observed between these IGSs, but homologous subrepeats were found in L. bicolor and T. matsutake. Analysis of IGS length polymorphism is therefore an efficient tool for investigating genetic relationships between genets and within progenies in natural fungal populations.

The NCBI accession number for the sequence reported in this paper is AF116534.

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