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Small-subunit ribosomal DNA of an ectomycorrhizal fungus tricholoma matsutake: sequence, structure and phylogenetic analysis.

A 2861 bp nucleotide sequence containing Tricholoma matsutake SSU rRNA gene and its flanking regions was determined and analyzed. Comparison with known SSU rDNA sequences and primer extension analysis revealed that the SSU rRNA coding region and intergenic spacer 2 (IGS2) are 1805 bp and 1043 bp in length, respectively. The IGS2 has an imperfect direct repeat (type 1) homologous to the region downstream to the 5S rRNA gene and the three imperfect tandem direct repeats (type 2) upstream to the SSU rRNA-encoding sequence. Structural analysis by a comparative method showed that the overall secondary structure of the SSU rRNA is generally similar to that of S. cerevisiae, whereas the secondary structures of the V4 regions predicted by the thermodynamics-based method showed different configurations between distantly related taxa, implying that these structural differences can provide phylogenetically informative features. Phylogenetic trees based on both the aligned SSU rRNA sequences with almost full-length sequences and V4 sequences revealed that T. matsutake is very closely related to other basidiomycetes belonging to Agaricales. Thus we propose that the V4 region is also a good source for the inference of phylogeny to support the SSU rRNA phylogeny.