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Evolutionary Diversification Indicated by Compensatory Base Changes in ITS2 Secondary Structures in a Complex Fungal Species, Rhizoctonia solani

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Abstract

The rRNA cistron (18S–ITS1–5.8S–ITS2–28S) is used widely for phylogenetic analyses. Recent studies show that compensatory base changes (CBC) in the secondary structure of ITS2 correlate with genetic incompatibility between organisms. Rhizoctonia solani consists of genetically incompatible strain groups (anastomosis groups, AG) distinguished by lack of anastomosis between hyphae of strains. Phylogenetic analysis of internal transcribed spacer (ITS) sequences shows a strong correlation with AG determination. In this study, ITS sequences were reannotated according to the flanking 5.8S and 28S regions which interact during ribogenesis. One or two CBCs were detected between the ITS2 secondary structure of AG-3 potato strains as compared to AG-3 tobacco strains, and between these two strains and all other AGs. When a binucleate Rhizoctonia species related to Ceratobasidiaceae was compared to the AGs of R. solani, which were multinucleate (3–21 nuclei per cell), 1–3 CBCs were detected. The CBCs in potato strains of AG-3 distinguish them from AG-3 tobacco strains and other AGs yielding further evidence that the potato strains of AG-3 originally described as R. solani are a species distinct from other AGs. The ITS1–5.8S–ITS2 sequences were analyzed by direct sequencing of PCR products from 497 strains of AG-3 isolated from potato. The same 10 and 4 positions in ITS1 and ITS2, respectively, contained variability in 425 strains (86%). Nine different unambiguous ITS sequences (haplotypes) could be detected in a single strain by sequencing cloned PCR products indicating that concerted evolution had not homogenized the rRNA cistrons in many AG-3 strains. Importantly, the sequence variability did not affect the secondary structure of ITS2 and CBCs in AG-3.

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Acknowledgements

We are grateful to M. Rännäli for skillful technical assistance, L. Paulin and P. Kristo for sequence analysis services, and A. Ogoshi and S. Naito for the AG reference strains. This work was funded by the Ministry of Agriculture and Forestry, Finland (grant 4655/501/2003), University of Helsinki, and the following Finnish companies and organizations: Berner Ltd., Chips Ltd., Finnamyl Ltd., Finnish Horticultural Products Society, Finnish Seed Potato Centre Ltd., HG Vilper Ltd., Jepuan Peruna Ltd., Järviseudun Peruna Ltd., Kesko, Kemira GrowHow, Krafts Food Ltd., MTT AgriFood Finland North Ostrobothnian Research Station, ProAgria Oulun maaseutukeskus, Pohjoisen Kantaperuna Ltd., Potwell Ltd., ProAgria Association of Rural Advisory Centers, Ravintoraisio Ltd., Ruokaperuna, Ruokakesko Ltd., Saarioinen Ltd. and Solanum Ltd.

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  1. Department of Applied Biology, University of Helsinki, P.O. Box 27, Helsinki, 00014, Finland

    Paavo Ahvenniemi, Mari J. Lehtonen, Paula Wilson, Malgorzata German-Kinnari & Jari P. T. Valkonen

  2. Department of Bioinformatics, Biocenter, University of Würzburg, 97074, Würzburg, Germany

    Matthias Wolf

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  1. Paavo Ahvenniemi
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  2. Matthias Wolf
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Correspondence to Jari P. T. Valkonen.

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239_2009_9260_MOESM1_ESM.jpg

Multiple global sequence-structure alignment (ITS2) of the strains of different anastomosis groups (AGs) of Rhizoctonia solani and a binucleate Rhizoctonia sp. (R92). The sequence length is given after the sequence name (JPG 2,846 kb)

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Ahvenniemi, P., Wolf, M., Lehtonen, M.J. et al. Evolutionary Diversification Indicated by Compensatory Base Changes in ITS2 Secondary Structures in a Complex Fungal Species, Rhizoctonia solani . J Mol Evol 69, 150–163 (2009). https://doi.org/10.1007/s00239-009-9260-3

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