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

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.

Formation of canker lesions on stems and black scurf on tubers in experimentally inoculated potato plants by isolates of AG2-1, AG3 and AG5 of Rhizoctonia solani: a pilot study and literature review

“…The data of this study indicate that the Finnish AG3 isolates are superior to those of AG2-1 and AG5 in formation of black scurf and thus also more likely to be efficiently spread with seed tubers. This is consistent with the fact that the great majority (98.9 %) of R. solani isolates infecting potato belong to AG3 in Finland (Ahvenniemi et al 2006, 2009) and in other northern potato production areas as discussed above. The other AGs infect many host species and would therefore be expected to be more common also in potato unless the differences in their abilities to form black scurf on potato tubers played an important role in dispersal, survival and prevalence in potato crops.…”

“…They were kindly provided by Prof. S. Naito (University of Hokkaido, Sapporo, Japan). A single isolate of AG4 was detected on potato in Finland (Ahvenniemi et al 2006(Ahvenniemi et al , 2009 but could not be maintained and was not available for experiments. One isolate of AG2-1 was not virulent on potato as tested in our previous study and was therefore excluded from experiments of this study.…”

“…The sequences of most of the isolates have been deposited to the NCBI sequence database [accession numbers DQ913037 (AG2-1 1734), DQ913034 (AG5-R96), DQ913014 (AG3-R11), DQ913026 (AG3-R98), EF532828 (AG2-1 PS-4) and EF532827 (AG5 Rh184)]. In addition, the anastomosis reactions of the Finnish isolates were determined using the tester isolates for comparison as reported previously , Ahvenniemi et al 2009). …”

“…therein). The secondary structures of ITS2 RNA sequences provide also additional evolutionary information in terms of compensatory base changes (CBC) occurring in the paired regions of a primary RNA transcript, which has revealed that strains of AG3 are a distinct species (Ahvenniemi et al 2009). This AG was originally described as R. solani by Kühn (1858) and in light of CBC analysis other AGs should be designated to new species different from R. solani (Ahvenniemi et al 2009).…”

“…In the survey that covered all main potato production areas of the country, a total of 503 isolates of R. solani were characterized and 497 of them (98.9 %) were found to belong to AG3. These isolates were collected from 281 potato fields and 31 cultivars (Ahvenniemi et al 2006, 2009. Only three isolates belonged to AG2-1 and one each to AG4, AG5 and an unknown binucleate Rhizoctonia sp.…”