Abstract
The haplotype variation and phylogeography of Rhizoctonia solani AG1-IA strains were estimated using rDNA5.8S-ITS and ß-actin gene sequences. Two haplotypes of ITS sequences were revealed, designated as ITSa and ITSb. Thirty-four SNPs from the ß-actin gene, which displayed more allele discriminations than rDNA-ITS, were identified. The SNPs were used to classify R. solani into 12 haplotypes, designated as H1–H12. Most SNPs occurred at the third codon position and resulted as silent mutations. Three SNPs occurred at the first codon position and one SNP occurred at the second position, which these four SNPs causing non-synonymous mutations. According to the translational amino acid sequences, the 12 nucleotide-inferred haplotypes were further classified into 5 groups, designated as ITRL, VARI, VARL, VTRI, and VAMI. Analysis of the geographical distribution of 12 haplotypes, showed that H1 and H9 were widely distributed in all studied locations and existed simultaneously in the strains collected in most areas. The results lead to the speculation that H1 and H9 could be the founder haplotypes of ß-actin gene, and other haplotypes might be derived from them.
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Acknowledgments
We thank Mr. Robert Harman II for critically reviewing this manuscript. This project was supported by National Transgenic Breeding Program of China (2012ZX08009001-002) and National Basic Research Program of China (2012CB722504).
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Yong Wei and Jiandong Bao equally contributed to this work.
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Figure S1
Neighbor-joining tree of different Rhizoctonia solani AG 1-IA isolates based on the nucleotide sequences of the rDNA ITS-5.8S. All the sequences within the same subgroup of AG1-IA collected from rice are clustered together and cannot be differentiated. The sequences described in this study were designated as either ITSa or ITSb. Other sequences were retrieved from NCBI with respective accession numbers (DOC 144 kb)
Table S1
Frequency of different SNP types in ß-actin sequence of R. solani AG1-IA strains (DOCX 12 kb)
Table S2
Groups based on the deduced amino acids and haplotypes based on SNPs in ß-actin sequence of R. solani AG1-IA strains (DOCX 11 kb)
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Wei, Y., Bao, J., Cao, H. et al. Haplotype variation and phylogeography of Rhizoctonia solani AG1-IA strains based on rDNA5.8S-ITS and ß-actin gene sequence analyses. Mycol Progress 13, 247–255 (2014). https://doi.org/10.1007/s11557-013-0909-3
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DOI: https://doi.org/10.1007/s11557-013-0909-3