LITERATURE CITED
- Aylor DL, Price EW, Carbone I. 2006. SNAP: combine and map modules for multilocus population genetic analysis. Bioinformatics 22:1399–1401.
- Bharathan N, Tavantzis SM. 1990. Genetic diversity of double-stranded RNA from Rhizoctonia solani. Phytopathology 80:631–635.
- ———, Saso H, Gudipati L, Bharathan S, Whited K, Anthony K. 2005. Double-stranded RNA: distribution and analysis among isolates of Rhizoctonia solani AG-2 to -13. Plant Pathol 54:196–203.
- Binder M, Hibbett DS, Larsson K-H, Larsson E, Langer E, Langer G. 2005. The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes). Syst Biodivers 3:113–157.
- Bowden LC, Price EW, Carbone I. 2008. SNAP Clade and Matrix, Version 2. Distributed over the Internet, http://www.cals.ncsu.edu/plantpath/faculty/carbone/home.html, Department of Plant Pathology, North Carolina State University.
- Carbone I, Liu YC, Hillman BI, Milgroom MG. 2004. Recombination and migration of Cryphonectria hypovirus 1 as inferred from gene genealogies and the coalescent. Genetics 166:1611–1629.
- ———, Jakobek JL, Ramirez-Prado JH, Horn BW. 2007. Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus. Mol Ecol 16:4401–4417.
- Carling DE. 1996. Grouping in Rhizoctonia solani by hyphal anastomosis reaction. In: Sneh B, Jabaji-Hare S, Neate S, Dijst G, eds. Rhizoctonia species: taxonomy, molecular biology, ecology, pathology and disease control. Dordrecht, Netherlands: Kluwer Academic Publishers. p 37–47.
- Castanho B, Butler EE. 1978. Rhizoctonia decline: a degenerative disease of Rhizoctonia solani. Phytopathology 68:1505–1510.
- Charlton ND. 2007. Evolutionary history and population dynamics of the M2 double-stranded RNA of Rhizoctonia solani [Doctoral dissertation]. Raleigh: North Carolina State Univ. 101 p.
- Cubeta MA, Vilgalys R. 2000. Rhizoctonia. In: Lederberg J, ed. Encyclopedia of Microbiology. San Diego: Academic Press. p 109–116.
- Deng F, Xu R, Boland GJ. 2003. Hypovirulence-associated double-stranded RNA from Sclerotinia homoeocarpa is conspecific with Ophiostoma novoulmi mitovirus 3a-Ld. Phytopathology 93:1407–1414.
- Finkler A, Koltin Y, Barash I, Sneh B, Pozniak D. 1985. Isolation of a virus from virulent strains of Rhizoctonia solani. J Gen Virol 66:1221–1232.
- Ghabrial SA. 1998. Origin, adaptation and evolutionary pathways of fungal viruses. Virus Gene 16:119–131.
- González D, Carling DE, Kuninaga S, Vilgalys R, Cubeta MA. 2001. Ribosomal DNA systematics of Ceratobasidium and Thanatephorus with Rhizoctonia anamorphs. Mycologia 93:1138–1150.
- ———, Cubeta MA, Vilgalys R. 2006. Phylogenetic utility of indels within ribosomal DNA and β-tubulin sequences from fungi in the Rhizoctonia solani species complex. Mol Phylogenet Evol 40:459–470.
- Griffiths RC, Tavaré S. 1994. Ancestral inference in population genetics. Stat Sci 9:307–319.
- Jian J, Lakshman DK, Tavantzis SM. 1997. Association of distinct double-stranded RNAs with enhanced or diminished virulence in Rhizoctonia solani infecting potato. MPMI 10:1002–1009.
- Kim S-O, Chung H-S, Lee Y-H. 1996. Double-stranded RNAs in Korean isolates of Rhizoctonia solani AG4. FEMS Microbiol Lett 141:203–206.
- Kousik CS, Snow JP, Valverde RA. 1994. Comparison of double-stranded RNA components and virulence among isolates of Rhizoctonia solani AG-1 IA and AG-1 IB. Phytopathology 84:44–49.
- Kuninga S, Natsuaki T, Takeuchi T, Yokosawa R. 1997. Sequence variation of the rDNA ITS regions within and between anastomosis groups in Rhizoctonia solani. Curr Genet 32:237–243.
- Lakshman DK, Tavantzis SM. 1994. Spontaneous appearance of genetically distinct double-stranded RNA elements in Rhizoctonia solani. Phytopathology 84: 633–639.
- ———, Jian J, Tavantzis SM. 1998. A double-stranded RNA element from a hypovirulent strain of Rhizoctonia solani occurs in DNA form and is genetically related to the pentafunctional AROM protein of the shikimate pathway. Proc Nat Acad Sci USA 95:6425–6429.
- Liu C, Lakshman DK, Tavantzis SM. 2003a. Expression of a hypovirulence-causing double-stranded RNA is associated with up-regulation of quinic acid pathway and down-regulation of shikimic acid pathway in Rhizoctonia solani. Curr Genet 42:284–291.
- ———, ———, Tavantzis SM. 2003b. Quinic acid induces hypovirulence and expression of a hypovirulence-associated double-stranded RNA in Rhizoctonia solani. Curr Genet 43:103–111.
- Liu YC, Linder-Basso D, Hillman BI, Kaneko S, Milgroom MG. 2003. Evidence for interspecies transmission of viruses in natural populations of filamentous fungi in the genus Cryphonectria. Mol Ecol 12:1619–1628.
- Lyngsø RB, Song YS, Hein J. 2005. Minimum recombination histories by branch and bound. Proc 5th Int Workshop Algorithms in Bioinformatics (lecture notes in Bioinformatics) 3692:239–250.
- Ogoshi A. 1987. Ecology and pathogenicity of anastomosis and intraspecific groups of Rhizoctonia solani Kühn. Annu Rev Phytopathol 25:125–143.
- Parmeter JR, ed. 1970. Rhizoctonia solani: biology and pathology. Berkeley: Univ. California Press. 255 p.
- Peever TL, Liu YC, Milgroom MG. 1997. Diversity of hypoviruses and other double-stranded RNAs in Cryphonectria parasitica in North America. Phytopathology 87:1026–1033.
- Price EW, Carbone I. 2005. SNAP: workbench management tool for evolutionary population genetic analysis. Bioinformatics 21:402–404.
- Robinson HL, Deacon JW. 2002. Double-stranded RNA elements in Rhizoctonia solani AG 3. Mycol Res 106:12–22.
- Salzman RA, Fujita T, Zhu-Salzman K, Hasegawa PM, Bressan RA. 1999. An improved RNA isolation method for plant tissues containing high levels of phenolic compounds or carbohydrates. Plant Mol Biol Rep 17: 11–17.
- Stalpers JA, Andersen TF. 1996. A synopsis of the taxonomy of teleomorphs connected with Rhizoctonia S.L. In: Sneh B, Jabaji-Hare S, Neate S, Dijst G, eds. Rhizoctonia species taxonomy, molecular biology, ecology, pathology and disease control. Dordrecht, Netherlands: Kluwer Academic Publishers. p 49–63.
- Swofford DL. 1998. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4.0. Sunderland, Massachusetts: Sinauer Associates.
- Thompson JD, Higgins DG, Gibson TJ. 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res 22:4673–4680.
- Vilgalys R. 1988. Genetic relatedness among anastomosis groups in Rhizoctonia as measured by DNA/DNA hybridization. Phytopathology 78:698–702.
- ———, González D. 1990. Ribosomal DNA restriction fragment length polymorphisms in Rhizoctonia solani. Phytopathology 80:151–158.
- Voth PD, Mairura L, Lockhart BE, May G. 2006. Phylogeography of Ustilago maydis virus H1 in the USA and Mexico. J Gen Virol 87:3433–3441.
- Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256–276.
- Zanzinger DH, Bandy BP, Tavantzis SM. 1984. High frequency of finding double-stranded RNA in naturally occurring isolates of Rhizoctonia solani. J Gen Virol 65: 1601–1605.