Phylogenetic utility of indels within ribosomal DNA and β-tubulin sequences from fungi in the Rhizoctonia solani species complex

Molecular Phylogenetics and Evolution

Volumn 40, Issue 2, 2006, Pages 459-470

  González, Dolores ^a   Cubeta, Marc A ^b   Vilgalys, Rytas ^c  

^a INSTITUTO DE ECOLOGÍA   (Mexico)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

^c DUKE UNIVERSITY   (United States)

Author keywords

Alignment; Coding indels; Parsimony; Sequence homology

Indexed keywords

RIBOSOME DNA; TUBULIN;

ARTICLE; GENETIC TRANSCRIPTION; GENETICS; HYPHOMYCETES; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT;

BASE SEQUENCE; DNA, RIBOSOMAL; PHYLOGENY; RHIZOCTONIA; SEQUENCE ALIGNMENT; TRANSCRIPTION, GENETIC; TUBULIN;

CERATOBASIDIUM; FUNGI; FUNGI IMPERFECTI; HYPHOMYCETES; RHIZOCTONIA; THANATEPHORUS; THANATEPHORUS CUCUMERIS;

EID: 33745811693     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.03.022     Document Type: Article

References (43)

1. Aagesen L., Petersen G., and Seberg O. Sequence length variation, indel costs, and congruence in sensitivity analysis. Cladistics 21 (2005) 15-30
2. Andersen T.F. A study of hyphal morphology in the form genus Rhizoctonia. Mycotaxon 37 (1990) 25-46
3. Andersen T.F. A comparative taxonomic study of Rhizoctonia sensu lato employing morphological, ultrastructural and molecular methods. Mycol. Res. 100 (1996) 1117-1128
4. Anderson N.A. The genetics and pathology of Rhizoctonia solani. Annu. Rev. Phytopathol. 20 (1982) 329-347
5. Burpee L.L., Sanders P.L., Junior H.C., and Sherwood R.T. Anastomosis groups among isolates of Ceratobasidium cornigerum and related fungi. Mycologia 72 (1980) 689-701
6. Coetzee M.P.A., Bloomer P., Ridley G.S., and Wingfield M.J. Molecular identification and phylogeny of Armillaria isolates from South America and Indo-Malaysia. Mycologia 95 (2003) 285-293
7. Cubeta M.A., Echandi E., Abernethy T., and Vilgalys R. Characterization of anastomosis groups of binucleate Rhizoctonia species using restriction analysis of an amplified ribosomal RNA gene. Phytopathology 81 (1991) 1395-1400
8. Cubeta M.A., and Vilgalys R. Rhizoctonia. In: Lederberg J. (Ed). Encyclopedia of Microbiology (2000), Academic Press, San Diego 109-116
9. González D. Codificación de las inserciones-deleciones en el análisis filogenético de secuencias génicas. Bol. Soc. Bot. México 59 (1996) 115-129
10. González D., Carling E.D., Kuninaga S., Vilgalys R., and Cubeta M.A. Ribosomal DNA systematics of Ceratobasidium and Thanatephorus with Rhizoctonia anamorphs. Mycologia 93 (2001) 1138-1150
11. Graybeal A. Is it better to add taxa or characters to a difficult phylogenetic problem?. Syst. Biol. 47 (1998) 9-17
12. Grubisha L.C., Trappe J.M., Molina R., and Spatafora J.W. Biology of the ectomycorrhizal genus Rhizopogon. VI. Re-examination of infrageneric relationships inferred from phylogenetic analyses of ITS sequences. Mycologia 94 (2002) 607-619
13. Hibbett D.S., and Thorn R.G. Homobasidiomycetes. In: McLaughlin D.J., McLaughlin E.G., and Lemke P.A. (Eds). The Mycota VII. Systematics and Evolution. Part B (2001), Springer, Berlin 121-168
14. Hibbett D.S., Fukumasa-Nakai Y., Tsuneda A., and Donoghue M.J. Phylogenetic diversity in shiitake inferred from nuclear ribosomal DNA sequences. Mycologia 87 (1995) 618-638
15. Higgins D.G., Bleasby A.J., and Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. CABIOS 8 (1992) 189-191
16. Hopple Jr. J.S., and Vilgalys R. Phylogenetic relationships in the mushroom genus Coprinus and dark-spored allies based on sequence data from the nuclear gene coding for the large ribosomal subunit RNA: divergent domains, outgroups, and monophyly. Mol. Phylogenet. Evol. 13 (1999) 1-19
17. Kitching I.L., Forey P.L., Humphries C.J., and Williams D.M. Cladistics: The Theory and Practice of Parsimony Analysis (1998), Oxford University Press, New York
18. Kotila J.E. A study of biology of a new spore-forming Rhizoctonia, Corticium praticola. Phytopathology 19 (1929) 1059-1099
19. Kropp B.R., Hansen D.R., Wolf P.G., Flint K.M., and Thomson S.V. A study on the phylogeny of Dyer's woad rust fungus and other species of Puccinia from crucifers. Phytopathology 87 (1997) 565-571
20. Kuninaga S., Natsuaki T., Takeuchi T., and Yokosawa R. Sequence variation of the rDNA ITS regions within and between anastomosis groups in Rhizoctonia solani. Curr. Genet. 32 (1997) 237-243
21. Lutzoni F., Wagner P., Reeb V., and Zoller S. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Syst. Biol. 49 (2000) 628-651
22. Matsumoto T., Yamamoto W., and Hirane S. Physiology and parasitology of the fungi generally referred to as Hypochnus sasakii Shirai. I. Differentiaton of the strains by mean of hyphal fusion and culture in differential media. J. Soc. Trop. Agric. 4 (1932) 370-388
23. Milinkovitch M.C., Meyer A., and Powell J.R. Phylogeny of all major groups of cetaceans based on DNA sequences from three mitochondrial genes. Mol. Biol. Evol. 11 (1994) 939-948
24. Moncalvo J.-M., Vilgalys R., Redhead S.A., Johnson J.E., James T.Y., Aime M.C., Hofstetter V., Verduin S.J.W., Larsson E., Baroni T.J., Thorn R.G., Jacobsson S., Clémençon H., and Miller Jr. O.K. One hundred and senventeen clades of euagarics. Mol. Phylogenet. Evol. 23 (2002) 357-400
25. Moore R.T. The dolipore/parenthesome septum in modern taxonomy. In: Sneh B., Jabaji-Hare S., Neate S., and Dijst G. (Eds). Rhizoctonia Species: Taxonomy, Molecular Biology, Ecology, Pathology and Disease Control (1996), Kluwer Academic Publishers, Dordrecht, The Netherlands 13-35
26. Müller W.H., Stalpers J.A., van Aelst A.C., vanderKrift T.P., and Boekhout T. Field emission gun-scanning electron microscopy of septal pore caps of selected species in the Rhizoctonia s.l. complex. Mycologia 90 (1998) 170-179
27. Ogoshi A. Ecology and pathogenicity of anastomosis and intraspecific groups of Rhizoctonia solani Kühn. Annu. Rev. Phytopathol. 25 (1987) 125-143
28. Olsen G.J. Phylogenetic analysis using ribosomal RNA. Methods Enzymol. 164 (1988) 793-838
29. Olsen G.J., and Woese C.R. Ribosomal RNA: a key to phylogeny. FASEB J. 7 (1993) 113-123
30. Parmeter Jr. J.R., Whitney H.S., and Platt W.D. Affinities of some Rhizoctonia species that resemble mycelium of Thanatephorus cucumeris. Phytopathology 57 (1967) 218-223
31. Parmeter Jr. J.R., and Whitney H.S. Taxonomy and nomenclature of the imperfect state. In: Parmeter J.R. (Ed). Rhizoctonia solani: Biology and Pathology (1970), Univ of Calif Press, Berkeley 7-19
32. Poe S. Sensitivity of phylogeny estimation to taxonomic sampling. Syst. Biol. 47 (1998) 18-31
33. Rehner S.A., and Buckley E. A Beauveria phylogeny inferred from nuclear ITS and EF1-α sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia 97 (2005) 84-98
34. Sanderson M.J. Confidence limits on phylogenies: the bootstrap revisited. Cladistics 5 (1989) 113-129
35. Schultz H. Vergleichende Untersuchungen zur Okologic, Morphologie und Systematik des Vermchrungspilzes. Abr.Biol. Reichsanst. Land-u Forstwirtsch Berl 22 (1936) 1-41
36. Simmons M.P., and Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49 (2000) 369-381
37. Soltis D., Soltis P.S., Chase M.W., Mort M.E., Albach D.C., Zanis M., Savolainen V., Hahn W.H., Hoot S.B., Fay M.F., Axtell M., Swensen S.M., Prince L.M., Kress W.J., Nixon K.C., and Farris J.S. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Bot. J. Linn. Soc. 133 (2000) 381-461
38. Stalpers J.A., and Andersen T.F. A synopsis of the taxonomy of teleomorphs connected with Rhizoctonia S.L. In: Sneth B., Jabaji-Hare S., Neate S., and Dijst G. (Eds). Rhizoctonia Species: Taxonomy, Molecular Biology, Ecology, Pathology and Disease Control (1996), Kluwer Academic Publishers, Dordrecht 49-63
39. Swofford, D.L., 2000. Phylogenetic analysis using parsimony (* and other methods). 4.0b4. Sunderland, Massachusetts. Sinauer Associates.
40. Talbot P.H.B. Taxonomy and nomenclature of the perfect state. In: Parmeter J.R. (Ed). Rhizoctonia solani: Biology and Pathology (1970), Univ. of Calif. Press, Berkeley
41. Tu C.C., Kimbrough J.W., and Aldrich H.C. Cytology and ultrastructure of Thanatephorus cucumeris and related taxa of the Rhizoctonia complex. Can. J. Bot. 5 (1977) 2419-2436
42. Tu C.C., and Kimbrough J.W. Systematics and phylogeny of fungi in the Rhizoctonia complex. Bot. Gaz. 139 (1978) 454-466
43. Vogler A.P., and DeSalle R. Evolution and phylogenetic information content of the ITS-1 region in the tiger beetle Cicindela dorsalis. Mol. Biol. Evol. 11 (1994) 393-405