Taxonomic aspects of Peronosporaceae inferred from Bayesian molecular phylogenetics

Canadian Journal of Botany

Volumn 81, Issue 7, 2003, Pages 672-683

  Goker M ^a   Voglmayr, H ^b   Riethmuller A ^c   Weiss M ^a   Oberwinkler, F ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b UNIVERSITY OF VIENNA   (Austria)

^c UNIVERSITY OF KASSEL   (Germany)

Author keywords

Bayesian phylogenetic analysis; Downy mildews; LSU rDNA; Peronosporales; Peronosporomycetes; Straminipila

Indexed keywords

DNA; ECOLOGY; GENES; MORPHOLOGY;

BIOTROPHISMS; PLASMORA SPECIES; RDNA; TAXONOMIC ASPECTS;

BIODIVERSITY;

MOLECULAR ANALYSIS; NEW GENUS; PHYLOGENETICS; TAXONOMY;

ANATOMY; BIODIVERSITY; ECOLOGY; GENES; NUCLEIC ACIDS;

BASIDIOPHORA; BREMIA; HYALOPERONOSPORA; PARAPERONOSPORA; PERONOSPORA; PERONOSPORA FARINOSA; PERONOSPORACEAE; PERONOSPORALES; PLASMOPARA; VIENNOTIA; VIENNOTIA OPLISMENI;

EID: 5344279619     PISSN: 00084026     EISSN: None     Source Type: Journal    
DOI: 10.1139/b03-066     Document Type: Article

References (44)

1. Angiosperm Phylogeny Group. 1998. An ordinal classification of the families of flowering plants. Ann. Mo. Bot. Gard. 85: 531-553.
2. Constantinescu, O. 2000. The fine structure of the sporangium in Pseudoperonospora humuli (Chromista, Oomycota, Peronosporales). Cryptogam. Mycol. 21: 93-101.
3. Constantinescu, O., and Fatehi, J. 2002. Peronospora-like fungi (Chromista, Peronosporales) parasitic on Brassicaceae and related hosts. Nova Hedwigia, 74: 291-338.
4. Cooke, D.E.L, Drenth, A., Duncan, J.M., Wagels, G., and Brasier, C.M. 2000. A molecular phylogeny of Phytophthora and related Oomycetes. Fungal Genet. Biol. 30: 17-32.
5. Cunningham, J.L. 1972. A miracle mounting fluid for permanent whole-mounts of microfungi. Mycologia, 64: 906-911.
6. Dick, M.W. 1999. Classification of the Peronosporomycetes. In Encyclopaedia of food microbiology. Vol. 2. Edited by R. Robinson, C. Batt, and P. Patel. Acacemic Press, London. pp. 871-882.
7. Dick, M.W. 2001. The Peronosporomycetes. In The Mycota. Vol. VIIA. Edited by D.J. McLaughlin, E.G. McLaughlin, and P.A. Lemke. Springer, Berlin, pp. 39-72.
8. Dick, M.W., Vick, M.C., Gibbings, J.G., Hedderson, T.A., and Lopez Lastra, C.C. 1999. 18S rDNA for species of Leptolegnia and other Peronosporomycetes: justification of the subclass taxa Saprolegniomycetidae and Peronosporomycetidae and division of the Saprolegniaceae sensu lato into the Leptolegniaceae and Saprolegniaceae. Mycol. Res. 103: 1119-1125.
9. Erwin, D.C., and Ribeiro, O.K. 1996. Phytophthora diseases worldwide. APS Press, St. Paul, Minn.
10. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39: 783-791.
11. Förster, H., Cummings, M.P., and Coffey, M.D. 2000. Phylogenetic relationship of Phytophthora species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI. Mycol. Res. 104: 1055-1061.
12. Fraymouth, J. 1956. Haustoria of the Peronosporales. Trans. Br. Mycol. Soc. 39: 79-107.
13. Garnica, S., Weiß, M., Oertel, B., and Oberwinkler, F. 2003. Phylogenetic relationships of European Phlegmacium species (Cortinarius, Agaricales). Mycologia, In press.
14. Gascuel, O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14: 685-695.
15. Gäumann, E. 1918. Über die Formen der Peronospora parasitica (Pers.) Fries. Beih. Biol. Zentbl. 35: 395-533.
16. Hawksworth, D.L., Kirk, P.M., Sutton, B.C., and Pegler, D.N. 1995. Ainsworth & Bisby's dictionary of the Fungi. 8th ed. CAB International, Wallingford, U.K.
17. Hennig, W. 1965. Phylogenetic systematics. Annu. Rev. Entomol. 10: 97-116.
18. Hennig, W., and Hennig, W. 1982. Phylogenetische Systematik. Parey, Berlin.
19. Hopple, J.S., and Vilgalys, R. 1999. 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: 1-19.
20. Hudspeth, D.S.S., Nadler, S.A., and Hudspeth, M.E.S. 2000. A COX2 molecular phylogeny of the Peronosporomycetes. Mycologia, 92: 674-684.
21. Huelsenbeck, J.P., and Ronquist, F.R. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17: 754-755.
22. Kenneth, R., and Kranz, J. 1973. Plasmopara penniseti sp. nov., a downy mildew of pearl millet in Ethiopia. Trans. Br. Mycol. Soc. 60: 590-593.
23. Larget, B., and Simon, D.L. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16: 750-759.
24. Leclerc, M.C., Guillot, J., and Deville, M. 2000. Taxonomic and phylogenetic analysis of Saprolegniaceae (Oomycetes) inferred from LSU rDNA and ITS sequence comparisons. Antonie Leeuwenhoek, 77: 369-377.
25. Maier, W., Begerow, D., Weiß, M., and Oberwinkler, F. 2003. Phylogeny of the rust fungi: an approach using nuclear large subunit ribosomal DNA sequences. Can. J. Bot. 81: 12-23.
26. Matsumoto, C., Kageyama, K., Suga, H., and Hyakumachi, M. 1999. Phylogenetic relationships of Pythiuin species based on ITS and 5.8S sequences of the ribosomal DNA. Mycoscience, 40: 321-331.
27. Mau, B., Newton, M.A., and Larget, B. 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics, 55: 1-12.
28. McNicol, R.J., and Williamson, B. 1989. Systemic infection of black currant flowers by Botrytis cinerea and its possible involvement in premature abscission of fruits. Ann. Appl. Biol. 114: 243-254.
29. Murphy, W.J., Eizirik, E., O'Brien, S.J., Madsen, O., Scally, M., Douady, C.J., Teeling, E., Ryder, O.A., Stanhope, M.J., De Jong, W.W., and Springer, M.S. 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science (Washington, D.C.), 294: 2348-2356.
30. Petersen, A.B., and Rosendahl, S. 2000. Phylogeny of the Peronosporomycetes (Oomycota) based on partial sequences of the large ribosomal subunit (LSU rDNA). Mycol. Res. 104: 1295-1303.
31. Posada, D., and Crandall, K.A. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics, 14: 817-818.
32. Rambaut, A. 1996. Se-Al. Sequence Alignment Editor v2.0. Available from http://evolve.zoo.ox.ac.uk/software/ [updated 22 January 2002; cited 17 October 2002].
33. Riethmüller, A., Weiß, M., and Oberwinkler, F. 1999. Phylogenetic studies of Saprolegniomycetidae and related groups based on nuclear large subunit DNA sequences. Can. J. Bot. 77: 1790-1800.
34. Riethmüller, A., Voglmayr, H., Göker, M., Weiß, M., and Oberwinkler, F. 2002. Phylogenetic relationships of the downy mildews (Peronosporales) and related groups based on nuclear large subunit ribosomal DNA sequences. Mycologia, 94: 834-849.
35. Rosenberg, M.S., and Kumar, S. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Nat. Acad. Sci. U.S.A. 98: 10751-10756.
36. Saitou, N., and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
37. Skalicky, V. 1966. Taxonomie der Gattungen der Familie Peronosporaceae. Preslia, 38: 117-129.
38. Swofford, D.L. 2001. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4b10. Sinauer Associates, Sunderland, Mass.
39. Swofford, D.L, Olsen, G.J., Waddell, P.J., and Hillis, D.M. 1996. Phylogenetic inference. In Molecular systematics. Edited by D.M. Hillis, C. Moritz, and B.K. Mable. Sinauer Associates, Inc., Sunderland, Mass. pp. 407-514.
40. Viennot-Bourgin, G. 1959. Champignons nouveaux de la Guinée. Bull. Soc. Mycol. Fr. 75: 33-37.
41. Waterhouse, G.M., and Brothers, M.P. 1981. The taxonomy of Pseudoperonospora. Mycol. Pap. 148: 1-28.
42. Whelan, S., Lio, P., and Goldman, N. 2001. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet. 17: 262-272.
43. Wubet, T., Weiß, M., Kottke, I., and Oberwinkler, F. 2003. Morphology and molecular diversity of arbuscular mycorrhizal fungi in wild and cultivated yew (Taxus baccata L.). Can. J. Bot. 81: 255-266.
44. Yerkes, D.R. Jr., and Shaw, C.G. 1959. Taxonomy of the Peronospora species on Cruciferae and Chenopodiaceae. Phytopathology, 49: 499-507.