Implications of molecular characters for the phylogeny of the Microbotryaceae (Basidiomycota: Urediniomycetes)

BMC Evolutionary Biology

Volumn 6, Issue , 2006, Pages

  Kemler, Martin ^a   Göker, Markus ^a   Oberwinkler, Franz ^a   Begerow, Dominik ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ANGIOSPERM; ANTHER; ARTICLE; BASIDIOMYCETES; CONTROLLED STUDY; DNA SEQUENCE; FAMILIA; MICROBOTRYACEAE; MOLECULAR BIOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARSIMONY ANALYSIS; PHYLOGENY; SMUT (PLANT DISEASE); CLASSIFICATION; GENETICS; MOLECULAR EVOLUTION; SEQUENCE ALIGNMENT;

ASTERACEAE; BASIDIOMYCOTA; CARYOPHYLLACEAE; DIPSACACEAE; LAMIACEAE; LENTIBULARIACEAE; MICROBOTRYACEAE; MICROBOTRYUM; POLYGONACEAE; PORTULACACEAE; UREDINIOMYCETES;

FUNGAL DNA; RIBOSOMAL SPACER DNA;

BASE SEQUENCE; BASIDIOMYCOTA; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; PHYLOGENY; SEQUENCE ALIGNMENT;

EID: 33746879970     PISSN: 14712148     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-6-35     Document Type: Article

References (60)

1. Hood ME, Antonovics J: Mating within the meiotic tetrad and the maintenance of genomic heterozygosity. Genetics 2004, 166:1751-1759.
2. Giraud T: Patterns of within population dispersal and mating of the fungus Microbotryum violaceum parasitising the plant Silene latifolia. Heredity 2004, 93:559-565.
3. Freeman AB, Duong KK, Shi TL, Hughes CF, Perlin MH: Isolates of Microbotryum violaceum from North American host species are phylogenetically distinct from European host-derived counterparts. Mol Phylogenet Evol 2002, 23:158-170.
4. Begerow D, Göker M, Lutz M, Stoll M: On the evolution of smut fungi and their hosts. In Frontiers in Basidiomycote Mycology Edited by: Agerer R, Piepenbring M, Blanz P. Eching: IHW Verlag; 2004:81-98.
5. Thrall PH, Biere A, Antonovics J: Plant-life history and disease susceptibility - the occurrence of Ustilago violacea on different species within the Caryophyllaceae. J Ecol 1993, 81:489-498.
6. Vánky K: The genus Microbotryum (smut fungi). Mycotaxon 1998, 67:33-118.
7. Lutz M, Göker M, Piatek M, Kemler M, Begerow D, Oberwinkler F: Anther smuts of Caryophyllaceae: molecular characters indicate host-dependent species delimitation. Mycol Prog 2005, 4(3):225-238.
8. Perlin MH: Pathovars or formae speciales of Microbotryum violaceum differ in electrophoretic karyotype. Int J Plant Sci 1996, 157:447-452.
9. Perlin MH, Hughes C, Welch J, Akkaraju S, Steinecker D, Kumar A, Smith B, Garr SS, Brown SA, Andom T: Molecular approaches to differentiate subpopulations or formae speciales of the fungal phytopathogen Microbotryum violaceum. Int J Plant Sci 1997, 158:568-574.
10. Bucheli E, Gautschi B, Shykoff JA: Host-specific differentiation in the anther smut fungus Microbotryum violaceum as revealed by microsatellites. J Evolution Biol 2000, 13:188-198.
11. Liro JI: Die Ustilagineen Finnlands I. Ann Acad Sci Fenn Ser A 1924, 17:1-636.
12. Bauer R, Oberwinkler F, Vánky K: Studies in heterobasidiomycetes, part 139. Ultrastructural markers and systematics in smut fungi and allied taxa. Can J Bot 1997, 75:1273-1314.
13. Vánky K, Berner D: Microbotryum sylibum sp. nov. (Microbotryales). Mycotaxon 2003, 85:307-311.
14. Vánky K: Taxonomic studies on Ustilaginomycetes - 24. Mycotaxon 2004, 89:55-118.
15. Weiss M, Bauer R, Begerow D: Spotlights on heterobasidiomycetes. In Frontiers in Basidiomycote Mycology Edited by: Agerer R, Piepenbring M, Blanz P. Eching: IHW Verlag; 2004:7-48.
16. Vánky K: Illustrated genera of smut fungi Stuttgart: Gustav Fischer Verlag; 1987.
17. Vánky K, Oberwinkler F: Ustilaginales on Polygonaceae - a taxonomic revision. Nova Hedwigia 1994:107.
18. Piepenbring M: Morphology of Liroa emodensis (Microbotryales, Basidiomycota) on Polygonum chinense. Fung Sci 2002, 17:55-64.
19. Piepenbring M: Comparative morphology of galls formed by smut fungi and discussion of generic concepts. In Frontiers in Basidiomycote Mycology Edited by: Agerer R, Piepenbring M, Blanz P. Eching: IHW Verlag; 2004:117-164.
20. Vánky K: The new classificatory system for smut fungi, and two new genera. Mycotaxon 1999, 70:35-49.
21. Begerow D, Lutz M, Oberwinkler F: Implications of molecular characters for the phylogeny of the genus Entyloma. Mycol Res 2002, 106:1392-1399.
22. Levy LA, Castlebury LM, Carris LJ, Meyer R, Pimentel G: Internal transcribed spacer sequence-based phylogeny and polymerase chain reaction-restriction fragment length polymorphismdifferentiation of Tilletia walkeri and T. indica. Phytopathology 2001, 91:935-940.
23. Stoll M, Piepenbring M, Begerow D, Oberwinkler F: Molecular phylogeny of Ustilago and Sporisorium species (Basidiomycota, Ustilaginales) based on internal transcribed spacer (ITS) sequences. Can J Bot 2003, 81:976-984.
24. Almaraz T, Roux C, Maumont S, Durrieu G: Phylogenetic relationships among smut fungi parasitizing dicotyledons based on ITS sequence analysis. Mycol Res 2002, 106:541-548.
25. Farris JS, Källersjö M, Kluge AC, Bult C: Testing significance of incongruence. Cladistics 1995, 10:315-319.
26. Barker FK, Lutzoni F: The utility of the incongruence length difference test. Syst Biol 2002, 51:625-637.
27. Mindell DP: Aligning DNA sequences: Homology and phylogenetic weighting. In Phylogenetic analysis of DNA sequences Edited by: Miyamoto MM, Cracraft J. New York/Oxford: Oxford University Press; 1991:73-89.
28. Morrison DA, Ellis JT: Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of Apicomplexa. Mol Biol Evol 1997, 14:428-441.
29. Thorne JL, Kishino H: Freeing phylogeny from artifacts of alignment. Mol Biol Evol 1992, 9:1148-1162.
30. Lake JA: The order of sequence alignment can bias the selection of tree topology. Mol Biol Evol 1991, 8:378-385.
31. Wheeler WC, Gatesy J, DeSalle R: Elision: A method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites. Mol Phylogen Evol 1995, 4:1-9.
32. Gatesy J, DeSalle R, Wheeler W: Alignment-ambiguous nucleotide sites and exclusion of systematic data. Mol Phylogenet Evol 1993, 2:152-157.
33. Lee MSY: Unalignable sequences and molecular evolution. Trends Ecol Evol 2001, 16:681-685.
34. Farris JS, Källersjö M, Crowe TM, Lipscomb DL, Johansson U: Frigatebirds, Tropicbirds, and Ciconiida: Excesses of confidence probability. Cladistics 1999, 15:1-7.
35. Farris JS: The retention index and the rescaled consistency index. Cladistics 1989, 5:417-419.
36. Katoh K, Misawa K, Kuma K, Miyata T: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002, 30:3059-3066.
37. Lassmann T, Sonnhammer ELL: Quality assessment of multiple alignment programs. FEBS Lett 2002, 529:126-130.
38. Pei J, Sadreyev R, Grishin NV: PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics 2003, 19:427-428.
39. Vánky K: European Smut Fungi. Gustav Fischer Verlag, Stuttgart; 1994.
40. Piepenbring M, Vánky K, Oberwinkler F: Aurantiosporium, a new genus for Ustilago subnitens (Ustilaginales). Pl Syst Evol 1996, 199:53-64.
41. Law R, Cook RED, Manlove RJ: The ecology of flower and bulbil production in Polygonum viviparum. Nord J Bot 1983, 3:559-565.
42. Bremer K, Backlund A, Sennblad B, Swenson U, Andreasen K, Hjertson M, Lundberg J, Backlund M, Bremer B: A phylogenetic analysis of 100+ genera and 50+ families of euasterids based on morphological and molecular data with notes on possible higher level morphological synapomorphies. Plant Syst Evol 2001, 229:137-169.
43. Caputo P, Cozzolino S, Moretti A: Molecular phylogenetics of Dipsacaceae reveals parallel trends in seed dispersal syndromes. Plant Syst Evol 2004, 246:163-175.
44. López-Villavicencio M, Enjalbert J, Hood ME, Shykoff JA, Raquin C, Giraud T: The anther smut disease on Gypsophila repens: a case of parasite sub-optimal performance following a recent host shift? Evol Biol 2005, 18:1293-1303.
45. Deml G, Oberwinkler F: Studies in heterobasidiomycetes, part 24. On Ustilago violacea (Pers.) Rouss. from Saponaria officinalis L. Phytopathol Z 1982, 104:345-356.
46. Moore RT: The genus Bauhinus gen. nov.: For species of Ustilago on dicot hosts. Mycotaxon 1992, 45:97-100.
47. Hennig W: Phylogenetic systematics. Ann Rev Entomol 1965, 10:97-116.
48. Gardes M, Bruns TD: ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol Ecol 1993, 2:113-118.
49. White TJ, Bruns TD, Lee S, Taylor JW: Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Edited by: Innis MA, Gelfand DH, Sninsky JJ, White TJ. PCR protocols, a guide to methods and applications, Academic Press, San Diego; 1990:315-322.
50. Morgenstern B: DIALIGN 2: improvement of the segment-tosegment approach to multiple sequence alignment. Bioinformatics 1999, 15:211-218.
51. Lee C, Grasso C, Sharlow M: Multiple sequence alignment using partial order graphs. Bioinformatics 2002, 18:452-464.
52. Thompson JD, Higgins DG, Gibson CWD: Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
53. Notredame C, Higgins DG, Heringa J: T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302:205-217.
54. Giribet G, Wheeler W: On gaps. Mol Phylogenet Evol 1999, 13:132-143.
55. Fitch WM: Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971, 20:406-416.
56. Felsenstein J: Confidence limits on phylogenies, an approach using the bootstrap. Evolution 1985, 39:783-791.
57. Posada D, Crandall KA: Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
58. Posada D, Buckley TR: Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst Biol 2004, 53:793-808.
59. Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52:696-704.
60. TREEBASE [http://www.treebase.org/]