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Investigation of fungal phylogeny on the basis of small ribosomal subunit RNA sequences

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Molecular Microbial Ecology Manual

Abstract

A study published in 1989 [15] on the evolutionary position of fungi within the eukaryotic realm as derived from the structure of small ribosomal subunit RNA comprised only 4 fungal SSU rRNA sequences (SSU rRNA is small ribosomal subunit RNA, i.e. the 16S rRNA of prokaryotes, the 18S rRNA of eukaryotes). At present, December 1993, more than 110 complete or nearly complete SSU rRNA sequences from fungi have been published. This increase can be ascribed to the fact that SSU rRNA has proven an excellent molecule for the reconstruction of phylogeny of bacterial as well as eukaryotic lineages, for reasons enumerated by Woese [41] and Sogin [30].

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References

  1. Barns SM, Lane DJ, Sogin ML, Bibeau C, Weisburg WG (1991) Evolutionary relationships among pathogenic Candida species and relatives. J Bacteriol 173: 2250–2255.

    PubMed  CAS  Google Scholar 

  2. Benson D, Lipman DJ, Ostell J (1993) GenBank. Nucl Acids Res 21: 2963–2965.

    Article  PubMed  CAS  Google Scholar 

  3. Berbee ML, Taylor JW (1992) Two ascomycete classes based on fruiting-body characters and ribosomal DNA sequences. Mol Biol Evol 9: 278–284.

    PubMed  CAS  Google Scholar 

  4. Bowman BH, Taylor JW, White TJ (1992) Molecular evolution of the fungi: human pathogens. Mol Biol Evol 9: 839–904.

    Google Scholar 

  5. Bowman BH, Taylor JW, Brownlee AG, Lee J, Lu S-D, White TJ (1992) Molecular evolution of the fungi: relationships of the basidiomycetes, ascomycetes, and chytridiomycetes. Mol Biol Evol 9: 285–296.

    PubMed  CAS  Google Scholar 

  6. Bruns TD, White TJ, Taylor JW (1991) Fungal molecular systematics. Annu Rev Ecol Syst 22: 525–564.

    Article  Google Scholar 

  7. Bruns TD, Vilgalys R, Barns SM, Gonzales D, Hibbett DS, Lane DJ, Simon L, Stickel S, Szaro TM, Weisburg WG, Sogin ML (1993) Evolutionary relationships within the fungi: analysis of nuclear small subunit rRNA sequences. Mol Phyl Evol 1: 231–241.

    Article  Google Scholar 

  8. Chan SC, Wong AKC, Chiu DKY (1992) A survey of multiple sequence comparison methods. Bull Math Biol 54: 563–698.

    PubMed  CAS  Google Scholar 

  9. Clark SP (1992) MALIGNED: a multiple sequence alignment editor. Comput Applic Biosci 8: 535–538.

    CAS  Google Scholar 

  10. De Rijk P, De Wachter R (1993) DCSE, an interactive tool for sequence alignment and secondary structure research. Comput Applic Biosci 9: 735–740.

    Google Scholar 

  11. De Soete G (1983) A least squares algorithm for fitting additive trees to proximity data. Psychometrika 48: 621–626.

    Article  Google Scholar 

  12. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.

    Article  Google Scholar 

  13. Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155: 279–284.

    Article  PubMed  CAS  Google Scholar 

  14. Gutell RR (1993) Collection of small subunit (16S- and 16S-like) ribosomal RNA structures. Nucl Acids Res 21: 3051–3054.

    Article  PubMed  CAS  Google Scholar 

  15. Hendriks L, Goris A, Neefs J-M, Van de Peer Y, Hennebert GL, De Wachter R (1989) The nucleotide sequence of the small ribosomal subunit RNA of the yeast Candida albicans and the evolutionary position of the fungi among the eukaryotes. Syst Appl Microbiol 12: 223–229.

    Article  CAS  Google Scholar 

  16. Hendriks L, Goris A, Van de Peer Y, Neefs J-M, Vancanneyt M, Kersters K, Berny J- F, Hennebert GL, De Wachter R (1992) Phylogenetic relationships among ascomyetes and ascomycete-like yeasts as deduced from small ribosomal subunit RNA sequences. Syst Appl Microbiol 15: 98–104.

    Article  CAS  Google Scholar 

  17. Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignments on a microcomputer. Gene 73: 237–244.

    Article  PubMed  CAS  Google Scholar 

  18. Higgins DG, Bleasby AJ, Fuchs R (1992) CLUSTAL V: improved software for multiple sequence alignment. Comput Applic Biosci 8: 189–191.

    CAS  Google Scholar 

  19. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian Protein Metabolism, pp. 21 132. New York: Academic Press.

    Google Scholar 

  20. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111–120.

    Article  PubMed  CAS  Google Scholar 

  21. Kreger-van Rij NJW, Kurtzman CP (1984) Classification of the ascosporogenous yeasts. In: NJW Kreger-van Rij (ed) The Yeasts, a Taxonomic Study, pp. 25–32. Amsterdam: Elsevier.

    Google Scholar 

  22. Larsen N, Olsen GJ, Maidak BL, McCaughey MJ. Overbeek R, Macke TJ, Marsh TL, Woese CR (1993) The ribosomal database project. Nucl Acids Res 21: 3021–3023.

    Article  PubMed  CAS  Google Scholar 

  23. Neefs J-M, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R (1993) Compilation of small ribosomal subunit RNA structures. Nucl Acid Res 21: 3025–3049.

    Article  CAS  Google Scholar 

  24. Rice CM, Fuchs R, Higgins DG, Stoehr PJ, Cameron GN (1993) The EMBL data library. Nucl Acids Res 21: 2967–2971.

    Article  PubMed  CAS  Google Scholar 

  25. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425.

    PubMed  CAS  Google Scholar 

  26. Saitou N, Imanishi T (1989) Relative efficiencies of the Fitch-Margoliash. maximum- parsimony, maximum-likelihood, minimum-evolution, and neighbour-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol Biol Evol 6: 514–525.

    CAS  Google Scholar 

  27. Sattath S, Tversky A (1977) Additive similarity trees. Psychometrika 42: 319–345.

    Article  Google Scholar 

  28. Simon L, Bousqet J, Lévesque RC, Lalonde M (1993) Origin and diversification of endomycorrhizal fungi and coincidence with vascular land plants. Nature 363: 67–69.

    Article  Google Scholar 

  29. Sneath PHA, Sokal RR (1973) Numerical Taxonomy. San Francisco: Freeman WH.

    Google Scholar 

  30. Sogin ML (1989) Evolution of eukaryotic microorganisms and their small subunit ribosomal RNAs. Amer Zool 29: 487–499.

    CAS  Google Scholar 

  31. Sourdis J, Nei M (1988) Relative efficiencies of the maximum parsimony and distance- matrix methods in obtaining the correct phylogenetic tree. Mol Biol Evol 5: 298–311.

    PubMed  CAS  Google Scholar 

  32. Swofford DL, Olsen GJ (1990) Phylogeny reconstruction. In: Hillis DM, Moritz C (eds) Molecular Systematics, pp. 411–501. Sunderland: Sinauer Associates.

    Google Scholar 

  33. Thirup S, Larsen NE (1990) ALMA, an editor for large sequence alignments. Proteins Struct Funct Genet 7: 291–291.

    Article  PubMed  CAS  Google Scholar 

  34. Van de Peer Y, Hendriks L, Goris A, Neefs J-M, Vancanneyt M, Kersters K, Berny J- F, Hennebert GL, De Wachter R (1992) Evolution of basidiomycetous yeasts as deduced from small ribosomal RNA sequences. Syst Appl Microbiol 15: 250–258.

    Article  Google Scholar 

  35. Van de Peer Y, De Wachter R (1993) TREECON: a software package for the construction and drawing of evolutionary trees. Comput Applic Biosci 9: 177–182.

    Google Scholar 

  36. Van de Peer Y, Neefs J-M, De Rijk P, De Wachter R (1993) Evolution of eukaryotes as deduced from small ribosomal subunit RNA sequences. Biochem Syst Ecol 21: 43–55.

    Article  Google Scholar 

  37. Van de Peer Y, Neefs J-M, De Rijk P, De Vos P, De Wachter R (1994) About the order of the major bacterial taxa. Syst Appl Microbiol 17: 32–38.

    Article  Google Scholar 

  38. Von Arx JA, Van der Walt JP (1987) Ophiostomatales and Endomycetales. Stud Mycol 30: 167–176.

    Google Scholar 

  39. Waterman MS (1989) Sequence alignments. In: Waterman MS (ed) Mathematical Methods for DNA Sequences, pp. 53–92. Boca Raton: CRC Press.

    Google Scholar 

  40. Wilmotte A, Van de Peer Y, Goris A, Chapelle S, De Baere R, Nelissen B, Neefs J-M, Hennebert GL, De Wachter R (1993) Evolutionary relationships among higher fungi inferred from small ribosomal subunit RNA sequence analysis. Syst Appl Microbiol 16: 436–444.

    Article  CAS  Google Scholar 

  41. Woese CR (1987) Bacterial evolution. Microbiol Rev 51: 221–271.

    PubMed  CAS  Google Scholar 

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© 1995 Springer Science+Business Media Dordrecht

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Van De Peer, Y., De Wachter, R. (1995). Investigation of fungal phylogeny on the basis of small ribosomal subunit RNA sequences. In: Akkermans, A.D.L., Van Elsas, J.D., De Bruijn, F.J. (eds) Molecular Microbial Ecology Manual. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-0351-0_21

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  • DOI: https://doi.org/10.1007/978-94-011-0351-0_21

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-010-4156-0

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