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].
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Barns SM, Lane DJ, Sogin ML, Bibeau C, Weisburg WG (1991) Evolutionary relationships among pathogenic Candida species and relatives. J Bacteriol 173: 2250–2255.
Benson D, Lipman DJ, Ostell J (1993) GenBank. Nucl Acids Res 21: 2963–2965.
Berbee ML, Taylor JW (1992) Two ascomycete classes based on fruiting-body characters and ribosomal DNA sequences. Mol Biol Evol 9: 278–284.
Bowman BH, Taylor JW, White TJ (1992) Molecular evolution of the fungi: human pathogens. Mol Biol Evol 9: 839–904.
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.
Bruns TD, White TJ, Taylor JW (1991) Fungal molecular systematics. Annu Rev Ecol Syst 22: 525–564.
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.
Chan SC, Wong AKC, Chiu DKY (1992) A survey of multiple sequence comparison methods. Bull Math Biol 54: 563–698.
Clark SP (1992) MALIGNED: a multiple sequence alignment editor. Comput Applic Biosci 8: 535–538.
De Rijk P, De Wachter R (1993) DCSE, an interactive tool for sequence alignment and secondary structure research. Comput Applic Biosci 9: 735–740.
De Soete G (1983) A least squares algorithm for fitting additive trees to proximity data. Psychometrika 48: 621–626.
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.
Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155: 279–284.
Gutell RR (1993) Collection of small subunit (16S- and 16S-like) ribosomal RNA structures. Nucl Acids Res 21: 3051–3054.
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.
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.
Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignments on a microcomputer. Gene 73: 237–244.
Higgins DG, Bleasby AJ, Fuchs R (1992) CLUSTAL V: improved software for multiple sequence alignment. Comput Applic Biosci 8: 189–191.
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian Protein Metabolism, pp. 21 132. New York: Academic Press.
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.
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.
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.
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.
Rice CM, Fuchs R, Higgins DG, Stoehr PJ, Cameron GN (1993) The EMBL data library. Nucl Acids Res 21: 2967–2971.
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425.
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.
Sattath S, Tversky A (1977) Additive similarity trees. Psychometrika 42: 319–345.
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.
Sneath PHA, Sokal RR (1973) Numerical Taxonomy. San Francisco: Freeman WH.
Sogin ML (1989) Evolution of eukaryotic microorganisms and their small subunit ribosomal RNAs. Amer Zool 29: 487–499.
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.
Swofford DL, Olsen GJ (1990) Phylogeny reconstruction. In: Hillis DM, Moritz C (eds) Molecular Systematics, pp. 411–501. Sunderland: Sinauer Associates.
Thirup S, Larsen NE (1990) ALMA, an editor for large sequence alignments. Proteins Struct Funct Genet 7: 291–291.
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.
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.
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.
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.
Von Arx JA, Van der Walt JP (1987) Ophiostomatales and Endomycetales. Stud Mycol 30: 167–176.
Waterman MS (1989) Sequence alignments. In: Waterman MS (ed) Mathematical Methods for DNA Sequences, pp. 53–92. Boca Raton: CRC Press.
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.
Woese CR (1987) Bacterial evolution. Microbiol Rev 51: 221–271.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1995 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
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
Download citation
DOI: https://doi.org/10.1007/978-94-011-0351-0_21
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-010-4156-0
Online ISBN: 978-94-011-0351-0
eBook Packages: Springer Book Archive