Skip to main content

Ribosomal RNA as a Phylogenetic Tool in Plant Systematics

  • Chapter
Molecular Systematics of Plants

Abstract

The traditional classification of plants into respective classes, orders, families, genera, and species has until recently been based on shared morphologic, cytologic, biochemical, and ecologic traits. The development of techniques in molecular biology including those for molecular hybridization, cloning, restriction endo-nuclease digestions, and protein and nucleic acid sequencing have provided many new tools for the investigation of phylogenetic relationships. At the molecular level, the most fundamental comparison possible is of the primary nucleotide sequences of homologous genes in different populations or species.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Appels, R., and Dvorak, J. (1982) The wheat ribosomal DNA spacer region: its structure and variation in populations and among species. Theor. Appl. Genet. 63, 337–348.

    CAS  Google Scholar 

  • Appels, R., and Honeycutt, R.L. (1986) rDNA: evolution over a billion years. In: DNA Systematics Vol. II: Plants (ed. S.K. Dutta), CRC Press, Boca Raton, FL., pp. 81–135.

    Google Scholar 

  • Arnheim, N. (1983) Concerted evolution of multigene families. In: Evolution of Genes and Proteins (eds. M. Nei and R.K. Koehn), Sinauer Assoc., Sunderland, MA., pp. 38–61.

    Google Scholar 

  • Birky, C.W., Jr., and Skavaril, R.V. (1976) Maintenance of genetic homogeneity in systems with multiple genomes. Genet. Res. 27, 249–263.

    PubMed  CAS  Google Scholar 

  • Brown, D.D., Wensink, P.C., and Jordan, E. (1972) Comparison of the ribosomal DNA’s of Xenopus laevis and Xenopus mulleri: the evolution of tandem genes. J. Mol. Biol. 63, 57–73.

    PubMed  CAS  Google Scholar 

  • Buchheim, M.A., Turmel, M., Zimmer, E.A., and Chapman, R.L. (1990) Phylogeny of Chlamydomonas (Chlorophyta): An investigation based on cladistic analysis of nuclear 18S rRNA sequence data. J. Phycol. 26, 689–699.

    Google Scholar 

  • Burger, W.C. (1977) The piperales and the monocots. Bot. Rev. 43, 345–393.

    Google Scholar 

  • Burger, W.C. (1981) Heresy revived: the monocot theory of angiosperm origin. Evol. Theo. 5, 189–225.

    Google Scholar 

  • Cech, T.R. (1983) RNA splicing: three themes with variations. Cell 34, 713–716.

    PubMed  CAS  Google Scholar 

  • Chapman, R.L., and Avery, D.W. (1989) Nuclear ribosomal RNA genes and the phylogeny of the Trentepohliales. J. Phycol. 25 (suppl.), 25.

    Google Scholar 

  • Clark, C.G., Tague, B.W., Ware, V.C., and Gerbi, S.A. (1984) Xenopus laevis 28S ribosomal RNA: a secondary structure model and its evolutionary and functional implications. Nucleic Acids Res. 12, 6197–6220.

    PubMed  CAS  Google Scholar 

  • Crane, P.R. (1985) Phylogenetic analysis of seed plants and the origin of angiosperms. Ann. Missouri Bot. Gard. 72, 716–793.

    Google Scholar 

  • Cronquist, A. (1968) The Evolution and Classification of Flowering Plants, Houghton Mifflin, Boston.

    Google Scholar 

  • Dahlberg, A.E. (1989) The functional role of ribosomal RNA in protein synthesis. Cell 57, 525–529.

    PubMed  CAS  Google Scholar 

  • Devereux, J., Haeverli, P., and Smithies, O. (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12, 387–395.

    PubMed  CAS  Google Scholar 

  • De Winter, R.F.J., and Moss, T. (1986) The ribosomal spacer in Xenopus laevis is transcribed as part of the primary ribosomal RNA. Nucleic Acids Res. 14, 6041–6051.

    PubMed  Google Scholar 

  • Doebley, J., Durbin, M., Golenberg, E.M., Clegg, M.T., and Ma, D.P. (1990) Evolutionary analysis of the large subunit of carboxylase (rbcL) nucleotide sequence among the grasses (Gramineae). Evolution 44, 1097–1108.

    CAS  Google Scholar 

  • Donoghue, M.J., and Doyle, J. A. (1989) Phylogenetic studies of seed plants and angiosperms based on morphological characters. In: The Hierarchy of Life (eds. B. Fernholm, K. Bremer, and H. Jörnvall), Elsevier Science Publishers, Amsterdam, pp. 181–195.

    Google Scholar 

  • Donoghue, M.J., Doyle, J.A., Gauthier, J., Kluge, A.G., and Rowe, T. (1989) The importance of fossils in phylogeny reconstruction. Ann. Rev. Ecol. Syst. 20, 431–460.

    Google Scholar 

  • Dover, G. (1982) Molecular drive: a cohesive mode of species evolution. Nature 299, 111–117.

    PubMed  CAS  Google Scholar 

  • Dover, G.A., and Flavell, R.B. (1984) Molecular coevolution: DNA divergence and the maintenance of function. Cell 38, 622–623.

    PubMed  CAS  Google Scholar 

  • Doyle, J.A., and Donoghue, M.J. (1986) Seed plant phylogeny and the origin of angiosperms: an experimental cladistic approach. Bot. Rev. 52, 321–431.

    Google Scholar 

  • Doyle, J.J., and Beachy, R.N. (1985) Ribosomal gene variation in soybean (Glycine max) and its relatives. Theor. Appl. Genet. 70, 369–376.

    CAS  Google Scholar 

  • Eckenrode, V.K., Arnold, J., and Meagher, R.B. (1985) Comparison of the nucleotide sequence of soybean 18S rRNA with the sequences of other small-subunit rRNAs. J. Mol. Evol. 21, 259–269.

    CAS  Google Scholar 

  • Edman, J.C., Kovacs, J.A., Masur, H., Santi, D.V., Elwood, H.J., and Sogin, M.L. (1988) Ribosomal RNA sequence shows Pneumocystis carinii to be a member of the fungi. Nature 334, 519–522.

    PubMed  CAS  Google Scholar 

  • Edward, K., and Koessel, H. (1981) The rRNA operon from Zea mays chloroplasts: nucleotide sequence of 23S rDNA and its homology with E. coli 23S rDNA. Nucleic Acids Res. 9, 2853–2869.

    Google Scholar 

  • Edwards, K., Bedbrook, K., Dyer, T., and Koessel, H. (1981) 4.5S rRNA from Zea mays shows a structural homology with the 3′ end of prokaryotic 23S rRNA. Biochem. Int. 2, 533–538.

    CAS  Google Scholar 

  • Farris, J.S. (1986) Hennig86 Manual, Port Jefferson Station, New York.

    Google Scholar 

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

    Google Scholar 

  • Field, K.G., Olsen, G.J., Lane, D.J., Giovannoni, S.J., Ghiselin, M.T., Raff, E.C., Pace, N.R., and Raff, R.A. (1988) Molecular phylogeny of the animal kingdom. Science 239, 748–753.

    PubMed  CAS  Google Scholar 

  • Flavell, R.B. (1986) The structure and control of expression of ribosomal RNA genes. Oxf. Surv. Pl. Mol. Cell Biol. 3, 251–274.

    CAS  Google Scholar 

  • Flavell, R.B., O’Dell, M., and Thompson, W.F. (1983) Cytosine methylation of ribosomal RNA genes and nucleolus organizer activity in wheat. In: Kew Chromosome Conference II (eds. P.E. Brandham and M.D. Bennett), George Allen and Unwin, London, pp. 11–17.

    Google Scholar 

  • Fogel, S., Mortimer, R., Lusnak, K., and Tavares, F. (1978) Meiotic gene conversion: a signal of the basic recombination event in yeast. Cold Spring Harbor Symp. Quant. Biol. 43, 1325–1341.

    Google Scholar 

  • Gerbi, S.A. (1985) Evolution of ribosomal RNA. In: Molecular Evolutionary Genetics (ed. R.J. MacIntyre), Plenum Press, New York, pp. 419–518.

    Google Scholar 

  • Givens, J.F., and Phillips, R.L. (1976) The nucleolus organizer region of maize (Zea mays L). Chromosoma 57, 103–117.

    CAS  Google Scholar 

  • Gould, F.W., and Shaw, R.B. (1985) Grass Systematics, Texas A&M University Press, College Station, TX., pp. 111–130.

    Google Scholar 

  • Gouy, M., and Li, W.-H. (1989a) Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree. Nature 339, 145–147.

    PubMed  CAS  Google Scholar 

  • Gouy, M., and Li, W.-H. (1989b) Molecular phylogeny of the kingdoms Animalia, Plantae, and Fungi. Mol. Biol. Evol. 6, 109–122.

    PubMed  CAS  Google Scholar 

  • Grummt, I., Roth, E., and Paule, M.R. (1982) Ribosomal RNA transcription in vitro is species specific. Nature 296, 173–174.

    PubMed  CAS  Google Scholar 

  • Gutell, R.R., and Fox, G.E. (1988) A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res. 16s, r175–203.

    Google Scholar 

  • Hamby, R.K., Issel, L.E., and Zimmer, E.A. (1987) Nuclear and organellar evolution in higher plants—ribosomal RNA as a marker molecule. Genetics 116, s20.

    Google Scholar 

  • Hamby, R.K., Sims, L.E., Issel, L.E., and Zimmer, E.A. (1988) Direct ribosomal RNA sequencing: optimization of extraction and sequencing methods for work with higher plants. Plant Mol. Biol. Rep. 6, 175–192.

    CAS  Google Scholar 

  • Hamby, R.K., and Zimmer, E.A. (1988) Ribosomal RNA sequences for inferring phylogeny within the grass family (Poaceae). Plant Syst. Evol. 160, 29–37.

    CAS  Google Scholar 

  • Hemleben, V., Ganal, M., Gerstner, J., Schiebel, K., and Torres, R.A. (1988) Organization and length heterogeneity of plant ribosomal RNA genes. In: Architecture of Eukaryotic Genes (ed. G. Kahl), VCH, Weinheim, Fed. Rep. Germany, pp. 371–383.

    Google Scholar 

  • Hendy, M.D., and Penny, D. (1982) Branch and bound algorithms to determine minimal evolutionary tree. Math. Biosci. 59, 277–290.

    Google Scholar 

  • Hillis, D.M., and Dixon, M.T. (1989) Vertebrate phylogeny: evidence from 28S ribosomal DNA sequences. In: The Hierarchy of Life (eds. B. Fernholm, K. Bremer, and H. Jörnvall), Elsevier Science Publishers, Amsterdam, pp. 355–367.

    Google Scholar 

  • Hood, L., Campbell, J.H., and Elgin, S.C.R. (1975) The organization, expression, and evolution of antibody genes and other multigene families. Ann. Rev. Genet. 9, 305–353.

    PubMed  CAS  Google Scholar 

  • Hori, H., Lim, B.-L, and Osawa, S. (1985) Evolution of green plants as deduced from 5S rRNA sequences. Proc. Natl. Acad. Sci. USA 82, 820–823.

    PubMed  CAS  Google Scholar 

  • Hori, H., and Osawa, S. (1987) Origin and evolution of organisms as deduced from 5S ribosomal RNA sequences. Mol. Biol. Evol. 4, 445–472.

    PubMed  CAS  Google Scholar 

  • Hui, A.S., Eaton, D.H., and de Boer, H.A. (1988) Mutagenesis at the mRNA decoding site in the 16S ribosomal RNA using the specialized ribosome system in Escherichia coli. EMBO J. 7, 4383–4388.

    PubMed  CAS  Google Scholar 

  • Ito, M. (1987) Phylogenetic systematics of the Nymphaeales. Bot. Mag. Tokyo 100, 17–35.

    Google Scholar 

  • Jacob, W.F., Santer, M., and Dahlberg, A.E. (1987) A single base change in the Shine-Dalgarno region of 16S rRNA of Escherichia coli affects translation of many proteins. Proc. Natl. Acad. Sci. USA 84, 4757–4761.

    PubMed  CAS  Google Scholar 

  • Jorgensen, R.A., and Cluster, P.D. (1988) Modes and tempos in the evolution of nuclear ribosomal DNA: new characters for evolutionary studies and new markers for genetic and population studies. Ann. Missouri Bot. Gard. 75, 1238–1247.

    Google Scholar 

  • Jukes, T.H., and Cantor, CR. (1969) Evolution of protein molecules. In: Mammalian Protein Metabolism (ed. H.N. Munro), Academic Press, New York, pp. 21–123.

    Google Scholar 

  • Jupe, E.R., and Zimmer, E.A. (1990) Unmethylated regions in the intergenic spacer of maize and teosinte ribosomal RNA genes. Plant Mol. Biol. 14, 333–347.

    PubMed  CAS  Google Scholar 

  • Kantz, T.S., Theriot, E.C., Zimmer, E.A., and Chapman, R.L. (1990) The Pleurastrophyceae and Micromonadophyceae: a cladistic analysis of nuclear rRNA sequence data. J. Phycol. 26, 711–721.

    Google Scholar 

  • Kellogg, E.A., and Campbell, C.S. (1987) Phylogenetic analysis of the Gramineae. In: Grass Systematic s and Evolution (eds. T.R. Soderstrom, K.W. Hilu, C.S. Campbell, and M.E. Barkworth), Smithsonian Institution Press, Washington, DC, pp. 310–322.

    Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Klein, H.L., and Petes, T.D. (1981) Intrachromosomal gene conversion in yeast. Nature 289, 144–148.

    PubMed  CAS  Google Scholar 

  • Knaak, C., Hamby, R.K., Arnold, M.L., LeBlanc, M.D., Chapman, R.L., and Zimmer, E.A. (1990) Ribosomal DNA variation and its use in plant biosystematics. In: Biological Approaches and Evolutionary Trends in Plants (ed. S. Kawano), Academic Press, New York, pp. 135–158.

    Google Scholar 

  • Kumazaki, T., Hon, H., and Osawa, S. (1983) Phylogeny of protozoa deduced from 5S rRNA sequences. J. Mol. Evol. 19, 411–419.

    PubMed  CAS  Google Scholar 

  • Labhart, P., and Reeder, R.H. (1986) Characterization of three sites of RNA 3′ end formation in the Xenopus ribosomal spacer. Cell 45, 431–433.

    PubMed  CAS  Google Scholar 

  • Lake, J. A. (1988) Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences. Nature 331, 184–186.

    PubMed  CAS  Google Scholar 

  • Lake, J. A. (1989) Origin of the eukaryotic nucleus determined by rate-invariant analyses of ribosomal RNA genes. In: The Hierarchy of Life (eds. B. Fernholm, K. Bremer, and H. Jörnvall), Elsevier Science Publishers, Amsterdam, pp. 87–101.

    Google Scholar 

  • Larson, A., and Wilson, A.C. (1989) Patterns of ribosomal RNA evolution in salamanders. Mol. Biol. Evol. 6, 131–154.

    PubMed  Google Scholar 

  • Li, W.-H., Luo, D.-C., and Wu, C.-I. (1985) Evolution of DNA sequences. In: Molecular Evolutionary Genetics (ed. R.J. Maclntyre), Plenum Press, New York, pp. 1–94.

    Google Scholar 

  • Long, E.O., and Dawid, I.B. (1980) Repeated genes in eukaryotes. Ann. Rev. Biochem. 49, 727–764.

    PubMed  CAS  Google Scholar 

  • Mascia, P.N., Rubenstein, I., Phillips, R.L., Wang, A.S., and Xiang, L.Z. (1981) Localization of the 5S rRNA genes and evidence for diversity in the 5S rDNA region of maize. Gene 14, 205–215.

    PubMed  Google Scholar 

  • McCarroll, R., Olsen, G.J., Stahl, Y.D., Woese, C.R., and Sogin, M.L. (1983) Nucleotide sequence of the Dictyostelium discoideum small-subunit ribosomal ribonucleic acid inferred from the gene sequence: evolutionary implications. Biochemistry 22, 5858–5868.

    CAS  Google Scholar 

  • McClintock, B. (1934) The relationship of a particular chromosomal element to the development of the nucleoli in Zea mays. Z. Zellforsch. Mikrosk. Anat. 21, 294 – 328.

    Google Scholar 

  • Meeuse, A.D.J. (1967) Again: the growth habit of the early angiosperms. Acta Bot. Neerl. 16, 33–41.

    Google Scholar 

  • Messing, J., Carlson, J., Hagen, G., Rubenstein, I., and Oleson, A. (1984) Cloning and sequencing of the ribosomal RNA genes in maize: the 17S region. DNA 3, 31–40.

    PubMed  CAS  Google Scholar 

  • Moazed, D., and Noller, H.F. (1987) Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature 327, 389–394.

    PubMed  CAS  Google Scholar 

  • Moazed, D., and Noller, H.F. (1989) Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell 57, 585–597.

    PubMed  CAS  Google Scholar 

  • Mullis, K.B., and Faloona, F.A. (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Meth. Enzym. 155, 335–350.

    PubMed  CAS  Google Scholar 

  • Murgola, E.J., Hijazi, K.A., Goringer, H.U., and Dahlberg, A.E. (1988) Mutant 16S ribosomal RNA: a codon-specific translational suppressor. Proc. Natl. Acad. Sci. USA 85, 4162–4165.

    PubMed  CAS  Google Scholar 

  • Nagylaki, T., and Petes, T.D. (1982) Intrachromosomal gene conversion and the maintenance of sequence homogeneity among repeated genes. Genetics 100, 315–337.

    PubMed  CAS  Google Scholar 

  • Nairn, C.J., and Ferl, R.J. (1988) The complete nucleotide sequence of the small-subunit ribosomal RNA coding region for the cycad Zamia pumila: phylogenetic implications. J. Mol. Evol. 27, 133–141.

    PubMed  CAS  Google Scholar 

  • Nei, M. (1987) Molecular Evolutionary Genetics, Columbia University Press, New York, p. 64.

    Google Scholar 

  • Nickrent, D.L., and Franchina, C.R. (1989) Phylogenies of parasitic flowering plants (Santalales) using ribosomal RNA sequences. Amer. J. Bot. 76 (suppl.), 262.

    Google Scholar 

  • Noller, H.F., Stern, S., Moazed, D., Powers, T., Svensson, P., and Changchien, L.-M. (1987) Cold Spring Harbor Symp. Quant. Biol. 52, 695–708.

    PubMed  CAS  Google Scholar 

  • Ohta, T. (1983) On the evolution of multigene families. Theor. Pop. Biol. 23, 216–240.

    CAS  Google Scholar 

  • Ohta, T. (1984) Some models of gene conversion for treating the evolution of multigene families. Genetics 106, 517–528.

    PubMed  CAS  Google Scholar 

  • Palmer, J.D. (1985) Evolution of chloroplast and mitochondrial DNA in plants and algae. In: Molecular Evolutionary Genetics (ed. R.J. Maclntyre), Plenum Press, New York, pp. 131–240.

    Google Scholar 

  • Penny, D., Hendy, M.D., Zimmer, E.A., and Hamby, R.K. (1990) Trees from sequences: panacea or Pandora’s box? Austral. Syst. Bot. 3, 21–38.

    Google Scholar 

  • Perasso, R., Baroin, A., Qu, L.H., Bachellerie, J.P., and Adoutte, A. (1989) Origin of the algae. Nature 339, 142–144.

    PubMed  CAS  Google Scholar 

  • Petes, T.D. (1980) Unequal meiotic recombination within tandem arrays of yeast ribosomal DNA genes. Cell 19, 765–774.

    PubMed  CAS  Google Scholar 

  • Phillips, R.L. (1978) Molecular cytogenetics of the nucleolus organizer region. In: Maize Breeding and Genetics (ed. D.B. Walden), John Wiley, New York, pp. 711–741.

    Google Scholar 

  • Raff, R.A., Field, K.G., Olsen, G.J., Giovannoni, S.J., Lane, D.J., Ghiselin, M.T., Pace, N.R., and Raff, E.C. (1989) Metazoan phylogeny based on analysis of 18S ribosomal RNA. In: The Hierarchy of Life (eds. B. Fernholm, K. Bremer, and H. Jörnvall), Elsevier Science Publishers, Amsterdam, pp. 247–260.

    Google Scholar 

  • Razin, A., and Riggs, A.D. (1980) DNA methylation and gene function. Science 210, 604–610.

    PubMed  CAS  Google Scholar 

  • Reeder, R.H. (1984) Enhancers and ribosomal gene spacers. Cell 38, 349–351.

    PubMed  CAS  Google Scholar 

  • Rivin, C.J., Cullis, C.A., and Walbot, V. (1986) Evaluating quantitative variation in the genome of Zea mays. Genetics 113, 1009–1019.

    PubMed  CAS  Google Scholar 

  • Rogers, S.O., Honda, S., and Bendich, A.J. (1986) Variation in the ribosomal RNA genes among individuals of Vicia faba. Plant Mol. Biol. 6, 339–345.

    CAS  Google Scholar 

  • Rogers, S.O., and Bendich, A.J. (1987) Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. Plant Mol. Biol. 9, 509–520.

    CAS  Google Scholar 

  • Saghai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A., and Allard, R.W. (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc. Natl. Acad. Sci. USA 81, 8014–8018.

    PubMed  CAS  Google Scholar 

  • Saiki, R.K., Scharf, S.J., Faloona, F., Mullis, K.B., Horn, G.T., Erlich, H.A., and Arnheim, N. (1985) Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230, 1350–1354.

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Schaal, B.A., and Learn, G.H., Jr. (1988) Ribosomal DNA variation within and among plant populations. Ann. Missouri Bot. Gard. 75, 1207–1216.

    Google Scholar 

  • Scharf, S.J. (1990) Cloning with PCR. In: PCR Protocols (eds. M.A. Innis, D.H. Gelfand, J.J. Sninsky, and T.J. White), Academic Press, San Diego, pp. 84–91.

    Google Scholar 

  • Schleifer, K.H., and Ludwig, W. (1989) Phylogenetic relationships among bacteria. In: The Hierarchy of Life (eds. B. Fernholm, K. Bremer, and H. Jörnvall), Elsevier Science Publishers, Amsterdam, pp. 103–117.

    Google Scholar 

  • Schwartz, Z., and Koessel, H. (1980) The primary structure of 16S rDNA from Zea mays chloroplast is homologous to Escherichia coli 16S rRNA. Nature 283, 739–742.

    Google Scholar 

  • Shermoen, A.W., and Kiefer, B.I. (1975) Regulation in rDNA-deficient Drosophila melanogaster. Cell 4, 275–280.

    PubMed  CAS  Google Scholar 

  • Smith, G.P. (1974) Unequal crossover and the evolution of multigene families. Cold Spring Harbor Symp. Quant. Biol. 38, 507–513.

    PubMed  CAS  Google Scholar 

  • Smith, G.P. (1976) Evolution of repeated DNA sequences by unequal crossover. Science 191, 528–535.

    PubMed  CAS  Google Scholar 

  • Sogin, M.L., Edman, U., and Elwood, H. (1989) A single kingdom of eukaryotes. In: The Hierarchy of Life (eds. B. Fernholm, K. Bremer, and H. Jörnvall), Elsevier Science Publishers, Amsterdam, pp. 133–143.

    Google Scholar 

  • Stebbins, G.L. (1974) Flowering Plants: Evolution Above the Species Level, Belknap Press, Cambridge, MA.

    Google Scholar 

  • Steffensen, D.M., and Patterson, E.B. (1979) Using translocations to map the 5S rRNA genes to chromosome 2L in maize. Genetics 9 (suppl.), s 123.

    Google Scholar 

  • Strauss, S.H., Palmer, J.D., Howe, G.T., and Doerksen, A.H. (1988) Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged. Proc. Natl. Acad. Sci USA 85, 3898–3902.

    PubMed  CAS  Google Scholar 

  • Stringer, S.L., Hudson, K., Blase, M.A., Walzer, P.D., Cushion, M.T., and Stringer, J.R. (1989) Sequence from ribosomal RNA of Pneumocystis carinii compared to those of four fungi suggests an ascomycetous affinity. J. Protozool. 36, 14S–16S.

    PubMed  CAS  Google Scholar 

  • Swofford, D.L. (1989) PAUP 3.0, Illinois Natural History Survey, Champaign, IL.

    Google Scholar 

  • Sytsma, K.J., and Schaal, B. A. (1985) Phylogenetics of the Lisianthius skinneri (Gentianaceae) species complex in Panama utilizing DNA restriction fragment analysis. Evolution 39, 594–608.

    CAS  Google Scholar 

  • Takaiwa, F., and Sugiura, M. (1982) The complete nucleotide sequence of a 23S rRNA gene from tobacco chloroplasts. Eur. J. Biochem. 124, 13–19.

    PubMed  CAS  Google Scholar 

  • Takaiwa, F., Oono, K., Iida, Y., and Sugiura, M. (1985a) The complete nucleotide sequence of a rice 25S ribosomal RNA gene. Gene 37, 255–289.

    PubMed  CAS  Google Scholar 

  • Takaiwa, F., Oono, K., and Sugiura, M. (1985b) Nucleotide sequence of the 17S–25S spacer region from rice rDNA. Plant Mol. Biol. 4, 355–364.

    CAS  Google Scholar 

  • Takaiwa, F., Oono, K., and Sugiura, M. (1984) The complete nucleotide sequence of a rice 17S ribosomal RNA gene. Nucleic Acids Res. 12, 5441–5448.

    PubMed  CAS  Google Scholar 

  • Takhtajan, A. (1969) Flowering Plants—Origin and Dispersal, Smithsonian Institution Press, Washington, DC.

    Google Scholar 

  • Tanaka, Y., Dyer, T.A., and Brownlee, G.G. (1980) An improved direct RNA sequence method: its application to Vicia faba 5.8S ribosomal RNA. Nucleic Acids Res. 8, 1259–1272.

    PubMed  CAS  Google Scholar 

  • Tartof, K.D. (1975) Redundant genes. Ann. Rev. Genet. 9, 355–385.

    PubMed  CAS  Google Scholar 

  • Taylor, D., and Hickey, L.J. (1990) An Aptian plant with attached leaves and flowers: implications for angiosperm origin. Science 247, 702–704.

    PubMed  CAS  Google Scholar 

  • Thorne, R.F. (1976) A phylogenetic classification of the Angiospermae. Evol. Biol. 9, 35–106.

    Google Scholar 

  • Tohdoh, N., and Sugiura, M. (1982) The complete nucleotide sequence of a 16S rRNA gene from tobacco chloroplasts. Gene 17, 213–218.

    PubMed  CAS  Google Scholar 

  • Trifonov, E.N. (1987) Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16S rRNA nucleotide sequences. J. Mol. Biol. 194, 643–652.

    PubMed  CAS  Google Scholar 

  • Turner, S., Burger-Wiersma, T., Giovannoni, S.J., Mur, L.R., and Pace, N.R. (1989) The relationship of a prochlorophyte Prochlorothrix hollandica to green chloroplasts. Nature 337, 380–382.

    PubMed  CAS  Google Scholar 

  • Vincentz, M., and Flavell, R.B. (1989) Mapping of ribosomal RNA transcripts in wheat. Plant Cell 1, 579–589.

    PubMed  CAS  Google Scholar 

  • Vossbrinck, C.R., Maddox, J.V., Friedman, S., Debrunner-Vossbrinck, B.A., and Woese, C.R. (1987) Ribosomal RNA sequence suggests microsporidia are extremely ancient eukaryotes. Nature 326, 411–414.

    PubMed  CAS  Google Scholar 

  • Watanabe, J.-I., Hori, H., Tanabe, K., and Nakamura, Y. (1989) 5S ribosomal RNA sequence of Pneumocystis carinii and its phylogenetic association with “Rhizopoda/Myxomycota/Zygomycota group.” J. Protozool. 36, 16S–17S.

    PubMed  CAS  Google Scholar 

  • Watson, L., Clifford, H.T., and Dallwitz, M.J. (1985) The classification of Poaceae: subfamilies and supertribes. Austral. J. Bot. 33, 433–484.

    Google Scholar 

  • Weiss, R.B., Dunn, D.M., Atkins, J.F., and Gesteland, R.F. (1987) Slippery runs, shifty stops, backward steps, and forward hops: −2, −1, +1, +2, +5, and +6 ribosomal frameshifting. Cold Spring Harbor Symp. Quant. Biol. 52, 687–693.

    PubMed  CAS  Google Scholar 

  • Weiss, R.B., Dunn, D.M., Dahlberg, A.E., Atkins, J.F., and Gesteland, R.F. (1988) Reading frame switch caused by base-pair formation between the 3′ end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli. EMBO J. 7, 1503–1507.

    PubMed  CAS  Google Scholar 

  • Wheeler, W.C., and Honeycutt, R.L. (1988) Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications. Mol. Biol. Evol. 5, 90–96.

    PubMed  CAS  Google Scholar 

  • Whitfield, P.R., and Bottomley, W. (1983) Organization and structure of chloroplast genes. Ann. Rev. Plant Physiol. 34, 279–310.

    Google Scholar 

  • Woese, CR. (1987) Bacterial evolution. Microbiol. Rev. 51, 221–271.

    PubMed  CAS  Google Scholar 

  • Wolfe, K.H., Gouy, M., Yang, Y.-W., Sharp, P.M., and Li, W.-H. (1989) Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc. Natl. Acad. Sci. USA 86, 6201–6205.

    PubMed  CAS  Google Scholar 

  • Yakura, K., Kato, A., and Tanifuji, S. (1984) Length heterogeneity of the large spacer of Vicia faba is due to the differing number of a 325 bp repetitive sequence element. Mol. Gen. Genet. 193, 400–405.

    CAS  Google Scholar 

  • Zechman, F.W., Theriot, E.C., Zimmer, E.A., and Chapman, R.L. (1990) Phylogeny of the Ulvophyceae (Chlorophyta): Cladistic analysis of nuclear-encoded rRNA sequence data. J. Phycol. 26, 700–710.

    CAS  Google Scholar 

  • Zimmer, E.A., Hamby, R.K., Arnold, M.L., LeBlanc, D.A., and Theriot, E.C. (1989) Ribosomal RNA phylogenies and flowering plant evolution. In: The Hierarchy of Life (eds. B. Fernholm, K. Bremer, and H. Jörnvall), Elsevier Science Publishers, Amsterdam, pp. 205–214.

    Google Scholar 

  • Zimmer, E.A., Martin, S.L., Beverley, S.M., Kan, Y.W., and Wilson, A.C. (1980) Rapid duplication and loss of genes coding for the a chains of hemoglobin. Proc. Natl. Acad. Sci. USA. 77, 2158–2162.

    PubMed  CAS  Google Scholar 

Download references

Authors

Editor information

Pamela S. Soltis Douglas E. Soltis Jeff J. Doyle

Rights and permissions

Reprints and permissions

Copyright information

© 1992 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Hamby, R.K., Zimmer, E.A. (1992). Ribosomal RNA as a Phylogenetic Tool in Plant Systematics. In: Soltis, P.S., Soltis, D.E., Doyle, J.J. (eds) Molecular Systematics of Plants. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-3276-7_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-4615-3276-7_4

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-0-412-02241-8

  • Online ISBN: 978-1-4615-3276-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics