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Evolution of the Nor and 5SDna Loci in the Triticeae

  • Chapter
Molecular Systematics of Plants

Abstract

The Nor and 5SDna loci are composed of tandem arrays of units that carry the genes coding for RNA products, as well as associated spacers. Extensive sequence data bases are available for the RNA products of both loci in a wide range of organisms (reviewed in Appels and Honeycutt, 1986; Erdmann and Wolters, 1986; Huysmans and DeWachter, 1986; Woese, 1987). The available information at the nucleotide sequence level has been used in both phenetic and cladistic analyses to assess the relationships between organisms (Hendriks et al., 1986; Dams et al., 1987; Woese, 1987; Wolters and Erdmann, 1988; Van den Eyne et al., 1988; Hamby and Zimmer, 1988; Johnson and Baverstock, 1989; Gouy and Li, 1989). The spacer regions separating the genes at these loci have also been studied in considerable detail (reviewed in Appels and Honeycutt, 1986), at both the restriction fragment length polymorphisms (RFLP) banding pattern level and sequence level. They were found to evolve at a rate that appears to be much faster than the gene regions. The depth of analysis of the Nor and 5SDna loci at the structure/function and evolutionary level is thus unique, and the available data suggest that the repetitive nature of the loci per se does not preclude them from being valuable taxonomic characters.

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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.

    Article  CAS  Google Scholar 

  • Appels, R., and Honeycutt, R.L. (1986) rDNA: evolution over a billion years. In: DNA Systematics. Vol. 2, (ed. S.K. Dutta), CRC Press, Boca Raton, FL., pp. 81–135.

    Google Scholar 

  • Appels, R., Gerlach, W., Dennis, E., Swift, H., and Peacock, W. (1980) Molecular and chromosomal organization of DNA sequences coding for the ribosomal RNAs in cereals. Chromosoma 78, 293–311.

    Article  CAS  Google Scholar 

  • Appels, R., McIntyre, C.L., and Clarke, B.C. (1986a) Alien chromatin in wheat: ribosomal DNA spacer probes for detecting specific nucleolar organiser region loci introduced into wheat. Can. J. Genet. Cytol. 28, 665–672.

    CAS  Google Scholar 

  • Appels, R., Moran, L.B., and Gustafson, J. P. (1986b) Structure of DNA from the rye (Secale cereale) Nor-R1 locus and its behavior in wheat backgrounds. Can. J. Genet. Cytol. 28, 673–685.

    CAS  Google Scholar 

  • Appels, R., Reddy, P., McIntyre, C.L., Moran, L.B., Frankel, O.H., and Clarke, B.C. (1989) The molecular-cytogenetic analysis of grasses and its application to studying relationships among species of the Triticeae. Genome 31, 122–133.

    Article  PubMed  CAS  Google Scholar 

  • Barker, R.F., Harberd, N.P., Jarvis, M.G., and Flavell, R.B. (1988) Structure and evolution of the intergenic spacer in ribosomal DNA repeat units of wheat. J. Mol. Biol. 21, 1–17.

    Article  Google Scholar 

  • Baum, B.R. (1973) The concept of relevance in taxonomy with special emphasis on automatic classification. Taxon 22, 329–332.

    Article  Google Scholar 

  • Baum, B.R. (1983) A phylogenetic analysis of the tribe Triticeae (Poaceae) based on morphological characters of the genera. Can. J. Bot. 61, 518–535.

    Article  Google Scholar 

  • Brettell, R.I.S., Pallotta, M.A., Gustafson, J.P., and Appels, R. (1985) Variation in the Nor loci in triticale derived from tissue culture. Theor. Appl. Genet. 71, 637–643.

    Google Scholar 

  • Cheung, W.Y., and Scott, N.S. (1989) A contiguous sequence in spinach nuclear DNA is homologous to three separated sequences in chloroplast DNA. Theor. Appl. Genet. 77, 625–633.

    Article  CAS  Google Scholar 

  • Dams, E., Yamada, T., De Baere, R., Huysmans, E., Vandenberghe, A., and DeWachter, R. (1987) Structure of 5S rRNA in Actinomycetes and relatives and evolution of eubacteria. J. Mol. Evol. 25, 255–260.

    Article  PubMed  CAS  Google Scholar 

  • Delcasso-Tremousaygue, D., Grellet, F., Panabieres, F., Ananiev, E., and Delseny, M. (1988) Structural and transcriptional characterization of the external spacer of a ribosomal RNA nuclear gene from a higher plant. Eur. J. Biochem. 466, 1–10.

    Google Scholar 

  • Denny, T.P., Gilmour, M.N., and Selander, R.K. (1988) Genetic diversity and relationships of two pathovars of Pseudomonas syringae. J. Gen. Microbiol. 134, 1949–1960.

    PubMed  CAS  Google Scholar 

  • Doyle, J.J., Doyle, J.L., and Brown, A.H.D. (1990) A chloroplast DNA phylogeny of the wild perennial relatives of soybean (Glycine subgenus Glycine): congruence with morphological and crossing groups. Evolution 44, 371–389.

    Article  CAS  Google Scholar 

  • Dvorak, J., Zhang, H.-B., Kota, R.S., and Lassner, M. (1989) Organization and evolution of the 5S ribosomal RNA gene family in wheat and related species. Genome 32, 1003–1016.

    Article  CAS  Google Scholar 

  • Erdmann, V.A., and Wolters, J. (1986) Collection of published 5S, 5.8S, and 4.5S ribosomal RNA sequences. Nucleic Acids Res. 14, r1–r59.

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein, J. (1989) PHYLIP: Phylogeny Inference Package, Version 3.2, Dept of Genetics, SK50, University of Washington, Seattle, WA.

    Google Scholar 

  • Gerbi, S.A., Savino, R., Stebbins-Boaz, B., Jeppesen, C., and Rivera-Leon, R. (1989) A role for U3 in the nucleolus? In: Ribosomes (eds. W. Hill, P. Moore, D. Schlessinger, A. Dahlberg, J. Warner, and R. Garrett), American Society for Microbiology, Washington, DC.

    Google Scholar 

  • Gerstner, J., Schiebel, K., von Waldburg, G., and Hemleben, V. (1988) Complex organization of the length heterogeneous 5′ external spacer of mung bean (Vigna radiata) ribosomal DNA. Genome 30, 723–733.

    Article  PubMed  CAS  Google Scholar 

  • Gill, B.S., and Appels, R. (1988) Relationships between Nor-loci from different Triticeae species. Plant Syst. Evol. 160, 77–90.

    Article  Google Scholar 

  • Gill, B.S., Morris, K.L., and Appels, R. (1988) Assignment of the genomic affinities of chromosomes from polyploid Elymus species added to wheat. Genome 30, 70–82.

    Article  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Govindaraju, D.R., Wagner, D.B., Smith, G.P., and Dancik, B.P. (1988) Chloroplast DNA variation within individual trees of a Pinus banksiana—Pinus contorta sympatric region. Can. J. For. Res. 18, 1347–1350.

    Article  Google Scholar 

  • Gower, J.C. (1971) A general coefficient of similarity and some of its properties. Biometrics 27, 857–871.

    Article  Google Scholar 

  • Gutell, R.R., Weiser, B., Woesse, C.R., and Noller, H.F. (1985) Comparative anatomy of 16S-like ribosomal RNA. Prog. Nucleic Acid Res. Mol. Biol. 32, 155–216.

    Article  PubMed  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.

    Article  CAS  Google Scholar 

  • Hendriks, L., Huysmans, E., Vandenberghe, A., and DeWachter, R. (1986) Primary structures of the 5S ribosomal RNAs of 11 arthropods and applicability of 5S RNA to the study of metozoan evolution. J. Mol. Evol. 24, 103–109.

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • Higgins, D.G., and Sharp, P.M. (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237–244.

    Article  PubMed  CAS  Google Scholar 

  • Higgins, D.G., and Sharp, P.M. (1989) Fast and sensitive multiple sequence alignments on a microcomputer. CABIOS 5, 151–153.

    PubMed  CAS  Google Scholar 

  • Huysmans, E., and DeWachter, R. (1986) Compilation of small ribosomal subunits of RNA sequences. Nucleic Acid Res. 14, r73–r118.

    PubMed  CAS  Google Scholar 

  • Johnson, A.M., and Baverstock, P.R. (1989) Rapid ribosomal RNA sequencing and the phylogenetic analysis of Protists. Parasitol. Today 5, 102–105.

    Article  PubMed  CAS  Google Scholar 

  • Kato, A., Yakura, K., and Tanifuji, S. (1985) Repeated DNA sequences found in the large spacer of Vicia faba rDNA. Biochim. Biophys. Acta 825, 411–415.

    Article  CAS  Google Scholar 

  • Kellogg, E.A. (1989) Comments on genomic genera in the Triticeae (Poaceae). Amer. J. Bot. 76, 796–805.

    Article  Google Scholar 

  • Kelly, R.J., and Siegel, A. (1989) The Cucurbita maxima ribosomal DNA intergenic spacer has a complex structure. Gene 80, 239–248.

    Article  PubMed  CAS  Google Scholar 

  • Klenk, H.-P., Haas, B., Schwass, V., and Zillig, W. (1986) Hybridization homology; a new parameter for the analysis of phylogenetic relations, demonstrated with the Urkingdom of the archaebacteria. J. Mol. Evol. 24, 167–173.

    Article  CAS  Google Scholar 

  • Kota, R.S., and Dvorak, J. (1986) Mapping of a chromosomal pairing gene and 5S rRNA genes in Triticum aestivum L. by a spontaneous deletion in chromosome arm 5. Can. J. Genet. Cytol. 28, 266–271.

    CAS  Google Scholar 

  • Kshirsagar, A.M. (1972) Multivariate Analysis. New York.

    Google Scholar 

  • Lagudah, E.S., Clarke, B.C., and Appels, R. (1989) Phylogenetic relationships of Triticum tauschii, the D genome donor of hexaploid wheat. 4. Variation and chromosomal location of 5 SDNA. Genome 32, 1017–1025.

    Article  PubMed  CAS  Google Scholar 

  • Lane, D.J., Pace, B., Olsen, G.J., Stahl, D.A., Sogin, M.L., and Pace, N.R. (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. USA 82, 6955–6959.

    Article  PubMed  CAS  Google Scholar 

  • Lassner, M., and Dvorak, J. (1986) Preferential homogenization between adjacent and alternate subrepeats in wheat rDNA. Nucleic Acids Res. 14, 5499–5512.

    Article  PubMed  CAS  Google Scholar 

  • Lassner, M., Anderson, O., and Dvorak, J. (1987) Hypervariation associated with a 12-nucleotide direct repeat and inferences on intergenomic homogenization of ribosomal RNA gene spacers based on the DNA sequence of a clone from the wheat Nor-D3 locus. Genome 29, 770–781.

    Article  CAS  Google Scholar 

  • Loukas, M., Delidakis, C., and Kafatos, F.C. (1986) Genomic blot hybridization as a tool of phylogenetic analysis: evolutionary divergence in the genus Drosophila. J. Mol. Evol. 24, 174–188.

    CAS  Google Scholar 

  • Löve, A. (1984) Conspectus of the Triticeae. Feddes Repert. 95, 425–521.

    Google Scholar 

  • May, C.E., and Appels, R. (1987) Variability and genetics of spacer DNA sequences between the ribosomal RNA genes of hexaploid wheat (Triticum aestivum). Theor. Appl. Genet. 74, 617–624.

    Article  CAS  Google Scholar 

  • McCarroll, R., Olsen, G.J., Stahl, Y.D., Woesse, 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.

    Article  CAS  Google Scholar 

  • McIntyre, C.L., Clarke, B.C., and Appels, R. (1988) DNA sequence analyses of the ribosomal spacer regions in the Triticeae. Plant Syst. Evol. 160, 91–104.

    Article  CAS  Google Scholar 

  • McMullen, M.D., Hunter, B., Phillips, R.L., and Rubenstein, I. (1986) The structure of the maize ribosomal DNA spacer region. Nucleic Acids Res. 14, 4953–5968.

    Article  PubMed  CAS  Google Scholar 

  • Molnar, S.J., Gupta, P.K., Fedak, G., and Wheatcroft, R. (1989) Ribosomal DNA repeat unit polymorphism in 25 Hordeum species. Theor. Appl. Genet. 78, 387–392.

    Article  CAS  Google Scholar 

  • Neale, D.B., Saghai-Maroof, M.A., Allard, R.W., Zhang, Q., and Jorgensen, R.A. (1988) Chloroplast DNA diversity in populations of wild and cultivated barley. Genetics 120, 1105–1110.

    PubMed  CAS  Google Scholar 

  • Olsen, G.J. (1988) Phylogenetic analysis using ribosomal RNA. In: Ribosomes (eds. H.F. Noller, Jr. and K. Moldave), Meth. Enzymol. 164, 793–812.

    Chapter  Google Scholar 

  • Olsen, G.J., and Woese, C.R. (1989) A brief note concerning archaebacterial phylogeny. Can. J. Microbiol. 35, 119–123.

    Article  PubMed  CAS  Google Scholar 

  • Palmer, J.D. (1986) Chloroplast DNA and phylogenetic relationships. In: DNA Systematics, Vol. 2 (ed. S.K. Dutta), CRC Press, Boca Raton, FL. pp. 63–80.

    Google Scholar 

  • Palmer, J.D., Jansen, R.K., Michaels, H.J., Chase, M.W., and Manhart, J.R. (1988) Chloroplast DNA variation and plant phylogeny. Ann. Missouri Bot. Gard. 75, 1180–1206.

    Article  Google Scholar 

  • Patterson, C. (1988) Homology in classical and molecular biology. Mol. Biol. Evol. 5, 603–625.

    PubMed  CAS  Google Scholar 

  • Procunier, J.D. and Kasha, K.J. (1991) Organization of the intergenic spacer region of rRNA genes of Hordeum bulbosum L., submitted.

    Google Scholar 

  • Qu, L.-H., Michot, B., and Bachellerie, J.-P. (1983) Improved methods for structure probing in large RNAs: a rapid “heterologous” sequencing approach is coupled to the direct mapping of nuclease accessible sites. Nucleic Acids Res. 11, 5903–5920.

    Article  PubMed  CAS  Google Scholar 

  • Qu, L.-H., Nicolson, M., and Bachellerie, J.-P. (1988) Phylogenetic calibration of the 5′ terminal domain of large rRNA achieved by determining twenty eucaryotic sequences. J. Mol. Evol. 28, 113–124.

    Article  PubMed  CAS  Google Scholar 

  • Reddy, P., and Appels, R. (1989) A second locus for the 5S multigene family in Secale L.: sequence divergence in two lineages of the family. Genome 32, 456–467.

    Article  CAS  Google Scholar 

  • Reddy, P., Appels, R., and Baum, B.R. (1990) Ribosomal DNA spacer-length variation in Secale (Poaceae). Plant Syst. Evol., in press.

    Google Scholar 

  • Samson, M.-L., and Wegnez, M. (1989) An approach to study the evolution of the Drosophila 5S ribosomal genes using P-element transformation. J. Mol. Evol. 28, 517–523.

    Article  PubMed  CAS  Google Scholar 

  • Sarle, W.S. (1985) Two-stage density linkage. In: SAS-User’s Guide: Statistics, SAS Institute Inc., Cary, NC, p. 267.

    Google Scholar 

  • Scoles, G.J., Gill, B.S., Xin, Z.-Y., Clarke, B.C., McIntyre, C.L., Chapman, C., and Appels, R. (1988) Frequent duplication and deletion events in the 5S RNA genes and the associated spacer region of the Triticeae. Plant Syst. Evol. 160, 105–122.

    Article  CAS  Google Scholar 

  • Smith, D.K. (1987) Concept and Use of Software for Pair-wise and Multiple Genetic Sequence Alignment, Technical Rept. No. 11, Canberra College of Advanced Education, ACT, Australia.

    Google Scholar 

  • Sneath, P.H.A. (1976) Phenetic taxonomy at the species level and above. Taxon 25, 437–450.

    Article  Google Scholar 

  • Song, K.M., Osborn, T.C., and Williams, P.H. (1988a) Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs). 1. Genome evolution of diploid and amphidiploid species. Theor. Appl. Genet. 75, 784–794.

    Article  CAS  Google Scholar 

  • Song, K.M., Osborn, T.C., and Williams, P.H. (1988b) Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs). 2. Preliminary analysis of subspecies within B. rapa (syn. campestris) and B. oleracea. Theor. Appl. Genet. 76, 593–600.

    Article  CAS  Google Scholar 

  • Stern, D.B., and Lonsdale, D.M. (1982) Mitochondrial and chloroplast genomes of maize have a 12-kilobase DNA sequence in common. Nature 299, 698–702.

    Article  PubMed  CAS  Google Scholar 

  • Taira, T., Kato, A., and Tanifuji, S. (1988) Difference between two major size classes of carrot rDNA repeating units is due to reiteration of sequences of about 460bp in the large spacer. Mol. Gen. Genet. 213, 170–174.

    Article  PubMed  CAS  Google Scholar 

  • Toloczyki, C., and Feix, G. (1986) Occurrence of 9 homologous repeat units in the external spacer region of a nuclear maize rDNA gene unit. Nucleic Acids Res. 14, 4969–4986.

    Article  PubMed  CAS  Google Scholar 

  • Van den Eyne, H., De Baere, R., De Roeck, E., Van de Peer, Y., Vandenberghe, A., Willekens, P., and de Wachter, R. (1988) The 5S ribosomal RNA sequences of a red algal rhodoplast and gymnosperm chloroplast. Implications for the evolution of plastids and cyanobacteria. J. Mol. Evol. 27, 126–132.

    Article  Google Scholar 

  • Veldkamp, J.F., and Scheindelen, van H.J. (1989) Australopyrum, Brachypodium, and Elymus (Gramineae) in Malesia. Blumea 34, 61–76.

    Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Waterman, M.S. (1988) Computer analysis of nucleic acid sequences. In: Ribosomes (eds. H.F. Noller, Jr. and K. Moldave), Meth. Enzymol. 164, 765–793.

    Chapter  Google Scholar 

  • West, J.G., McIntyre, C.L., and Appels, R. (1988) Evolution and systematic relationships in the Triticeae (Poaceae). Plant Syst. Evol. 160, 1–28.

    Article  Google Scholar 

  • Wilbur, W.J., and Lipman, D.J. (1984) The context dependent comparison of biological sequences. SIAM J. Appl. Math. 44, 557–567.

    Article  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Wolters, J., and Erdmann, V.A. (1988) Cladistic analysis of ribosomal RNAs—the phylogeny of eukaryotes with respect to the endosymbiotic theory. Biosystems 21, 209–214.

    Article  PubMed  CAS  Google Scholar 

  • Youvan, D., and Hearst, J. (1981) A sequence from Drosophila melanogaster 18S rRNA bearing the conserved hyper-modified nucleoside amU: analysis by reverse transcription and high-performance liquid chromatography. Nucleic Acids Res. 9, 1723–1741.

    Article  PubMed  CAS  Google Scholar 

  • Zucker, M., and Stiegler, P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9, 133–148.

    Article  Google Scholar 

  • Zurawski, G., and Clegg, M.T. (1987) Evolution of higher-plant chloroplast DNA-encoded genes: implications for structure-function and phylogenetic studies. Ann. Rev. Plant Physiol. 38, 391–418.

    Article  CAS  Google Scholar 

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

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Appels, R., Baum, B. (1992). Evolution of the Nor and 5SDna Loci in the Triticeae. 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_5

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