Skip to main content

The chloroplast generps 4 as a tool for the study ofPoaceae phylogeny

Abstract

Phylogenetic analyses of 28Poaceae species based on the chloroplastrps 4 gene are presented using parsimony and distance methods. Two monocots from other families were used as outgroups. The chloroplast generps 4 was amplified, cloned, and sequenced for each species. The inferred phylogenetic trees were compared to recent classifications and are shown to fit their general features. There is a dichotomy in our tree between the pooid group and the other grasses. This is in contradiction with other molecular phylogenies, where the bamboos appear first within the family. This result led us to discuss some hypotheses about the relationships of the bambusoids with the other groups of grasses, and also about the relative position of rice and bamboo, which are found close to each other in our trees.

This is a preview of subscription content, access via your institution.

References

  • Birnboim, H. C., Doly, J., 1979: A rapid alkaline extraction procedure for screening recombinant plasmid DNA. — Nucleic Acids Res.7: 1513–1523.

    Google Scholar 

  • Chase, M. W., Soltis, D. E., Olmstead, R. G., Morgan, D., Les, D. H., Mishler, B. D., Duvall, M. R., Price, R. A., Hills, H. G., Qiu, Y.-L., Kron, K. A., Rettig, J. H., Conti, E., Palmer, J. D., Manhart, J. R., Sytsma, K. J., Michaels, H. J., Kress, W. J., Karol, K. G., Clark, W. D., Hedrén, M., Gaut, B. S., Jansen, R. K., Kim, K.-J., Wimpee, C. F., Smith, J. F., Furnier, G. R., Strauss, S. H., Xiang, Q. Y., Plunkett, G. M., Soltis, P. S., Swensen, S., Williams, S. E., Gadek, P. A., Quinn, C. J., Eguiarte, L. E., Goldenberg, E., Learn, G. H. J., Graham, S. W., Barret, S. C. H., Dayanandan, S., Albert, V. A., 1993: DNA sequence phylogenetics of seed plants: an analysis of the plastid generbcL. — Ann. Missouri Bot. Gard.80: 528–586.

    Google Scholar 

  • Clayton, W. D., Renvoize, S. A., 1986: GeneraGraminum, grasses of the world. — Kew Bull. Ser. XIII. — London: HMSO Publications.

    Google Scholar 

  • Dahlgren, R. M. T., Clifford, H. T., Yeo, P. F., 1985: The families of the monocotyledons (structure, evolution, and taxonomy). — Berlin: Springer.

    Google Scholar 

  • Doebley, J., Durbin, M., Golenberg, E. M., Clegg, M. T., Ma, D. P., 1990: Evolutionary analysis of the large subunit of the carboxylase (rbcL) nucleotide sequence among the grasses (Gramineae). — Evolution44: 1097–1108.

    Google Scholar 

  • —, 1992: Chloroplast DNA variation and the phylogeny ofHordeum (Poaceae). — Amer. J. Bot.79: 576–584.

    Google Scholar 

  • Downie, S. R., Palmer, J. D., 1992: Use of chloroplast DNA rearrangements in reconstructing phylogeny. — InSoltis, P. S., Soltis, D. E., Doyle, J. J., (Eds): Molecular systematics of plants, pp. 14–35. — New York, London: Chapman & Hall.

    Google Scholar 

  • Doyle, J. J., Doyle, J. L., 1987: A rapid DNA isolation procedure for small quantities of fresh leaf tissue. — Phytochem. Bull.19: 11–15.

    Google Scholar 

  • Enomoto, S. I., Ogihara, Y., Tsunewaki, K., 1985: Studies on the origin of crop species by restriction endonuclease analysis of organellar DNA. I. Phylogenetic relationships among ten cereals revealed by the restriction fragment patterns of chloroplast DNA. — Japan J. Genet.60: 411–424.

    Google Scholar 

  • Felsenstein, J., 1990: PHYLIP: Phylogeny inference package. Version 3.3. — Seattle: University of Washington.

    Google Scholar 

  • Giannasi, D. E., Zurawski, G., Learn, G., Clegg, M. T., 1992: Evolutionary relationships of theCaryophyllidae based on comparativerbcL sequences. — Syst. Bot.17: 1–15.

    Google Scholar 

  • Gould, F. W., 1968: Grass systematics. — New York: McGraw-Hill.

    Google Scholar 

  • Hamby, R. K., Zimmer, E. A., 1992: Ribosomal RNA as a phylogenetic tool. — InSoltis, P. S., Soltis, D. E., Doyle, J. J., (Eds): Molecular systematics of plants, pp. 50–91. — New York, London: Chapman & Hall.

    Google Scholar 

  • Hennig, W., 1966: Phylogenetic systematics. — Urbana: University of Illinois Press.

    Google Scholar 

  • Higgins, D. G., Sharp, P. M., 1988: CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. — Gene73: 237–244.

    Google Scholar 

  • Hilu, K. W., 1987: Chloroplast DNA in the systematics and evolution of thePoaceae. — InSoderstrom, T. R., Hilu, K. W., Campbell, C. S., Barkworth, M. E., (Eds): Grass systematics and evolution, pp. 265–276. — Washington: Smithsonian Institution Press.

    Google Scholar 

  • —, 1985: Trends of variation and systematics ofPoaceae. — Taxon34: 102–114.

    Google Scholar 

  • —, 1982: Systematics ofGramineae: a cluster analysis study. — Taxon31: 9–36.

    Google Scholar 

  • Hiratsuka, J., Shimada, H., Whittier, R., Ishibashi, T., Sakamoto, M., Mori, M., Kondo, C., Honji, Y., Sun, C. R., Meng, B. Y., Li, Y. Q., Kanno, A., Nishizawa, Y., Hirai, A., Shinozaki, K., Sugiura, M., 1989: The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of cereals. — Mol. Gen. Genet.217: 185–194.

    Google Scholar 

  • Hubbard, C. E., 1984: Grasses, 3rd edn. — London: Penguin Books.

    Google Scholar 

  • Kellog, E. A., 1992: Tools for studying the chloroplast genome in theTriticeae (Gramineae): anEco RI map, a diagnostic deletion, and support forBromus as an outgroup. — Amer. J. Bot.72: 186–197.

    Google Scholar 

  • Les, D. H., Garvin, D. K., Wimpee, C. F., 1991: Molecular evolutionary history of ancient aquatic angiosperms. — Proc. Natl. Acad. Sci. USA88: 10119–10123.

    Google Scholar 

  • MacFarlane, T. D., 1987:Poaceae subfamilyPooideae. — InSoderstrom, T. R., Hilu, K. W., Campbell, C. S., Barkworth, M. E., (Eds): Grass systematics and evolution, pp. 265–276. — Washington: Smithsonian Institution Press.

    Google Scholar 

  • —, 1982: The classification ofPoaceae subfamilyPooideae. — Taxon31: 178–203.

    Google Scholar 

  • Maddison, W. P., Maddison, D. R., 1992: MacClade: analysis of phylogeny and character evolution. Version 3.0. — Sunderland, Massachusetts: Sinauer.

    Google Scholar 

  • Martin, P. G., Dowd, J. M., 1991: A comparison of 18s ribosomal RNA and Rubisco large subunit sequences for studying angiosperm phylogeny. — J. Mol. Evol.33: 274–282.

    Google Scholar 

  • Palmer, J. D., Zamir, D., 1982: Chloroplast DNA evolution and phylogenetic relationships inLycopersicon. — Proc. Natl. Acad. Sci. USA79: 5006–5010.

    Google Scholar 

  • —, 1988: Chloroplast DNA variation and plant phylogeny. — Ann. Missouri Bot. Gard.75: 1180–1206.

    Google Scholar 

  • Philippe, H., 1992: MUST: management utilitarians for sequences and trees. — Orsay: University of Paris-Sud.

    Google Scholar 

  • Ritland, K., Clegg, M. T., 1987: Evolutionary analysis of plant DNA sequences. — Amer. Naturalist130: S 74-S 100.

    Google Scholar 

  • Saitou, N., Nei, M., 1987: The Neighbor-joining Method: a new method for reconstructing phylogenetic trees. — Mol. Biol. Evol.4: 406–425.

    Google Scholar 

  • Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Hayashida, N., Matsubayashi, T., Zaita, N., Chungwongse, J., Obokata, J., Yamaguchi-Shinozaki, K., Meng, B. Y., Sugita, M., Deno, H., Kamogashira, T., Yamada, K., Kusuda, J., Takaiwa, F., Kato, A., Tohdoh, N., Shimada, H., Sugiura, M., 1986: The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression. — EMBO J.5: 2043–2049.

    Google Scholar 

  • Soltis, D. E., Soltis, P. S., Clegg, M. T., Durbin, M., 1990:rbcL sequence divergence and phylogenetic relationship inSaxifragaceae sensu lato. — Proc. Natl. Acad. Sci. USA87: 4640–4644.

    Google Scholar 

  • —, —, 1992: Intraspecific chloroplast DNA variation: systematic and phylogenetic implications. — InSoltis, P. S., Soltis, D. E., Doyle, J. J., (Eds): Molecular systematics of plants, pp. 117–150. — New York, London: Chapman & Hall.

    Google Scholar 

  • Soreng, R. J., Davis, J. I., Doyle, J. J., 1990: A phylogenetic analysis of chloroplast DNA restriction site variation in thePoaceae subfam.Pooideae. — Pl. Syst. Evol.172: 83–97.

    Google Scholar 

  • Stebbins, G. L., 1956: Cytogenetics and evolution of the grass family. — Amer. J. Bot.43: 890–905.

    Google Scholar 

  • Subramanian, A. R., Steinmetz, A., Bogorad, L., 1983: Maize chloroplast DNA encodes a protein sequence homologous to the bacterial ribosome assembly protein S4. — Nucleic Acids Res.11: 5277–5287.

    Google Scholar 

  • Swofford, D. L., 1990: PAUP: phylogenetic analysis using parsimony. Version 3.0. — Champaign, Illinois: Illinois Natural History Survey.

    Google Scholar 

  • Tahar, S. B., Bottomley, W., Whitfeld, P. R., 1986: Characterization of the spinach chloroplast genes for the S4 ribosomal protein, tRNA-Thr (UGU) and tRNA-Ser (GGA). — Pl. Mol. Biol.7: 63–70.

    Google Scholar 

  • Tutin, T. G., Heywood, V. H., Burges, N. A., Valentine, D. H., Walters, S. M., Webb, D. A., (Eds), 1980: Flora Europaea5. — Cambridge: Cambridge University Press.

    Google Scholar 

  • Tzvelev, N. N., 1989: The system of grasses (Poaceae) and their evolution. — The Bot. Rev.55: 141–203.

    Google Scholar 

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

    Google Scholar 

  • Wilson, M. A., Gaut, B., Clegg, M. T., 1990: Chloroplast DNA evolves slowly in the Palm family (Arecaceae). — Mol. Biol. Evol.7: 303–314.

    Google Scholar 

  • Wolfe, K. H., Gouy, M., Yang, Y. W., Sharp, P. M., Li, W. H., 1989: Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. — Proc. Natl. Acad. Sci. USA86: 6201–6205.

    Google Scholar 

  • Wolfe, K. H., Li, W. H., Sharp, P. M., 1987: Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. — Proc. Natl. Acad. Sci. USA84: 9054–9058.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Nadot, S., Bajon, R. & Lejeune, B. The chloroplast generps 4 as a tool for the study ofPoaceae phylogeny. Pl Syst Evol 191, 27–38 (1994). https://doi.org/10.1007/BF00985340

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00985340

Key words

  • Poaceae
  • Phylogenetic analyses
  • rps 4 gene