Use of Chloroplast DNA Rearrangements in Reconstructing Plant Phylogeny

  • Stephen R. Downie
  • Jeffrey D. Palmer


Reconstructing phytogenies among genera and at higher taxonomic levels always has been fraught with difficulties. Conventional plant classifications employ a diverse array of approaches (phytochemical, anatomic, morphologic, etc.) and often offer a synthesis of these data sets. Many of these traditional characters are susceptible to convergent evolution by natural selection; the ensuing homoplasy largely precludes robust phytogenies. Only recently have we been able to examine the genetic material itself to investigate phylogenetic relationships. Chloroplast DNA (cpDNA) variation has proven to be immensely valuable in reconstructing phytogenies at the species level, and the application of cpDNA comparisons at higher taxonomic levels is now being pursued actively.


Land Plant Chloroplast Genome Filter Hybridization Restriction Site Variation Large Inverted Repeat 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Arnheim, N., White, T., and Rainey, W.E. (1990) Application of PCR: organismal and population biology. Bioscience 40, 174–182.CrossRefGoogle Scholar
  2. Baldauf, S., and Palmer, J.D. (1990) Evolutionary transfer of the chloroplast tufA gene to the nucleus. Nature 344, 262–265.PubMedCrossRefGoogle Scholar
  3. Baldwin, B.G., Kyhos, D.W., and Dvořák, J. (1990) Chloroplast DNA evolution and adaptive radiation in the Hawaiian silversword alliance (Asteraceae-Madiinae). Ann. Missouri Bot. Gard. 77, 96–109.CrossRefGoogle Scholar
  4. Blasko, K., Kaplan, S.A., Higgins, K.G., Wolfson, R., and Sears, B.B. (1988) Variation in copy number of a 24-base pair tandem repeat in the chloroplast DNA of Oenothera hookeri strain Johansen. Curr. Genet. 14, 287–292.PubMedCrossRefGoogle Scholar
  5. Bowman, C.M., Barker, R.F., and Dyer, T.A. (1988) In wheat ctDNA, segments of ribosomal protein genes are dispersed repeats, probably conserved by nonreciprocal recombination. Curr. Genet. 14, 127–136.PubMedCrossRefGoogle Scholar
  6. Bruzdzinski, C.J., and Gelehrter, T.D. (1989) Determination of exon-intron structure: a novel application of the polymerase chain reaction technique. DNA 8, 691–696.PubMedCrossRefGoogle Scholar
  7. Bruneau, A., Doyle, J.J., and Palmer, J.D. (1990) A chloroplast DNA inversion as a subtribal character in the Phaseoleae (Leguminosae). Syst. Bot. 15, 378–386.CrossRefGoogle Scholar
  8. Calie, P.J., and Hughes, K.W. (1987) The consensus land plant chloroplast gene order is present, with two alterations, in the moss Physcomitrella patens. Mol. Gen. Genet. 208, 335–341.CrossRefGoogle Scholar
  9. Chase, M.W., and Palmer, J.D. (1989) Chloroplast DNA systematics of lilioid monocots: resources, feasibility, and an example from the Orchidaceae. Amer. J. Bot. 76, 1720–1730.CrossRefGoogle Scholar
  10. Coates, D., and Cullis, C.A. (1987) Chloroplast DNA variability among Linum species. Amer. J. Bot. 74, 260–268.CrossRefGoogle Scholar
  11. Cronquist, A. (1981) An Integrated System of Classification of Flowering Plants, Columbia University Press, New York.Google Scholar
  12. Crouse, E.J., Schmitt, J.M., and Bohnert, H. (1985) Chloroplast and cyanobacterial genomes, genes and RNAs: a compilation. Plant Mol. Biol. Reporter 3, 43–89.CrossRefGoogle Scholar
  13. Dang, L.A., and Pring, D.R. (1986) A physical map of the sorghum chloroplast genome. Plant Mol. Biol. 6, 119–123.CrossRefGoogle Scholar
  14. de Heij, H.T., Lustig, H., Moeskops, D.M., Bovenberg, W.A., Bisanz, C., and Groot, G.S.P. (1983) Chloroplast DNAs of Spinacia, Petunia, and Spirodela have a similar gene organization. Curr. Genet. 7, 1–6.CrossRefGoogle Scholar
  15. dePamphilis, C.W., and Palmer, J.D. (1989) Evolution and function of plastid DNA: a review with special reference to nonphotosynthetic plants. In: Physiology, Biochemistry, and Genetics of Nongreen Plastids (eds. C.D. Boyer, J.C. Shannon, and R.C. Hardison), American Society of Plant Physiologists, pp. 182–202.Google Scholar
  16. Doebley, J.F., Ma, D.P., and Renfroe, W.T. (1987a) Insertion/deletion mutations in the Zea chloroplast genome. Curr. Genet. 11, 617–624.PubMedCrossRefGoogle Scholar
  17. Doebley, J., Renfroe, W., and Blanton, A. (1987b) Restriction site variation in the Zea chloroplast genome. Genetics 117, 139–147.PubMedGoogle Scholar
  18. Downie, S.R., Olmstead, R.G., Zurawski, G., Soltis, D.E., Soltis, P.S., Watson, J.C, and Palmer, J.D. (1991) Six independent losses of the chloroplast DNA rpl2 intron in dicotyledons: molecular and phylogenetic implications. Evolution, in press.Google Scholar
  19. Gounaris, I., Michalowski, C.B., Bohnert, H.J., and Price, C.A. (1986) Restriction and gene maps of plastid DNA from Capsicum annuum. Curr. Genet. 11, 7–16.CrossRefGoogle Scholar
  20. Green, R.M., Vardi, A., and Galun, E. (1986) The plastome of Citrus. Physical map, variation among Citrus cultivars and species and comparison with related genera. Theor. Appl. Genet. 72, 170–177.CrossRefGoogle Scholar
  21. Hallick, R.B. (1989) Proposals for the naming of chloroplast genes. II. Update to the nomenclature of genes for thylakoid membrane polypeptides. Plant Mol. Biol. Reporter 7, 266–275.CrossRefGoogle Scholar
  22. Hallick, R.B., and Bottomley, W. (1983) Proposals for the naming of chloroplast genes. Plant Mol. Biol. Reporter 1, 38–43.CrossRefGoogle Scholar
  23. Hansmann, P. (1987) Daffodil chromoplast DNA: comparison with chloroplast DNA, physical map, and gene localization. Z. Naturforsch. 42c, 118–122.Google Scholar
  24. Hasebe, M., and Iwatsuki, K. (1990) Chloroplast DNA from Adiantum capillus-veneris L., a fern species (Adiantaceae); clone bank, physical map and unusual gene localization in comparison with angiosperm chloroplast DNA. Curr. Genet. 17, 359–364.CrossRefGoogle Scholar
  25. Heinhorst, S., Gannon, G.C., Galun, E., Kenschaft, L., and Weissbach, A. (1988) Clone bank and physical and genetic map of potato chloroplast DNA. Theor. Appl. Genet. 75, 244–251.CrossRefGoogle Scholar
  26. Herrmann, R.G., Westhoff, P., Alt, J., Winter, P., Tittgen, J., Bisanz, C., Sears, B.B., Nelson, N., Hurt, E., Hauska, G., Viebrock, A., and Sebald, W. (1983) Identification and characterization of genes for polypeptides of thylakoid membrane. In: Structure and Function of Plant Genomes (eds. O. Ciferri and L. Dure), Plenum Press, New York, pp. 143–153.CrossRefGoogle Scholar
  27. Heyraud, F., Serror, P., Kuntz, M., Steinmetz, A., and Heizmann, P. (1987) Physical map and gene localization on sunflower (Helianthus annuus) chloroplast DNA: evidence for an inversion of a 23.5-kbp segment in the large single copy region. Plant Mol. Biol. 9, 485–496.CrossRefGoogle Scholar
  28. 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., and 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 the cereals. Mol. Gen. Genet. 217, 185–194.PubMedCrossRefGoogle Scholar
  29. Howe, C.J. (1985) The endpoints of an inversion in wheat chloroplast DNA are associated with short repeated sequences containing homology to att-lambda. Curr. Genet. 10, 139–145.PubMedCrossRefGoogle Scholar
  30. Howe, C.J., Barker, R.F., Bowman, C.M., and Dyer, M. (1988) Common features of three inversions in wheat chloroplast DNA. Curr. Genet. 13, 343–349.PubMedCrossRefGoogle Scholar
  31. Hudson, K.R., and Gardner, R.C. (1988) Organisation of the chloroplast genome of kiwifruit (Actinidia deliciosa). Curr. Genet. 13, 339–342.CrossRefGoogle Scholar
  32. Jansen, R.K., and Palmer, J.D. (1987a) Chloroplast DNA from lettuce and Barnadesia (Asteraceae): structure, gene localization, and characterization of a large inversion. Curr. Genet. 11, 553–564.CrossRefGoogle Scholar
  33. Jansen, R.K., and Palmer, J.D. (1987b) A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae). Proc. Natl. Acad. Sci. USA 84, 5818–5822.PubMedCrossRefGoogle Scholar
  34. Jansen, R.K., and Palmer, J.D. (1988) Phylogenetic implications of chloroplast DNA restriction site variation in the Mutisieae (Asteraceae). Amer. J. Bot. 75, 753–766.CrossRefGoogle Scholar
  35. Jansen, R.K., Holsinger, K.E., Michaels, H.J., and Palmer, J.D. (1990) Phylogenetic analysis of chloroplast DNA restriction site data at higher taxonomic levels: an example from the Asteraceae. Evolution 44, 2089–2105.CrossRefGoogle Scholar
  36. Kishima, Y., Mikami, T., Hirai, A., Sugiura, M., and Kinoshita, T. (1987) Beta chloroplast genomes: analysis of fraction I protein and chloroplast DNA variation. Theor. Appl. Genet. 73, 330–336.CrossRefGoogle Scholar
  37. Kuhsel, M.G., Strickland, R., and Palmer, J.D. (1990) An ancient Group I intron shared by eubacteria and chloroplasts. Science 250, 1570–1573.PubMedCrossRefGoogle Scholar
  38. Kung, S.D., Zhu, Y.S., and Shen, G.F. (1982) Nicotiana chloro-plast genome III. Chloroplast DNA evolution. Theor. Appl. Genet. 61, 73–79.CrossRefGoogle Scholar
  39. Lavin, M., Doyle, J.J., and Palmer, J.D. (1990) Evolutionary significance of the loss of chloroplast-DNA inverted repeat in the Leguminosae subfamily Papilionoideae. Evolution 44, 390–402.CrossRefGoogle Scholar
  40. Lidholm, J., Szmidt, A.E., Hällgren, J.E., and Gustafsson P. (1988) The chloroplast genomes of conifers lack one of the rRNA-encoding inverted repeats. Mol. Gen. Genet. 212, 6–10.CrossRefGoogle Scholar
  41. Ma, C., and Smith, M. A. (1985) Construction and mapping of safflower chloroplast DNA recombinants and location of selected gene markers. Theor. Appl. Genet. 70, 620–627.CrossRefGoogle Scholar
  42. Meyer, T.E., Cusanovich, M.A., and Kamen, M.D. (1986) Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees. Proc. Natl. Acad. Sci. USA 83, 217–220.PubMedCrossRefGoogle Scholar
  43. Milligan, B.G., Hampton, J.N., and Palmer, J.D. (1989) Dispersed repeats and structural reorganization in subclover chloroplast DNA. Mol. Biol. Evol. 6, 355–368.PubMedGoogle Scholar
  44. Morden, C.W., and Golden, S.S. (1989) psbA genes indicate common ancestry of prochlorophytes and chloroplasts. Nature 337, 382–385.PubMedCrossRefGoogle Scholar
  45. Murai, K., and Tsunewaki, K. (1987) Chloroplast genome evolution in the genus Avena. Genetics 116, 613–621.PubMedGoogle Scholar
  46. Murai, K., Naiyu, X., and Tsunewaki, K. (1989) Studies on the origin of crop species by restriction endonuclease analysis of organellar DNA. III. Chloroplast DNA variation and interspecific relationships in the genus Secale. Jap. J. Genet. 64, 35–47.CrossRefGoogle Scholar
  47. Ngernprasirtsiri, J., and Kobayashi, H. (1990) Application of an efficient strategy with a phage λ vector for constructing a physical map of the amyloplast genome of sycamore (Acer pseudoplatanus). Arch. Biochem. Biophys. 276, 172–179.PubMedCrossRefGoogle Scholar
  48. Ogihara, Y., and Tsunewaki, K. (1988) Diversity and evolution of chloroplast DNA in Triticum and Aegilops as revealed by restriction fragment analysis. Theor. Appl. Genet. 76, 321–332.CrossRefGoogle Scholar
  49. Ohyama, K., Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T., Sano, S., Umesono, K., Shiki, Y., Takeuchi, M., Chang, Z., Aota, S., Inokuchi, H., and Ozeki, H. (1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchanda polymorpha chloroplast DNA. Nature 322, 572–574.CrossRefGoogle Scholar
  50. Ohyama, K., Kohchi, T., Sano, T., and Yamada, Y. (1988) Newly identified groups of genes in chloroplasts. TIBS 13, 19–22.PubMedGoogle Scholar
  51. Palmer, J.D. (1985a) 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.CrossRefGoogle Scholar
  52. Palmer, J.D. (1985b) Comparative organization of chloroplast genomes. Ann. Rev. Genet. 19, 325–354.PubMedCrossRefGoogle Scholar
  53. Palmer, J.D. (1991) Plastid chromosomes: structure and evolution. In: Cell Culture and Somatic Cell Genetics in Plants, Vol. 7, The Molecular Biology of Plastids (eds. L. Bogorad and I.K. Vasil), Academic Press, New York, pp. 5–53.Google Scholar
  54. Palmer, J.D., and Stein, D.B. (1986) Conservation of chloroplast genome structure among vascular plants. Curr. Genet. 10, 823–833.CrossRefGoogle Scholar
  55. Palmer, J.D., and Thompson, W.F. (1982) Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell 29, 537–550.PubMedCrossRefGoogle Scholar
  56. Palmer, J.D., Jorgensen, R.A., and Thompson, W.F. (1985) Chloroplast DNA variation and evolution in Pisum: patterns of change and phylogenetic analysis. Genetics 109, 195–213.PubMedGoogle Scholar
  57. Palmer, J.D., Nugent, J.M., and Herbon, L.A. (1987a) Unusual structure of geranium chloroplast DNA: a triple-sized inverted repeat, extensive gene duplications, multiple inversions, and two repeat families. Proc. Natl. Acad. Sci. USA 84, 769–773.PubMedCrossRefGoogle Scholar
  58. Palmer, J.D., Osorio, B., Aldrich, J., and Thompson, W.F. (1987b) Chloroplast DNA evolution among legumes: loss of a large inverted repeat occurred prior to other sequence rearrangements. Curr. Genet. 11, 275–286.CrossRefGoogle Scholar
  59. Palmer, J.D., Jansen, R.K., Michaels, H.J., Chase, M.W., and Manhart, J.R. (1988a) Chloroplast DNA variation and plant phylogeny. Ann. Missouri Bot. Gard. 75, 1180–1206.CrossRefGoogle Scholar
  60. Palmer, J.D., Osorio, B., and Thompson, W.F. (1988b) Evolutionary significance of inversions in legume chloroplast DNAs. Curr. Genet. 14, 65–74.CrossRefGoogle Scholar
  61. Perl-Treves, R., and Galun, E. (1985) The Cucumis plastome: physical map, intrageneric variation and phylogenetic relationships. Theor. Appl. Genet. 71, 417–429.Google Scholar
  62. Quigley, F., and Weil, J.H. (1985) Organization and sequence of five tRNA genes and of an unidentified reading frame in the wheat chloroplast genome: evidence for gene rearrangements during the evolution of chloroplast genomes. Curr. Genet. 9, 495–503.PubMedCrossRefGoogle Scholar
  63. Ritland, K., and Clegg, M.T. (1987) Evolutionary analysis of plant DNA sequences. Am. Nat. 130, S74–S100.CrossRefGoogle Scholar
  64. Sasaki, Y., Nagano, Y., Morioka, S., Ishikawa, H., and Matsuno, R. (1989) A chloroplast gene encoding a protein with one zinc finger. Nucleic Acids Res. 17, 6217–6227.PubMedCrossRefGoogle Scholar
  65. Schilling, E.E., and Jansen, R.K. (1989) Restriction fragment analysis of chloroplast DNA and the systematics of Viguiera and related genera (Asteraceae: Heliantheae). Amer. J. Bot. 76, 1769–1778.CrossRefGoogle Scholar
  66. Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Hayashida, N., Matsubayashi, T., Zaita, N., Chunwongse, J., Obokata, J., Yamaguchi-Shinozaki, K., Ohto, C., Torazawa, K., Meng, B.-Y., Sugita, M., Deno, H., Kamogashira, T., Yamada, K., Kusuda, J., Takaiwa, F., Kato, A., Tohdoh, N., Shimada, H., and Sugiura, M. (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5, 2043–2049.PubMedGoogle Scholar
  67. Smith, R.L., and Sytsma, K.J. (1990) Evolution of Populus nigra L. (sect. Aigeiros): introgressive hybridization and the chloroplast contribution of Populus alba L. (sect. Populus). Amer. J. Bot. 11, 1176–1187.CrossRefGoogle Scholar
  68. Soltis, D.E., Soltis, P.S., Ranker, T.A., and Ness, B.D. (1989) Chloroplast DNA variation in a wild plant, Tolmiea menziesii. Genetics 121, 819–826.PubMedGoogle Scholar
  69. Soltis, D.E., Soltis, P.S., and Bothel, K.D. (1990) Chloroplast DNA evidence for the origins of the monotypic Bensoniella and Conimitella (Saxifragaceae). Syst. Bot. 15, 349–362.CrossRefGoogle Scholar
  70. Spielmann, A., Roux, E., Allmen, J. von, and Stutz, E. (1988) The soybean chloroplast genome: complete sequence of the rps19 gene, including flanking parts containing exon2 of rpl2 (upstream), but not rpl22 (downstream). Nucleic Acids Res. 16, 1199.PubMedCrossRefGoogle Scholar
  71. Stein, D.B., Palmer, J.D., and Thompson, W.F. (1986) Structural evolution and flip-flop recombination of chloroplast DNA in the fern genus Osmunda. Curr. Genet. 10, 835–841.CrossRefGoogle Scholar
  72. Stewart, W.N. (1983) Paleobotany and the Evolution of Plants, Cambridge University Press, Cambridge, UK.Google Scholar
  73. 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.PubMedCrossRefGoogle Scholar
  74. Sugiura, M. (1989) The chloroplast chromosomes in land plants. Ann. Rev. Cell Biol. 5, 51–70.PubMedCrossRefGoogle Scholar
  75. Sugiura, M., Shinozaki, K., Zaita, N., Kusuda, M., and Kumano, M. (1986) Clone bank of the tobacco (Nicotiana tabacum) chloroplast genome as a set of overlapping restriction endonuclease fragments: mapping of eleven ribosomal protein genes. Plant Sci. 44, 211–216.CrossRefGoogle Scholar
  76. Sundberg, S.D., Denton, M.F., and Rehner, S.A. (1990) Structural map of Sedum oreganum (Crassulaceae) chloroplast DNA. Biochem. Syst. Ecol. 18, 409–411.CrossRefGoogle Scholar
  77. Sytsma, K.J., and Gottlieb, L.D. (1986) Chloroplast DNA evolution and phylogenetic relationships in Clarkia sect. Peripetasma (Onagraceae). Evolution 40, 1248–1261.CrossRefGoogle Scholar
  78. Sytsma, K.J., Smith, J.F., and Gottlieb, L.D. (1990) Phylogenetics in Clarkia (Onagraceae): restriction site mapping of chloroplast DNA. Syst. Bot. 15, 280–295.CrossRefGoogle Scholar
  79. Sytsma, K.J., Smith, J.F., and Berry, P.E. (1991) Biogeography and evolution of morphology, breeding systems, flavonoids, and chloroplast DNA in the four Old World species of Fuchsia (Onagraceae). Syst. Bot. 16, 257–269.CrossRefGoogle Scholar
  80. Terauchi, R., Terachi, T., and Tsunewaki, K. (1989) Physical map of chloroplast DNA of aerial yam, Dioscorea bulbifera L. Theor. Appl. Genet. 78, 1–10.CrossRefGoogle Scholar
  81. White, E.E. (1990) Chloroplast DNA in Pinus monticola. 1. Physical map. Theor. Appl. Genet. 79, 119–124.Google Scholar
  82. Whitfeld, P.R., and Bottomley, W. (1983) Organization and structure of chloroplast genes. Ann. Rev. Plant Physiol. 34, 279–310.CrossRefGoogle Scholar
  83. Wolfe, K.H., and Sharp, P.M. (1988) Identification of functional open reading frames in chloroplast genomes. Gene 66, 215–222.PubMedCrossRefGoogle Scholar
  84. 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.CrossRefGoogle Scholar
  85. Zurawski, G., Bottomley, W., and Whitfeld, P.R. (1984) Junctions of the large single copy region of the inverted repeats in Spinacia oleracea and Nicotiana debneyi chloroplast DNA: sequence of the genes for tRNAHIS and the ribosomal proteins S19 and L2. Nucleic Acids Res. 12, 6547–6558.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 1992

Authors and Affiliations

  • Stephen R. Downie
  • Jeffrey D. Palmer

There are no affiliations available

Personalised recommendations