SEARCH

SEARCH BY CITATION

References

  • Al-Shehbaz, I.A., Beilstein, M.A. & Kellogg, E.A. 2006. Systematics and phylogeny of Brassicaceae (Cruciferae): an overview. Plant Syst. Evol. 259: 89120.
  • Bailey, C.D., Carr, T.G., Harris, S.A. & Huges, C.E. 2003. Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Mol. Phylogenet. Evol. 29: 435455.
  • Bailey, C.D., Koch, M.A., Mayer, M., Mummenhoff, K., O'kane, S., Warwick, S.I., Windham, D. & Al-Shehbaz, I. 2006. Toward a global phylogeny of the Brassicaceae. Mol. Biol. Evol. 23: 21422160.
  • Bailey, C.D., Price, R.A. & Doyle, J.J. 2002. Systematics of the halimolobine Brassicaceae: evidence from three loci and morphology. Syst. Bot. 27: 18332.
  • Birky, C.W. 1995. Uniparental inheritance of mitochondrial and chloroplast genes. Proc. Natl Acad. Sci. U.S.A. 92: 1133111338.
  • Birky, C.W. 2001. The inheritence of genes in mitochondria and chloroplasts, mechanisms and models. Annu. Rev. Genet. 35: 125148.
  • Bleeker, W. & Hurka, H. 2001. Introgressive hybridisation in Rorippa (Brassicaceae): gene flow and its consequences in natural and anthroprogenic habitats. Mol. Ecol. 10: 20132022.
  • Bowmann, C.M., Barker, R.F. & Dyer, T.A. 1988. The location and possible evolutionary significance of small dispersed repeats in wheat ctDNA. Curr. Genet. 10: 931941.
  • Ceplitis, A., Su, Y.T. & Lascoux, M. 2006. Bayesian inference of evolutionary history from chloroplast microsatellite in the cosmopolitan weed Capsella bursa-pastoris (Brassicaceae). Mol. Ecol. 14: 42214233.
  • Chuang, S. & Blattner, F.R. 1994. Ultra-fast DNA recovery from agarose by centrifugation through a paper slurry. Biotechniques 17: 634.
  • Coates, D.J. & Byrne, M. 2005. Genetic variation in plant populations. In: Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants (R. J.Henry, ed.), pp. 139164. CABI Publishing, Cambridge, MA.
  • Corrivea, J.L. & Coleman, A.W. 1988. Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. Am. J. Bot. 75: 14431458.
  • Cosner, M.E., Jansen, R.K., Palmer, J.D. & Downie, S.R. 1997. The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families. Curr. Genet. 31: 419429.
  • Cosner, M.E., Raubeson, L.A. & Jansen, R.K. 2004. Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. Evol. Biol. 4: 27.
  • Cozzolino, S., Cafasso, D., Pellegrino, G., Musacchio, A. & Widmer, A. 2003. Molecular evolution of a plastid tandem repeat locus in an orchid lineage. J. Mol. Evol. 57: S41S49.
  • Deng, X.-W., Wing, R.A. & Gruissem, W. 1989. The chloroplast genome exists in multimeric forms. Proc. Natl Acad. Sci. U.S.A. 86: 41564169.
  • Doyle, J.J. & Doyle, J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19: 1115.
  • Drábkova, L., Kirschner, J., Vlček, Č. & Paček, V. 2004. TrnL–trnF intergenic spacer and trnL intron define major clades within Luzula and Juncus (Juncaceae): importance of structural mutations. J. Mol. Evol. 59: 110.
  • Franzke, A. & Hurka, H. 2000. Molecular systematics and biogeography of the Cardamine pratensis complex (Brassicaceae). Plant Syst. Evol. 224: 213234.
  • Golenberg, E.M., Clegg, M.T., Doebley, D.J. & Ma, D.P. 1993. Evolution of a non-coding region of the chloroplast genome. Mol. Phylogenet. Evol. 2: 5264.
  • Hall, T.A. 1999. BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program. North Carolina State University, Raleigh, NC.
  • Heenan, P.B., Mitchell, A.D., Koch, M. 2002. Molecular systematics of the New Zealand Pachycladon (Brassicaceae) complex: generic circumscription and relationship to Arabidopsis sens. lat. and Arabis sens. lat. N. Z. J. Bot. 40: 543562.
  • Hewitt, G.M. 2004. Genetic consequences of climate oscillations in the quaternary. Philos. Trans. R. Soc. B 359: 183195.
  • Hey, J. & Wakeley, J. 1997. A coalescent estimator of the population recombination rate. Genetics 145: 833846.
  • Hipkins, V.D., Marshall, K.A., Neale, D.B., Rottmann, W.H. & Strauss, S.H. 1995. A mutation hotspot in the chloroplast genome of a conifer (Douglas-fir: Pseudotsuga) is caused by variability in the number of direct repeats derived from a partially duplicated tRNA gene. Curr. Genet. 27: 572579.
  • Hiratsuka, J., Shimada, H., Whitter, R. et al. (12 co-authors) 1989. The complete sequence of the rice (Orzya 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: 185194.
  • Hoot, S.B. & Palmer, J.D. 1994. Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera. J. Mol. Evol. 38: 274281.
  • Hupfer, H., Swiatek, M., Hornung, S., Herrmann, R.G., Maier, R.M., Chiu, W.L. & Sears, B.B. 2000. Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of five distinguishable Euoenothera plastomes. Mol. Gen. Genet. 263: 581585.
  • Huson, D. & Bryant, D. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23: 254267.
  • Ingvarsson, P.K., Ribstein, S. & Taylor, D.R. 2003. Molecular evolution of insertions and deletions in the chloroplast genome of Silene. Mol. Biol. Evol. 20: 17371740.
  • Jales, J. & Suominen, J. 1994. Cardaminopsis petraea. In: Atlas of the Floraea Europaea, Volume 10. Cruciferae (Sisymbrium to Aubrieta) (J.Jales & J.Suominen, eds.), pp. 180181. Helsinki University Press, Helsinki, Finland.
  • Kanno, A., Watanabe, N., Nakamua, I. & Hirai, A. 1993. Variation in chloroplast DNA from rice (Oryza sativa): differences between deletions mediated by short-direct repeat sequences within a single species. Theor. Appl. Genet. 86: 579584.
  • Kano, A., Lee, Y.-O. & Kameya, T. 1997. The structure of the chloroplast genome in members of the genus Asparagus. Theor. Appl. Genet. 95: 11961202.
  • Kawata, M., Harada, T., Shimamoto, K., Ono, K. & Takaiwa, F. 1997. Short inverted repeats function as hotspots of intermolecular recombination giving rise to oligomers of deleted plastid DNA (ptDNAs). Curr. Genet. 31: 179184.
  • Kelchner, S.A. 2000. The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann. Mo. Bot. Gard. 87: 482498.
  • Kelchner, S.A. & Wendel, J.F. 1996. Hairpins create minute inversions in non-coding regions of chloroplast DNA. Curr. Genet. 30: 259262.
  • Kim, K.J. & Lee, H.L. 2004. Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 other vascular plants. DNA Res. 11: 247261.
  • Koch, M.A., Al-Shehbaz, I.A. & Mummenhoff, K. 2003. Molecular systematics, evolution, and population biology in the mustard family (Brassicaceae). Ann. Mo. Bot. Gard. 90: 151171.
  • Koch, M.A., Dobeš, C., Kiefer, C., Schmickl, R., Klimes, L. & Lysak, M.A. 2007. Supernetwork identifies multiple events of plastid trnF(GAA) pseudogene evolution in the Brassicaceae. Mol. Biol. Evol. 24: 6373.
  • Koch, M.A., Dobeš, C., Matschinger, M., Bleeker, W., Vogel, J., Kiefer, C. & Mitchell-Olds, T. 2005. Evolution of the trnF(GAA) gene in Arabidopsis relatives and the Brassicaceae family: monophyletic origin and subsequent diversification of a plastidic pseudogene. Mol. Biol. Evol. 22: 10321043.
  • Koch, A.M., Haubold, B. & Mitchell-Olds, T. 2001. Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear CHS sequences. Am. J. Bot. 88: 534544.
  • Lavin, M., Doyle, J. & Palmer, J.D. 1990. Evolutionary significance of the loss of the chloroplast DNA inverted repeat in the Leguminosae subfamily Papilionoideae. Evolution 44: 390402.
  • Levinson, G. & Gutman, G.A. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4: 203221.
  • Lindholm, J. & Gustafsson, T. 1991. The chloroplast genome of the gymnosperm Pinus contorta: a physical map and a complete collection of overlapping clones. Curr. Genet. 20: 161166.
  • Lihová, J., Aguilar, J.F., Marhold, K. & Feliner, G.N. 2004. Origin of the disjunct tetraploid Cardamine amporitana (Brassicaceae) assessed with nuclear and chloroplast DNA sequence data. Am. J. Bot. 91: 12311242.
  • Martin, A.P. & Burg, T.M. 2002. Perils of paralogy: using HSP70 genes for inferring organismal phylogenies. Syst. Biol. 51: 570587.
  • Mitchell-Olds, T. 2001. Arabidopsis thaliana and its wild relatives: a model system for ecology and evolution. Trends Ecol. Evol. 16: 693700.
  • Mitchell-Olds, T., Al-Shehbaz, I.A., Koch, M.A. & Sharbel, T.F. 2005. Crucifer evolution in the post-genomic era. In: Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants (Henry, R.J., ed.), pp. 119136. CABI Publishing, Cambridge, MA.
  • Mummenhoff, K., Bruggeman, H. & Bowman, J.L. 2001. Chloroplast DNA phylogeny and biogeography of Lepidium (Brassicaceae). Am. J. Bot. 81: 20512063.
  • Mummenhoff, K., Franzke, A. & Koch, M. 1997. Molecular data reveal convergence in fruit characters used in the classisification of Thlaspi s.l. (Brassicaceae). Bot. J. Linn. Soc. 125: 183199.
  • Muse, S.V. 2000. Examining rates and patterns of nucleotide substitutions in plants. Plant Mol. Biol. 42: 481490.
  • O'Kane, S.L. & Al-Shehbaz, I.A. 1997. A synopsis of Arabidopsis (Brassicaceae). Novon 7: 323327.
  • Ogihara, Y., Isono, K., Kojima, T., et al. (19 co-authors) 2002. Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol. Gen. Genom. 266: 740746.
  • Ogihara, Y., Terachi, T. & Sasakuma, T. 1988. Intramolecular recombination of chloroplast genomes mediated by short direct-repeat sequences in wheat species. Proc. Natl Acad. Sci. U.S.A. 85: 85738577.
  • Ohnishi, Y., Tajiri, H., Matsuoka, Y. & Tsunewaki, K. 1999. Molecular analysis of a 21.1 kbp fragment of wheat chloroplast DNA bearing RNA polymerase subunit (rpo) genes. Genome 42: 10421049.
  • 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 (L.Bogorad & I. K.Vasil, eds), pp. 553. Academic Press, San Diego, CA.
  • Palmer, J.D., Jansen, R.K., Michaels, H., Manhart, J. & Chase, M. 1988. Chloroplast DNA variation and plant phylogeny. Ann. Mo. Bot. Gard. 75: 11801206.
  • Perry, A.S., Brennan, S., Murphy, D.J., Kavanagh, T.A. & Wolfe, K.H. 2002. Evolutionary re-organisation of a large operon in Aduzi bean chloroplast DNA caused by inverted repeat movement. DNA Res. 9: 157162.
  • Provan, J., Soranzo, N., Wilson, N.J., Goldstein, D.B. & Powell, W. 1999. A low mutation rate for chloroplast microsatellites. Genetics 153: 943947.
  • Pyke, K.A. 1999. Plastid divisons and development. Plant Cell 11: 549556.
  • Quandt, D., Müller, K., Stech, M., Frahm, J.-P., Frey, W., Hilu, W. & Borsch, T. 2004. Molecular evolution of the chloroplast TRNL-F region in land plants. Monogr. Syst. Bot. Mo. Bot. Gard. 98: 1337.
  • Razafimandimbison, S.G., Kellogg, E.A. & Bremer, B. 2004. Recent origin and phylogenetic utility of divergent ITS putative pseudogenes: a case study from Naucleceae (Rubiaceae). Syst. Biol. 53: 177192.
  • Raubson, L.A. & Jansen, R.K. 2005. Chloroplast genomes of plants. In: Plant Diversity and Evolution: Genotypic and phenotypic variation in higher plants (R. J.Henry, ed.), pp. 4568. CABI Publishing, Cambridge, MA.
  • Sambrook, J., Fritsch, E.F. & Maniatas, T. 1989. Molecular Cloning, A Laboratory Manual, 2nd edn. Cold Spring Harbour laboratory press, New York.
  • Sang, T., Crawford, D.J. & Stussey, T.D. 1997. Chloroplast DNA phylogeny, reticulate evolution and biogeography of Paeonia (Paeoniaceae). Am. J. Bot. 84: 11201136.
  • Sato, S., Nakamura, Y., Kaneko, T., Asamitzu, E. & Tabata, S. 1999. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6: 283290.
  • Schaal, B.A., Hayworth, D.A., Olsen, K.M., Rauscher, J.T. & Smith, W.A. 1998. Phylogeographic studies in plants: problems and prospects. Mol. Ecol. 7: 465475.
  • Schmitz-Linneweber, C., Maier, R.M., Alcaraz, J.P., Cottet, A., Herrmann, R.G. & Mache, R. 2001. The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol. Biol. 45: 307315.
  • Taberlet, P., Gielly, L., Pautou, G. & Bouvet, J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17: 11051109.
  • Vijverberg, K. & Bachman, K. 1999. Molecular evolution of a tandemly repeated trnF (GAA) gene in the chloroplast genomes of Micoseris (Asteraceae) and the uses of structural mutations in phylogenetic analyses. Mol. Biol. Evol. 16: 13291340.
  • Wakasugi, T.J., Sugita, M., Tsudzuki, T. & Sugiura, M. 1998. Updated gene map of tobacco chloroplast DNA. Plant Mol. Biol. Rep. 16: 231241.
  • Wakasugi, T.J., Tsudzuki, T.J., Ito, S., Nakashima, K., Tsudzuki, T. & Sugiura, M. 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of black pine Pinus thunbergii. Proc. Natl Acad. Sci. U.S.A. 91: 97949798.
  • Wittzell, H. 1999. Chloroplast DNA variation and reticulated evolution in sexual and apomictic sections of dandelions. Mol. Ecol. 8: 20232035.
  • Wolfe, K.H., Morden, C.W. & Palmer, J.D. 1992. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc. Natl Acad. Sci. U.S.A. 89: 1064810652.
  • Yukawa, M., Tsudzuki, T. & Sugiura, M. 2005. 2005 version of the chloroplast DNA sequence from tobacco (Nicotiana tabacum). Plant Mol. Biol. Rep. 23: 359365.
  • Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridisation prediction. Nucleic Acid Res. 31: 34063415.