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Chloroplastrps16 intron phylogeny of the tribeSileneae (Caryophyllaceae)

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Abstract

Intron sequences of the chloroplast generps16 from 46 species were used to examine phylogenetic relationships indicated by nrDNA ITS sequence variation in the tribeSileneae (Caryophyllaceae, Caryophylloideae). This region has previously not been utilized for phylogenetic purposes but the results presented here suggest that it is a consistent and valuable complement to the ITS sequences. Therps16 intron trees are largely congruent with the ITS trees. All the major hypotheses suggested by the ITS data are supported, often at similar bootstrap levels. The joint usage ofrps16 intron and ITS sequences provides a powerful tool for resolving many of the difficult taxonomic issues in the tribeSileneae.

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References

  • Baldwin, B. G., Sanderson, M. J., Porter, J. M., Wojciechowski, M. F., Campbell, C. S., Donoghue, M. J., 1995: The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. — Ann. Missouri Bot. Gard.82: 247–277.

    Google Scholar 

  • Böhle, U.-R., Hilger, H., Cerff, R., Martin, W. F., 1994: Non-coding chloroplast DNA for plant molecular systematics at the infrageneric level. — InSchierwater, B., Streit, B., Wagner, G. P., DeSalle, R., (Eds): Molecular ecology and evolution: approaches and applications, pp. 391–402. — Basel: Birkhäuser.

    Google Scholar 

  • Bremer, K., 1988: The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. — Evolution42: 795–803.

    Google Scholar 

  • Chowdhuri, P. K., 1957: Studies in the genusSilene. — Notes Roy. Bot. Gard. Edinburgh22: 221–278.

    Google Scholar 

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

    Google Scholar 

  • —, 1996: Phylogenetic analysis ofApiaceae subfamilyApioideae using nucleotide sequences from the chloroplastrpoCl intron. — Molec. Phylogenet. Evol.6: 1–18.

    PubMed  Google Scholar 

  • Doyle, J. J., 1992: Gene trees and species trees: molecular systematics as one-character taxonomy. — Syst. Bot.17: 144–163.

    Google Scholar 

  • —, 1995: Multiple independent losses of two genes and one intron from legume chloroplast genomes. — Syst. Bot.20: 272–294.

    Google Scholar 

  • Ehrendorfer, F., Manén, J.-F., Natali, A., 1994: cpDNA intergene sequences corroborate restriction site data for reconstructingRubiaceae phylogeny. — Pl. Syst. Evol.190: 245–258.

    Google Scholar 

  • Eriksson, T., Wikström, N., 1995: AutoDecay. Version 3.03. — Stockholm: Stockholms Universitet (distributed by the authors).

    Google Scholar 

  • Farris, J. S., 1989: The retention index and the rescaled consistency index. — Cladistics5: 417–419.

    Google Scholar 

  • Felsenstein, J., 1978: Cases in which parsimony and compatibility methods will be positively misleading. — Syst. Zool.27: 401–410.

    Google Scholar 

  • Gielly, L., Taberlet, P., 1994: The use of chloroplast DNA to resolve plant phylogenies: noncoding versusrbcL sequences. — Molec. Biol. Evol.11: 769–777.

    PubMed  Google Scholar 

  • —, 1996: Phylogenetic use of noncoding regions in the genusGentiana L.: chloroplasttrnL (UAA) intron versus nuclear ribosomal internal transcribed spacer sequences. — Molec. Phylogenet. Evol.5: 460–466.

    PubMed  Google Scholar 

  • Golenberg, E. M., Clegg, M. T., Durbin, M. L., Doebley, J., Ma, D. P., 1993: Evolution of a noncoding region of the chloroplast genome. — Molec. Phylogenet. Evol.2: 52–64.

    PubMed  Google Scholar 

  • Greuter, W., 1995:Silene (Caryophyllaceae) in Greece: a subgeneric and sectional classification. — Taxon44: 543–581.

    Google Scholar 

  • Harshman, J., 1994: The effect of irrelevant characters to bootstrap values. — Syst. Biol.43: 419–424.

    Google Scholar 

  • Holmgren, K. P., Holmgren, H. N., Barnett, L. C., 1990: Index Herbariorum 1: The herbaria of the world, 8th edn. — Regnum Veg.120.

  • Hoot, S., Culham, A., Crane, P. R., 1995: The utility ofatpB gene sequences in resolving phylogenetic relationships: comparison withrbcL and 18S ribosomal DNA sequences in theLardizabalaceae. — Ann. Missouri Bot. Gard.82: 194–207.

    Google Scholar 

  • Johnson, L. A., Soltis, D. E., 1995: Phylogenetic inference inSaxifragaceae sensu stricto andGilia (Polemoniaceae) usingmatK sequences. — Ann. Missouri Bot. Gard.82: 149–175.

    Google Scholar 

  • Jordan, W. C., Courtney, M. W., Neigel, J. E., 1996: Low levels of intraspecific genetic variation at a rapidly evolving chloroplast DNA locus in North American duckweeds (Lemnaceae). — Amer. J. Bot.83: 430–439.

    Google Scholar 

  • Lidén, M., Fukuhara, T., Rylander, J., Oxelman, B., 1997: The phylogeny and classification ofFumariaceae with emphasis onDicentra sensu lato based on the chloroplast generps16 intron. — Pl. Syst. Evol.206: 411–420.

    Google Scholar 

  • Maddison, W. P., Maddison, D. R., 1992: MacClade: analysis of phylogeny and character evolution. Version 3.05 — Sunderland, Mass.: Sinauer.

    Google Scholar 

  • Nagano, Y., Matsuno, R., Sasaki, Y., 1991: Sequence and transcriptional analysis of the gene clustertrnQ-zfpA-psaI-ORF231-petA in pea chloroplasts. — Curr. Genet.20: 431–436.

    PubMed  Google Scholar 

  • Neuhaus, H., Scholz, A., Link, G., 1989: Structure and organisation of a split chloroplast gene from mustard (Sinapis alba): ribosomal protein generps16 reveals unusual transcriptional features and complex RNA maturation. — Curr. Genet.15: 63–70.

    PubMed  Google Scholar 

  • Ohyama, K., Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T., Sano, S., Umesono, K., Shiki, Y., Takeuchi, M., Chang, Z., Aota, S., Inokuchi, H., Ozeki, H., 1986: Chloroplast gene organization deduced from complete sequence of liverwortMarchantia polymorpha chloroplast DNA. — Nature322: 572–574.

    Google Scholar 

  • Olmstead, R. G., Reeves, P. A., 1995: Evidence for the polyphyly of theScrophulariaceae based on chloroplastrbcL andndsF sequences. — Ann. Missouri Bot. Gard.82: 176–193.

    Google Scholar 

  • Oxelman, B., 1995: Systematic studies in the genusSilene L. (Caryophyllaceae) — morphological and molecular approaches. — Ph.D. thesis, Västra Frölunda: Göteborgs Universitet.

    Google Scholar 

  • —, 1996: LongRangerTM gels versus standard polyacrylamide gels on ALFExpressTM automated sequencers. — FMC Resolutions12(2): 2–4.

    Google Scholar 

  • —, 1995: Generic boundaries in the tribeSileneae (Caryophyllaceae) as inferred from nuclear rDNA sequences. — Taxon44: 525–542.

    Google Scholar 

  • Pamilo, P., Nei, M., 1991: Relationships between gene trees and species trees. — Molec. Biol. Evol.5: 568–583.

    Google Scholar 

  • Rieseberg, L. H., Soltis, D. E., 1991: Phylogenetic consequences of cytoplasmic gene flow in plants. — Evol. Trends Pl.5: 65–84.

    Google Scholar 

  • Rohrbach, P., 1869: Monographie der GattungSilene. — Leipzig: Engelmann.

    Google Scholar 

  • Sexton, D., Jones, J. T., Mullet, J. E., 1990: Sequence and transcriptional analysis of the barley ctDNA region upstream of psbD-psbC encoding trnK(UUU), rps16, trnQ(UUG), psbK, psbI, and trnS(GCU). — Curr. Genet.17: 445–454.

    PubMed  Google Scholar 

  • Sheen, J.-Y., Seed, B., 1988: Electrolyte gradient gels for DNA sequencing. — Bio/Techniques6: 942–943.

    Google Scholar 

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

    Google Scholar 

  • Soltis, P. S., Soltis, D. E., 1995: Alternative genes for phylogenetic reconstruction in plants: introduction. — Ann. Missouri Bot. Gard.82: 147–148.

    Google Scholar 

  • Swofford, D., 1993: PAUP: phylogenetic analysis using parsimony. — Champaign: Illinois Natural History Survey.

    Google Scholar 

  • Talavera, S., 1979: Revision de la sect.Erectorefractae del generoSilene L. — Lagascalia8: 135–164.

    Google Scholar 

  • Thein, S. L., 1990: A simplified method of direct sequencing of PCR amplified DNA with Sequenase*T7 DNA polymerase. — USB Comments17: 26–27.

    Google Scholar 

  • Tzudsuki, J., Nakashima, K., Tzudsuki, T., Hiratsuka, J., Shibata, M., Wakasugi, T., Sugiura, M., 1992: Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences oftrnQ,trnK,psbA,trnI, andtrnH and the absence ofrps16. — Molec. Gen. Genet.232: 206–214.

    PubMed  Google Scholar 

  • Wendel, J. F., Schnabel, A., Seelanan, T., 1995: Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). — Proc. Natl. Acad. Sci. USA92: 280–284.

    PubMed  Google Scholar 

  • 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. USA89: 10648–10652.

    PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Systematic Botany, Carl Skottsbergs Gata 22B, S-413 19, Göteborg, Sweden

    Bengt Oxelman, Magnus Lidén & Daniel Berglund

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  1. Bengt Oxelman
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  2. Magnus Lidén
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  3. Daniel Berglund
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Dedicated to emer. Univ.-Prof. DrFriedrich Ehrendorfer on the occasion of his 70th birthday

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Oxelman, B., Lidén, M. & Berglund, D. Chloroplastrps16 intron phylogeny of the tribeSileneae (Caryophyllaceae). Pl Syst Evol 206, 393–410 (1997). https://doi.org/10.1007/BF00987959

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  • DOI: https://doi.org/10.1007/BF00987959

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