Molecular evolution of a tandemly repeated trnF(GAA) gene in the chloroplast genomes of Microseris (Asteraceae) and the use of structural mutations in phylogenetic analyses

Molecular Biology and Evolution

Volumn 16, Issue 10, 1999, Pages 1329-1340

  Vijverberg, Kitty ^a   Bachmann, Konrad ^b  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

Asteraceae; cpDNA phylogeny; Interchromosomal recombination; Microseris; Pseudogenes; trnF(GAA)

Indexed keywords

DNA; TRANSFER RNA;

ARTICLE; CHLOROPLAST; CHROMOSOME; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENOME; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PLANT; SOUTHERN BLOTTING; TANDEM REPEAT;

ASTERACEAE; CICHORIEAE; EMBRYOPHYTA; MICROSERIS; UROPAPPUS;

EID: 0032875444     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026043     Document Type: Article

References (66)

1. BANDELT, H.-J., and A. W. M. DRESS. 1992. Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol. Phylogenet. Evol. 1:242-252.
2. BIRKY, C. W. JR. 1995. Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution. Proc. Natl. Acad. Sci. USA 92:11331-11338.
3. BLASKO, K., S. A. KAPLAN, K. G. HIGGINS, R. WOLFSON, and B. B. SEARS. 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.
4. BONNARD, G., J-H. WEIL, and A. STEINMETZ. 1985. The intergenic region between the Vicia faba chloroplast tRNA-Leu(CAA) and tRNA-Leu(UAA) genes contains a partial copy of the split tRNA-Leu(UAA) gene. Curr. Genet. 9: 417-422.
5. BOWMAN, C. M., R. F. BARKER, and T. A. DYER. 1988. In wheat ctDNA, segments of ribosomal protein genes are dispersed repeats, probably conserved by nonreciprocal recombination. Curr. Genet. 14:127-136.
6. BOWMAN, C. M., and T. A. DYER. 1986. The location and possible evolutionary significance of small dispersed repeats in wheat ctDNA. Curr. Genet. 10:931-941.
7. CHAMBERS, K. L. 1955. A biosystematic study of the annual species of Microseris. Contrib. Dudley Herb. 4:207-312.
8. CLEGG, M. T., and G. ZURAWSKI. 1992. Chloroplast DNA and the study of plant phylogeny: present status and future prospects. Pp. 1-13 in P. S. SOLTIS, D. E. SOLTIS, and J. J. DOYLE, eds. Molecular systematics of plants. Chapman and Hall, New York.
9. COSNER, M. E., R. K. JANSEN, J. D. PALMER, and S. R. DOWNIE. 1997. The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contradiction, transposition, insertions/deletions, and several repeat families. Curr. Genet. 31:419-429.
10. DENG, X.-W., R. A. WING, and W. GRUISSEM. 1989. The chloroplast genome exists in multimeric forms. Proc. Natl. Acad. Sci. USA 86:4156-4160.
11. DONOGHUE, M. J., and M. J. SANDERSON. 1992. The suitability of molecular and morphological evidence in reconstructing plant phylogeny. Pp. 340-368 in P. S. SOLTIS, D. E. SOLTIS, and J. J. DOYLE, eds. Molecular systematics of plants. Chapman and Hall, New York.
12. DOWNIE, S. R., R. G. OLMSTEAD, G. ZURAWSKI, D. E. SOLTIS, P. S. SOLTIS, L. C. WATSON, and J. D. PALMER. 1991. Six independent losses of the chloroplast DNA rpl2 intron in dicotyledons: molecular and phylogenetic implications. Evolution 45:1245-1259.
13. DOWNIE, S. R., and J. D. PALMER. 1992. Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. Pp. 14-35 in P. S. SOLTIS, D. E. SOLTIS, and J. J. DOYLE, eds. Molecular systematics of plants. Chapman and Hall, New York.
14. DOYLE, J. J., and J. I. DAVIS. 1998. Homology in molecular phylogenetics: a parsimony perspective. Pp. 101-131 in D. E. SOLTIS, P. S. SOLTIS, and J. J. DOYLE, eds. Molecular systematics of plants II. Kluwer Academic Publishers, Dordrecht, the Netherlands.
15. DOYLE, J. J., J. I. DAVIS, R. J. SORENG, D. GRAVIN, and M. J. ANDERSON. 1992. Chloroplast inversions and the origin of the grass family (Poaceae). Proc. Natl. Acad. Sci. USA 89: 7722-7726.
16. DUMOLIN-LAPEGUE, S., M.-H. PEMONGE, and R. J. PETIT. 1997. An enlarged set of consensus primers for the study of organelle DNA in plants. Mol. Ecol. 6:393-397.
17. EDDY, S. R., and R. DURBIN. 1994. RNA sequence analysis using covariance models. Nucleic Acids Res. 22:2079-2088.
18. FICHANT, G. A., and C. BURKS. 1991. Identifying potential tRNA genes in genomic DNA sequences. J. Mol. Biol. 220: 659-671.
19. GLICKMAN, B. W., and L. S. RIPLEY. 1984. Structural intermediates of deletion mutagenesis: a role for palindromic DNA. Proc. Natl. Acad. Sci. USA 81:512-516.
20. HIPKINS, V. D., K. A. MARSHALL, D. B. NEALE, W. H. ROTTMANN, and S. H. STRAUSS. 1995. A mutation hotspot in the chloroplast genome of a conifer (Douglas-fir: Pseudotsuga) is caused by variability in the number of direct repeats from a partially duplicated tRNA gene. Curr. Genet. 27:527-579.
21. HIRATSUKA, J., H. SHIMADA, R. WHITTIER et al. (16 co-authors). 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.
22. HOOT, S. B., and J. D. PALMER. 1994. Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera. J. Mol. Evol. 38: 274-281.
23. 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.
24. HOWE, C. J., R. F. BARKER, C. M. BOWMAN, and T. A. DYER. 1988. Common features of three inversions in wheat chloroplast DNA. Curr. Genet. 13:343-349.
25. JANSEN, R. K., H. J. MICHAELS, R. S. WALLACE, K.-J. KIM, S. C. KEELEY, L. E. WATSON, and J. D. PALMER. 1992. Chloroplast DNA variation in the Asteraceae: phylogenetic and evolutionary implications. Pp. 252-279 in P. S. SOLTIS, D. E. SOLTIS, and J. J. DOYLE, eds. Molecular systematics of plants. Chapman and Hall, New York.
26. JANSEN, R. K., and J. D. PALMER. 1987a. A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae). Proc. Natl. Acad. Sci. USA 84: 5818-5822.
27. _. 19876. Chloroplast DNA from lettuce and Barnadesia (Asteraceae): structure, gene localization, and characterization of a large inversion. Curr. Genet. 11:553-564.
28. JANSEN, R. K., J. L. WEE, and D. MILLIE. 1998. Comparative utility of chloroplast DNA restriction site and DNA sequence data for phylogenetic studies in plants. Pp. 87-100 in D. E. SOLTIS, P. S. SOLTIS, and J. J. DOYLE, eds. Molecular systematics of plants II. Kluwer Academic Publishers, Dordrecht, the Netherlands.
29. KAWATA, M., T. HARADA, Y. SHIMAMOTO, K. OONO, and F. TAKAIWA. 1997. Short inverted repeats function as hotspots of intermolecular recombination giving rise to oligomers of deleted plastid DNAs (ptDNA). Curr. Genet. 31:179-184.
30. KOLODNER, R., and K. K. TEWARI. 1979. Inverted repeats in chloroplast DNA from higher plants. Proc. Natl. Acad. Sci. USA 76:41-45.
31. LIDHOLM, J., A. SZMIDT, and P. GUSTAFSSON. 1991. Duplication of the psbA. gene in the chloroplast genome of two Pinus species. Mol. Gen. Genet. 226:345-352.
32. MAIER, R. M., K. NECKERMANN, G. L. IGLOI, and H. KOSSEL. 1995. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251: 614-628.
33. MARÉCHAL-DROUARD, L., J. H. WEIL, and A. DIETRICH. 1993. Transfer RNAs and transfer RNA genes in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 44:13-32.
34. MES, T. H. M., N. FRIESEN, R. M. FRITSCH, M. KLAAS, and K. BACHMANN. 1997. Criteria for sampling in Allium based on chloroplast DNA PCR-RFLPs. Syst. Bot. 22:701-712.
35. MORTON, B. R., and M. T. CLEGG. 1993. A chloroplast DNA mutational hotspot and gene conversion in a noncoding region near rbcL in the grass family (Poaceae). Curr. Genet. 24:357-365.
36. MUBUMBILA, M., E. J. CROUSE, and J. H. WEIL. 1984. Transfer RNAs and tRNA genes of Vicia faba chloroplasts. Curr. Genet. 8:379-385.
37. NIMZYK, R., T. SCHÖNDORF, and W. HACHTEL. 1993. In-frame length mutations associated with short tandem repeats are located in unassigned open reading frames of Oenothera chloroplast DNA. Curr. Genet. 23:265-270.
38. OGIHARA, Y., T. TERACHI, and T. SASAKUMA. 1988. Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species. Proc. Natl. Acad. Sci. USA 85:8573-8577.
39. _. 1992. Structural analysis of length mutations in a hotspot region of wheat chloroplast DNAs. Curr. Genet. 22: 251-258.
40. OHYAMA, K., H. FUKUZAWA, T. KOHCHI et al. (13 co-authors). 1986. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha. Nature 322:572-574.
41. OLMSTEAD, R. G., and J. D. PALMER. 1994. Chloroplast DNA systematics: a review of methods and data analysis. Am. J. Bot. 81:1205-1224.
42. PALMER, J. D. 1991. Plastid chromosomes: structure and evolution. Pp. 5-53 in L. BOGORAD and I. K. VASIL, eds. Cell culture and somatic cell genetics in plants, Vol. 7. The molecular biology of plastids. Academic Press, San Diego.
43. PALMER, J. D., J. M. NUGENT, and L. A. HERBON. 1987. 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.
44. PALMER, J. D., B. OSORIO, J. ALDRICH, and W. F. THOMPSON. 1987. Chloroplast DNA evolution among legumes: loss of a large inverted repeat occurred prior to other sequence rearrangements. Curr. Genet. 11:275-286.
45. PALMER, J. D., and W. F. THOMPSON. 1982. Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell 29:537-550.
46. PAVESI, A., F. CONTERIO, A. BOLCHI, G. DIECI, and S. OTTONELLO. 1994. Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions. Nucleic Acids Res. 22:1247-1256.
47. QUIGLEY, F., and J. H. WEIL. 1985. Organization and sequence of five tRNA genes and of an unidentified reading frame in the wheat chloroplast genome: evidence for gene rearrangements during evolution of chloroplast genomes. Curr. Genet. 9:495-503.
48. SANG, T., D. J. CRAWFORD, and T. F. STUESSY. 1997. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). Am. J. Bot. 84:1120-1136.
49. SHIMADA, H., and M. SUGIURA. 1989. Pseudogenes and short repeated sequences in the rice chloroplast genome. Curr. Genet. 16:293-301.
50. SHINOZAKI, K., M. OHME, M. TANAKA et al. (23 co-authors). 1986. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5:2043-2049.
51. SNEDDON, B. V. 1977. A biosystematic study of Microseris subgenus Monermos (Compositae; Cichorieae). Ph.D. thesis, Victoria University of Wellington, New Zealand.
52. SOLTIS, D. E., and P. S. SOLTIS. 1998. Choosing an approach and an appropriate gene for phylogenetic analysis. Pp. 1-42 in D. E. SOLTIS, P. S. SOLTIS, and J. J. DOYLE, eds. Molecular systematics of plants II. Kluwer Academic Publishers, Dordrecht, the Netherlands.
53. SOLTIS, D. E., P. S. SOLTIS, and K. D. BOTHEL. 1990. Chloroplast DNA evidence for the origins of the monotypic Bensoniella and Conimitella (Saxifragaceae). Syst. Bot. 15: 349-362.
54. SOLTIS, D. E., P. S. SOLTIS, T. A. RANKER, and B. D. NESS. 1989. Chloroplast DNA variation in a wild plant, Tolmiea menziesii. Genetics 121:819-826.
55. SOLTIS, P. S., D. E. SOLTIS, and J. J. DOYLE. 1992. Molecular systematics of plants. Chapman and Hall, New York.
56. SPRINZL, M., C. HORN, M. BROWN, A. IOUDOVITCH, and S. STEINBERG. 1998. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26:148-153.
57. STOIKE, L. L., and B. B. SEARS. 1998. Plastome mutator-induced alterations arise in Oenothera chloroplast DNA through template slippage. Genetics 149:347-353.
58. STRAUSS, S. H., J. D. PALMER, G. T. HOWE, and A. H. DOERKSEN. 1988. Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged. Proc. Natl. Acad. Sci. USA 85:3898-3902.
59. TABERLET, P., L. GIELLY, G. PAUTOU, and J. BOUVET. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17:1105-1109.
60. TSAI, C.-H., and S. H. STRAUSS. 1989. Dispersed repetitive sequences in the chloroplast genome of Douglas-fir. Curr. Genet. 16:211-218.
61. TSUDZUKI, J., S. ITO, T. TSUDZUKI, T. WAKASUGI, and M. SUGIURA. 1994. A new gene encoding tRNA-Pro (GGG) is present in the chloroplast genome of black pine: a compilation of 32 tRNA genes from black pine chloroplasts. Curr. Genet. 26:153-158.
62. VIJVERBERG, K., T. H. M. MES, and K. BACHMANN. 1999. Chloroplast DNA evidence for the evolution of Microseris (Asteraceae) in Australian and New Zealand after long-distance dispersal from western North America. Am. J. Bot. (in press).
63. WAKASUGI, T., J. TSUDZUKI, S. ITO, K. NAKASHIMA, T. TSUDZUKI, and M. SUGIURA. 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc. Natl. Acad. Sci. USA 91:9794-9798.
64. WALLACE, R. S., and R. K. JANSEN. 1990. Systematic implications of chloroplast DNA variation in the genus Microseris (Asteraceae: Lactuceae). Syst. Bot. 15:606-616.
65. WOLFE, K. H. 1988. The site of a deletion of the inverted repeat in pea chloroplast DNA contains duplicated gene fragments. Curr. Genet. 13:97-99.
66. WOLFSON, R., K. G. HIGGINS, and B. B. SEARS. 1991. Evidence for replications slippage in the evolution of Oenothera chloroplast DNA. Mol. Biol. Evol. 8:709-720.