Noncoding sequences from the slowly evolving chloroplast inverted repeat in addition to rbcL data do not support gnetalean affinities of angiosperms

Molecular Biology and Evolution

Volumn 13, Issue 2, 1996, Pages 383-396

  Goremykin, Vadim ^a,b   Bobrova, Vera ^a   Pahnke, Jens ^b   Troitsky, Aleksey ^a   Antonov, Andrew ^a   Martin, William ^b  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

Author keywords

angiosperms; chloroplast inverted repeat; ferns; Gnetales; gymnosperms; molecular evolution; molecular phylogeny; noncoding DNA

Indexed keywords

CHLOROPLAST RNA; RIBOSOME RNA; RIBULOSEBISPHOSPHATE CARBOXYLASE;

ARTICLE; CHLOROPLAST; CONTROLLED STUDY; EVOLUTION; GENETIC POLYMORPHISM; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PHYLOGENY; PLANT; RNA SEQUENCE; SPECIES DIFFERENCE;

EMBRYOPHYTA; FILICOPHYTA; GNETALES; GYMNOSPERMAE; MAGNOLIOPHYTA; NYMPHAEA; SPERMATOPHYTA;

EID: 0030052344     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025597     Document Type: Article

References (60)

1. ALBERT, V. A., A. BACKLUND, K. BREMER, M. W. CHASE, J. R. MANHARDT, B. D. MISHLER, and K. C. NIXON. 1994. Functional constraints and rbcL evidence for land plant phylogeny. Ann. Mo. Bot. Gard. 81:534-567.
2. ANSORGE, W., B. S. SPROAT, J. STEGEMANN, and C. SCHWAGER. 1986. A non-radioactive automated method for DNA sequence determination. J. Biochem. Biophys. Methods 13: 315-323.
3. BAUM, D. 1994. rbcL and seed plant phytogeny. Trends Ecol. Evol. 9:39-41.
4. BOBROVA, V. K., A. V. TROITSKY, A. G. PONOMAREV, and A. S. ANTONOV. 1987. Low-molecular-weight rRNA sequences and plant phylogeny reconstruction: nucleotide sequences of chloroplast 4.5S rRNAs from Acorus calamus (Araceae) and Ligularia calthifolia (Asteraceae). Plant Syst. Evol. 156:13-27.
5. BÖHLE, U.-R., H. H. HILGER, R. CERFF, and W. MARTIN. 1994. Non-coding chloroplast DNA for plant molecular systematics at the infrageneric level. Pp. 391-403 in B. SCHIERWATER, B. STREIT, G. WAGNER, and R. DESALLE, eds. Molecular ecology and evolution: approaches and applications. Birkhäuser, Basel.
6. BOULTER, D., J. A. M. RAMSHAW, E. W. THOMPSON, M. RICHARDSON, and R. H. BROWN. 1972. A phylogeny of higher plants based on the amino acid sequences of cytochrome c and its biological implications. Proc. R. Soc. Lond. B 181: 441-455.
7. CHASE, M. W., D. E. SOLTIS, R. G. OLMSTEAD et al. (42 co-authors). 1993. DNA sequence phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Ann. Mo. Bot. Gard. 80:528-580.
8. CHAW, S.-M., H.-M. SUNG, H. LONG, A. ZHARKIKH, and W.-H. LI. 1994. Phylogeny of the major subclasses of angiosperms and date of the monocot-dicot divergence. Am. J. Bot. 81: S146.
9. CLEGG, M. T. 1993. Chloroplast gene sequences and the study of plant evolution. Proc. Nad. Acad. Sci. USA 90:363-367.
10. CLEGG, M. T., and G. ZURAWSKI. 1992. Chloroplast DNA and the study of plant phytogeny. Pp. 1-13 in P. S. SOLTIS, J. J. DOYLE, and D. E. SOLTIS, eds. Molecular systematics of plants. Chapman & Hall, New York.
11. CRANE, P. W., E. M. FRIIS, and K. R. PEDERSEN. 1995. The origin and early diversification of angiosperms. Nature 374: 27-33.
12. DEVEREUX, J., P. HAEBERLI, and O. SMITHIES. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387-395.
13. DOWNIE, S. R., and J. D. PALMER. 1992. Use of Chloroplast DNA rearrangements in reconstructing phylogeny. Pp. 14-35 in P. S. SOLTIS, J. J. DOYLE, and D. E. SOLTIS, eds. Molecular systematics of plants. Chapman & Hall, New York.
14. DOYLE, J. A., M. J. DONOGHUE, and E. A. ZIMMER. 1994. Integration of morphological and ribosomal RNA data on the origin of the angiosperms. Ann. Mo. Bot. Gard. 81:419-450.
15. EHRENDORFER, F. 1991. Evolution und Systematik. Pp. 666-826 in P. SITTE, H. ZIEGLER, F. EHERENDORFER, and A. BREZINSKY, eds. Lehrbuch der Botanik. Gustav Fischer Verlag, Stuttgart.
16. ENDRESS, P. 1994 Floral structure and evolution of primitive angiosperms: recent advances. Pl Syst. Evol. 192:79-97.
17. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: a maximum-likelihood appoach. J. Mol. Evol. 17:368-376.
18. _. 1989. PHYLIP - phylogeny inference package (version 3.2). Cladistics 5:164-166.
19. FRIEDMANN, W. 1990. Double fertilization in Ephedra, a non-flowering seed plant: its bearing on the origin of angiosperms. Science 247:951-954.
20. _. 1994. The evolution of embryogeny in seed plants and the developmental origin and early history of endosperm. Am. J. Bot. 81:1468-1486.
21. GAUT, B. S., S. V. MUSE, W. D. CLARK, and M. T. CLEGG. 1992. Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. J. Mol. Evol. 35:292-303.
22. HAMBY, R. K., and E. A. ZIMMER. 1992. Ribosomal RNA as a phylogenetic tool in plant systematics. Pp. 50-91 in P. S. SOLTIS, J. J. DOYLE, and D. E. SOLTIS, eds. Molecular systematics of plants. Chapman & Hall, New York.
23. HASEBE, M., M. ITO, R. KOFUJI, K. UEDA, and K. IWATSUKI. 1993. Phylogenetic relationships of ferns deduced from rbcL gene sequence. J. Mol. Evol. 37:476-482.
24. HASEBE, M., R. KOFUJI, M. ITO, M. KATO, K. IWATSUKI, and K. UEDA. 1992. Phylogeny of the gymnosperms inferred from rbcL gene sequences. Bot. Mag. Tokyo 105:673-679.
25. HASEBE, M., T. OMORI, M. NAKAZAWA, T. SANO, M. KATO, and K. IWATSUKI. 1994. rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns. Proc. Natl. Acad. Sci. USA 91:5730-5734.
26. HERVÉ, P., A. CHENUIL, and A. ADOUTTE. 1994. Can the Cambrian explosion be inferred through molecular phylogeny? Development (Supplement) 15-25.
27. HORI, H., B.-L. LIM, and S. OSAWA. 1985. Evolution of green plants as deduced from 5S rRNA sequences. Proc. Natl. Acad. Sci. USA 82:820-823.
28. JIN, L., and M. NEI. 1990. Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol. Biol. Evol. 7: 82-102.
29. KIMURA, M. 1980. A simple method for estimating evolutionary rate of base subsitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
30. KRAMER, K. U. 1990. Notes on the higher level classification of the recent ferns. Pp. 49-52 in K. U. KRAMER and P. S. GREEN, eds. The families and genera of vascular plants. Vol. I. Pteridophytes and gymnosperms. Springer Verlag, Berlin.
31. LECOINTRE, G., P. HERVÉ, H. L. V. LE, and H. LE GUYADER. 1994. How many nucleotides are required to resolve a phylogenetic problem? The use of a new statistical method applicable to available sequences. Mol. Phylogenet. Evol. 3: 292-309.
32. LES, D. H., D. K. GARVIN, and C. F. WIMPEE. 1991. Molecular evolutionary history of ancient aquatic angiosperms. Proc. Natl. Acad. Sci. USA 88:10119-10123.
33. LI, W.-H., C.-I. WU, and C.-C. LUO. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150-174.
34. MANHART, J. R. 1994. Phylogenetic analysis of green plant rbcL sequences. Mol. Phylogenet. Evol. 3:114-127.
35. MARTIN, P. G., and A. C. JENNINGS. 1983. The study of plant phytogeny using amino acid sequences of ribulose-1,5-bisphosphate carboxylase. Aust. J. Bot. 31:395-409.
36. MARTIN, W., A. GIERL, and H. SAEDLER. 1989. Molecular evidence for pre-Cretaceous angiosperm origins. Nature 339:46-48.
37. MARTIN, W., D. LYDIATE, H. BRINKMANN, G. FORKMANN, H. SAEDLER, and R. CERFF. 1993. Molecular phytogenies in angiosperm evolution. Mol. Biol. Evol. 10:140-162.
38. MARTIN, W., C. C. SOMERVILLE, and S. LOISEAUX-DE GOER. 1992. Molecular phytogenies of plastid origins and algal evolution. J. Mol. Evol. 35:385-403.
39. MURRAY, M. G., and W. F. THOMPSON. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8: 4321-4325.
40. NEI, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
41. NEI, M., and T. GOJOBORI. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous substitutions. Mol. Biol. Evol. 3:418-426.
42. NIESBACH-KLOSGEN, U., E. BARZEN, J. BERNHARDT, W. ROHDE, Zs. SCHWARZ-SOMMER, H.-J. REIF, U. WIENAND, and H. SAEDLER. 1987. Chalcone synthase genes in plants: a tool to study evolutionary relationships. J. Mol. Evol. 26:213-225.
43. NIXON, K. C., W. L. CREPET, D. STEVENSON, and E. M. FRIIS. 1994. A reevaluation of seed plant phytogeny. Ann. Mo. Bot. Gard. 81:484-533.
44. OTA, T., and M. NEI. 1994. Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites. J. Mol. Evol. 38:642-643.
45. PALMER, J. D. 1985. Comparative organization of chloroplast genomes. Ann. Rev Genet. 19:325-354.
46. PALMER, J. D., and W. F. THOMPSON. 1981. Rearrangements in the chloroplast genomes of mung bean and pea. Proc. Natl. Acad. Sci. USA 78:5533-5537.
47. PALMER, J. D., R. K. JANSEN, H. J. MICHEALS, M. W. CHASE, and J. R. MANHART. 1988. Chloroplast DNA variation and plant phylogeny. Ann. Mo. Bot. Gard. 75:1180-1206.
48. PICHI-SERMOLLI, R. E. G. 1958. The higher taxa of Pteridophyta and their classification. Syst. Today (Uppsala Universitets Aarsskrift) 6:70-90.
49. RAKHIMOVA, G. M., A. V. TROITSKY, I. N. KLIKUNOVA, and A. S. ANTONOV. 1989. Phylogenetic analysis of partial nucleotide sequences of 18S rRNA of 14 plant species. Mol. Biol. (Moscow) 23:830-842.
50. RAUBESON, L. A., and R. K. JANSON. 1992. Chloroplast DNA evidence on the acient evolutionary split in vascular land plants. Science 255:1697-1699.
51. SAITOU, N., and M. NEI 1987. The neighbor-joining method: a new method for the reconstruction of phylogenetic trees. Mol. Biol. Evol. 4:406-425.
52. SAMBROOK, J., E. F. FRITSCH, and T. MANIATIS. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
53. TABOR, S., and C. C. RICHARDSON. 1987. DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc. Natl. Acad. Sci. USA 84:4767-4771.
54. TROITSKY, A. V., and V. K. BOBROVA. 1986. 23S-derived small ribosomal RNAs: their structure and evolution with regard to plant phylogenies. Pp. 137-170 in K. S. DUTTA, ed. DNA systematics. Vol. II. CRC Press, Boca Raton.
55. TROITSKY, A. V., Y. F. MELEKHOVETS, G. M. RAKHIMOVA, V. K. BOBROVA, K. M. VALIEJO-ROMAN, and A. S. ANTONOV. 1991. Angiosperm origin and early seed plant evolution deduced from rRNA sequence comparisons. J. Mol. Evol. 32: 253-261.
56. VAN DE PEER, Y., and R. DE WACHTER. 1993. TREECON: a software package for the construction and drawing of evolutionary trees. Comput. Appl. Biosci. 9:177-182.
57. WOLFE, K. H., M. GOUY, Y. W. YANG, P. SHARP, and W-H. LI. 1989. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc. Natl. Acad. Sci. USA 86:6201-6205.
58. WOLFE, K. H., W.-H. LI, and P SHARP. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. USA 84: 9054-9058.
59. WOLFE, K. H., C. W. MORDEN, and J. D. PALMER. 1992. Function and evolution of a minimal plastid genome from a non-photosynthetic parasitic plant. Proc. Natl. Acad. Sci. USA 89: 10648-10652.
60. ZIMMER, E. A., R. K. HAMBY, M. L. ARNOLD, D. A. LEBLANC, and E. L. THERIOT. 1989. Ribosomal RNA phylogenies and flowering plant evolution. Pp. 205-226 in B. FERNHOLM, K. BREMER, and H. JORNVALL, eds. The hierarchy of life. Elsevier, Amsterdam.