Sequence variations in the large-subunit ribosomal RNA gene of Ammonia (foraminifera, protozoa) and their evolutionary implications

Journal of Molecular Evolution

Volumn 43, Issue 2, 1996, Pages 145-151

  Holzmann, Maria ^a   Piller, Werner ^a   Pawlowski, Jan ^b  

^a UNIVERSITY OF VIENNA   (Austria)

^b UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

Foraminifera; LSU rRNA gene; Phylogeny; Sequence dissimilarity

Indexed keywords

RIBOSOME DNA; RIBOSOME RNA;

ARTICLE; BENTHOS; DNA FLANKING REGION; DNA SEQUENCE; EVOLUTION; GENE SEQUENCE; GENETIC VARIABILITY; NONHUMAN; PHYLOGENY; PROTOZOON; RNA GENE;

EID: 0029742237     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02337359     Document Type: Article

References (46)

1. Bairoch A (1989) PC/Gene, IntelliGenetics, Inc
2. Christen R (1994) Molecular phylogeny and the origin of Metazoa. In: Bengtson S (ed) Early life on earth, Nobel symposium No. 84. Columbia University Press, New York, pp 467-474
3. Clark CG (1987) On the evolution of ribosomal RNA. J Mol Evol 25:343-350
4. Clark CG, Tague BW, Ware VC, Gerbi SA (1984) Xenopus laevis 28S ribosomal RNA: a secondary structure and its evolutionary and functional implications. Nucleic Acids Res 12:6197-6220
5. De Rijk P, Van de Peer Y, Chapelle S, De Wachter R (1994) Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res 22:3495-3501
6. Dover AG (1988) rDNA world falling to pieces. Nature 336:623-624
7. Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22:521-565
8. Gerbi SA, Jeppesen C, Stebbins-Boaz B, Ares M Jr (1987) Evolution of eukaryotic rRNA: constraints imposed by RNA interactions. Cold Spring Harb Symp Quant Biol 11:709-719
9. Goldstein ST, Moodley L (1993) Gametogenesis and the life cycle of the foraminifera Ammonia beccarii (Linne) Forma tepida (Cushman). J Foraminiferal Res 23:213-220
10. Gonzalez IL, Gorski JL, Campen TJ, Dorney DJ, Erickson JM, Sylvester JE, Schmickel RD (1985) Variation among human 28S ribosomal RNA genes. Proc Natl Acad Sci USA 82:7666-7670
11. Gonzalez IL, Sylvester JE, Schmickel RD (1988) Human 28S ribosomal RNA sequences heterogeneity. Nucleic Acids Res 16: 10213-10224
12. Gunderson JH, Sogin ML, Wollett G, Hollingdale M, De La Cruz VF, Waters AP, Mc Cutchan TF (1987) Structurally distinct, stage-specific ribosomes occur in Plasmodium. Science 238:933-937
13. Hadjiolov AA, Georgiev OI, Nosikov VV, Yavachec LP (1984) Primary and secondary structure of rat 28S ribosomal RNA. Nucleic Acids Res 12:3677-3693
14. Hamby RK, Zimmer EA (1991) Ribosomal RNA as a phylogenetic tool in plant systematics. In: Soltis P, Soltis D, Doyle JJ (eds) Molecular systematics in plants. Routledge, Chapman and Hall, New York, pp 50-91
15. Hancock JM, Dover GA (1988) Molecular coevolution among cryptically simple expansion segments of eukaryotic 26S/28S rRNAs. Mol Biol Evol 5:377-392
16. Hancock JM, Dover GA (1990) "Compensatory slippage" in the evolution of ribosomal RNA genes. Nucleic Acids Res 18:5949-5954
17. Hassouna N, Michot B, Bachellerie JP (1984) The complete nucleotide sequence of mouse 28 S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes. Nucleic Acids Res 12:3563-3583
18. Haynes JR (1992) Supposed pronounced ecophenotypy in foraminifera. J Micropaleontol 11:59-63
19. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
20. Larsen NGJ, Maidak BL, McCaughey MJ, Overbeek R, Macke TJ, Marsh TL, Woese CR (1993) The ribosomal database project. Nucleic Acids Res 21:3021-3023
21. Larson A, Wilson AC (1989) Patterns of ribosomal RNA evolution in salamanders. Mol Biol Evol 6:131-153
22. Lee JJ, Faber WW Jr, Anderson RO, Pawlowski J (1992) Life cycles of foraminifera. In: Lee JJ, Anderson RO (eds) Biology of foraminifera. Academic press, San Diego, pp 285-334
23. Leffers H, Andersen AH (1993) The sequence of 28S ribosomal RNA varies within and between human cell lines. Nucleic Acids Res 21:1449-1455
24. Lenaers G, Scholin C, Bhaud Y, Saint-Hilaire D, Herzog M (1991) A molecular phylogeny of dinoflagellate protists (Pyrrhophyta) inferred from the sequence of 24S r RNA divergent domains D1 and D8. J Mol Evol 32:53-63
25. Liu Y, Rocourt M, Pan S, Leibowitz MJ (1992) Sequence and variability of the 5.8S and 26S rRNA genes of Pneumocystis carinii. Nucleic Acids Res 20:3763-3772
26. Maden BE, Dent CL, Farrell TE, Garde J, McCallum F, Wakeman JA (1987) Human rRNA heterogeneity. Biochem J 246:519-527
27. McCutchan TF, De La Cruz VF, Lal AA, Gunderson JH, Elwood HJ, Sogin M (1988) Primary sequence of two small subunit ribosomal RNA genes from Plasmodium falciparum. Mol Biochem Parasitol 28:63-68
28. Michot B, Qu HL, Bachellerie JP (1990) Evolution of large-subunit rRNA structure; the diversification of divergent D3 domain among major phylogenetic groups. Eur J Biochem 188:219-229
29. Murray JW (1991) Ecology and paleoecology of benthic foraminifera. Longman, Harlow
30. Mylvaganam S, Denis PP (1992) Sequence heterogeneity between the two genes encoding 16S rRNA from thehalophilic archaebacterium Haloarcula marismortui. Genetics 130:399-410
31. Pace NR, Olsen GJ, Woese CR (1986) Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell 45:325-326
32. Pélandakis M, Solignac M (1993) Molecular phylogeny of Drosophila based on ribosomal RNA sequences. J Mol Evol 37:525-543
33. Pawlowski J, Bolivar I, Guiard-Maffia J, Gouy M (1994) Phylogenetic position of Foraminifera interred from LSU rRNA gene sequences. Mol Biol Evol 11:929-938
34. Pawlowski J, Bolivar I, Fahrni J, Zaninetti L (1995) DNA analysis of "Ammonia beccarii" morphotypes: one or more species? Marine Micropaleontol 26:171-178
35. Qu LH, Nicoloso M, Bachellerie JP (1988) Phylogenetic calibration of the 5′terminal domain of large rRNA achieved by determining twenty eucaryotic sequences. J Mol Evol 28:113-114
36. Rousset F, Pélandakis M, Solignac M (1991) Evolution of compensatory substitutions through G-U intermediate state in Drosophila rRNA. Proc Natl Acad Sci USA 88:10032-10036
37. Ruiz Linares A, Hancock JM, Dover GA (1991) Secondary structure constraints on the evolution of Drosophila 28S ribosomal RNA expansion segments. J Mol Biol 219:381-390
38. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
39. Schlegel M (1991) Protist evolution and phylogeny as discerned from small subunit RNA sequence comparisons. Eur J Protistol 27:207-219
40. Sogin ML (1991) Early evolution and the origin of eukaryotes. Curr Opin Genet Dev 1: 457-463
41. Sogin ML (1994) The origin of eukaryotes and evolution into major kingdoms. In: Bengtson S (ed) Early life on earth, Nobel Symposium No. 84. Columbia U.P., New York, pp 181-192
42. Tautz D, Hancock JM, Webb DA, Tautz C, Dover GA (1988) Complete sequences of the rRNA genes of Drosophila melanogaster. Mol Biol Evol 5:366-376
43. Walton WR, Sloan BJ (1990) The genus Ammonia Brünnich, 1772: its geographic distribution and morphologic variability. J Foraminiferal Res 20:128-156
44. Weekers PHH, Gast RJ, Fuerst PA, Byers TJ (1994) Sequence variations in small-subunit ribosomal RNAs of Hartmanella vermiformis and their phylogenetic implications. Mol Biol Evol 11:684-690
45. Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archae, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576-4579
46. Zuker M (1989) On finding all suboptimal foldings of an RNA molecule. Science 244:48-52