Sequence and secondary structure variation in the Gyrodactylus (Platyhelminthes: Monogenea) ribosomal RNA gene array

Journal of Parasitology

Volumn 86, Issue 3, 2000, Pages 567-576

  Cunningham, Carey O ^b   Aliesky, Holly ^a,b   Collins, Catherine M ^a,b  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b MARINE LABORATORY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENETIC TRANSCRIPTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLATYHELMINTH; PREDICTION; PROTEIN SECONDARY STRUCTURE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RNA SEQUENCE; RNA STRUCTURE;

DIGENEA; GYRODACTYLUS; INVERTEBRATA; MONOGENEA; NEMATODA; PLATYHELMINTHES;

EID: 0033944805     PISSN: 00223395     EISSN: None     Source Type: Journal    
DOI: 10.1645/0022-3395(2000)086[0567:sassvi]2.0.co;2     Document Type: Article

References (33)

1. CHILTON, N. B., R. B. GASSER, AND I. BEVERIDGE. 1995. Differences in a ribosomal DNA sequence of morphologically indistinguishable species within the Hypodontus macropi complex (Nematoda: Strongyloidea). International Journal for Parasitology 25: 647-651.
2. _, HOSTE, H., L. A. NEWTON, I. BEVERIDGE, AND R. B. GASSER. 1998. Common secondary structures for the second internal transcribed spacer pre-RNA of two subfamilies of trichostrongylid nematodes. International Journal for Parasitology 28: 1765-1773.
3. CUNNINGHAM, C. O. 1997. Species variation within the internal transcribed spacer (ITS) region of Gyrodactylus (Monogenea; Gyrodactylidae) ribosomal RNA genes. Journal of Parasitology 83: 215-219.
4. _, D. M. MCGILLIVRAY, AND K. MACKENZIE. 1995. Phylogenetic analysis of Gyrodactylus salaris Malmberg, 1957 based on the small subunit (18S) ribosomal RNA gene. Molecular and Biochemical Parasitology 71: 139-142.
5. _, _, _, AND W. T. MELVIN. 1995. Discrimination between Gyrodactylus salaris, G. derjavini and G. truttae (Platyhelminthes: Monogenea) using restriction fragment length polymorphisms and an oligonucleotide probe within the small subunit ribosomal RNA gene. Parasitology 111: 87-94.
6. DOUDNA, J. A. 1997. A molecular contortionist. Nature 388: 830-831.
7. ELLIS, J., AND D. MORRISON. 1995. Effects of sequence alignment on the phylogeny of Sarcocystis deduced from 18S rDNA sequences. Parasitology Research 81: 696-699.
8. GASSER, R. B. 1997. Mutation scanning methods for the analysis of parasite genes. International Journal for Parasitology 27: 1449-1463.
9. _, AND H. HOSTE. 1995. Genetic markers for closely-related parasitic nematodes. Molecular and Cellular Probes 9: 315-320.
10. JAEGER, J. A., D. H. TURNER, AND M. ZUKER. 1990. Predicting optimal and suboptimal secondary structure for RNA. Methods in Enzymology 183: 281-306.
11. JOHNSTON, D. J., R. A. KANE, AND D. ROLLINSON. 1993. Small subunit (18S) ribosomal RNA gene divergence in the genus Schistosoma. Parasitology 107: 147-156.
12. KJER, K. M. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from the frogs. Molecular Phylogenetics and Evolution 4: 314-330.
13. LEWIN, B. 1997. Genes VI. Oxford University Press, Oxford, U.K., 1,260 p.
14. LITTLEWOOD, D. T. J., AND D. A. JOHNSTON. 1995. Molecular phylogenetics of the four Schistosoma groups determined with partial 28S ribosomal RNA gene sequences. Parasitology 111: 167-175.
15. LUMB, S. M., R. A. BRAY, AND D. ROLLINSON. 1993. Partial small subunit (18S) rRNA gene sequences from fish parasites of the families Lepocreadiidea and Fellodistomidae (Digenea) and their use in phylogenetic analyses. Systematic Parasitology 26: 141-149.
16. MICHOT, B., J.-P. BACHELLERIE, AND F. RAYNAL. 1982. Sequence and secondary structure of mouse 28S rRNA 5′-terminal domain. Organisation of the 5.8S-28S rRNA complex. Nucleic Acids Research 10: 5273-5283.
17. _, L. DESPRES, F. BONHOMME, AND J.-P. BACHELLERIE. 1993. Conserved secondary structures in the ITS2 of trematode pre-rRNA. FEBS 316: 247-252.
18. MORGAN, J. A. T., AND D. BLAIR. 1998. Trematode and monogenean rRNA ITS2 secondary structures support a four-domain model. Journal of Molecular Evolution 47: 406-419.
19. MORRISON, D. A., AND J. T. ELLIS. 1997. Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of Apicomplexa. Molecular Biology and Evolution 14: 428-441.
20. MUSE, S. V. 1995. Evolutionary analyses of DNA sequences subject to constraints on secondary structure. Genetics 139: 1429-1439.
21. NAIMI, A., G. BECK, AND C. BRANLANT. 1997. Primary and secondary structures of rRNA spacer regions in enterococci. Microbiology 143: 823-834.
22. NEEFS, J.-M., Y. VAN DE PEER, P. DE RIJK, S. CHAPPELLE, AND R. DE WACHTER. 1993. Compilation of small ribosomal subunit RNA structures. Nucleic Acids Research 21: 3025-3049.
23. NOTREDAME, C. E. A. O'BRIEN, AND D. G. HIGGINS. 1997. RAGA: RNA sequence alignment by genetic algorithm. Nucleic Acids Research 25: 4570-4580.
24. OMER ALI, P., A. J. G. SIMPSON, R. ALLEN, A. P. WATERS, C. J. HUMPHRIES, D. A. JOHNSTON, AND D. ROLLINSON. 1991. Sequence of a small subunit rRNA gene of Schistosoma mansoni and its use in phylogenetic analysis. Molecular and Biochemical Parasitology 46: 201-208.
25. RAUÉ, H. A., W. MUSTERS, C. A. RUTGERS, J. V. T. RIET, AND R. J. PLANTA. 1990. rRNA: from structure to function. In The ribosome: Structure, function and evolution, W. E. Hill, A. Dahlberg, R. A. Garrett et al. (eds.). American Society for Microbiology, Washington, D.C., p. 217-235.
26. SCHULENBURG, J. H. G. V. D., U. ENGLISCH, AND J.-W. WAGELE. 1999. Evolution of ITS1 rDNA in the Digenea (Platyhelminthes: Trematoda): 3′ end sequence conservation and its phylogenetic utility. Journal of Molecular Evolution 48: 2-12.
27. THOMPSON, J. D., T. J. GIBSON, F. PLEWNIAK, F. JEANMOUGIN, AND D. G. HIGGINS. 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876-4882.
28. TOURASSE, N. J., AND M. GOUY. 1997. Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony. Molecular Biology and Evolution 14: 287-298.
29. VAN DER SANDE, C. A. F. M., M. KWA, R. W. VAN NUES, H. VAN HEERIKHUIZEN, H. A. RAUÉ, AND R. J. PLANTA. 1992. Functional analysis of internal transcribed spacer 2 of Saccharomyces cerevisiae ribosomal DNA. Journal of Molecular Biology 223: 899-910.
30. VAWTER, L., AND W. M. BROWN. 1993. Rates and patterns of base change in ssu rRNA gene. Genetics 143: 597-608.
31. WALKER, T. A., Y. ENDO, W. H. WHEAT, I. G. WOOL, AND N. R. PACE. 1983. Location of 5.8S rRNA contact sites in 28S rRNA and the effect of alpha-sarcin on the association of 5.8S rRNA with 28S rRNA. Journal of Biological Chemistry 258: 333-338.
32. ZHU, X., R. B. GASSER, M. PODOLSKA, AND N. B. CHILTON. 1998. Characterisation of anisakid nematodes with zoonotic potential by nuclear ribosomal DNA sequences. International Journal for Parasitology 28: 1911-1921.
33. ZUKER, M., D. H. MATHEWS, AND D. H. TURNER. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In RNA biochemistry and biotechnology, J. Barciszewski and B. F. C. Clark (eds.). NATO ASI Series, Kluwer Academic Publishers, Dordrecht, Netherlands, p. 11-44.