Molecular Characterization of Nuclear Small Subunit (18S)-rDNa Pseudogenes in a Symbiotic Dinoflagellate (Symbiodinium, Dinophyta)

Journal of Eukaryotic Microbiology

Volumn 50, Issue 6, 2003, Pages 417-421

  Santos, Scott R ^a,b   Kinzie III, Robert A ^c   Sakai, Kazuhiko ^d   Coffroth, Mary Alice ^a  

^a UNIVERSITY AT BUFFALO   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

^c UNIVERSITY OF HAWAII   (United States)

^d UNIVERSITY OF THE RYUKYUS   (Japan)

Author keywords

Culture; Truncated genes; Zooxanthellae

Indexed keywords

PRIMER DNA; RIBOSOME DNA; RNA 18S;

DINOFLAGELLATE;

ANIMAL; ARTICLE; DINOFLAGELLATE; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PSEUDOGENE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SYMBIOSIS;

ANIMALS; BASE SEQUENCE; DINOFLAGELLIDA; DNA PRIMERS; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PSEUDOGENES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 18S; SYMBIOSIS;

ANIMALIA; DINOPHYCEAE; PROTISTA; SYMBIODINIUM;

EID: 0348226830     PISSN: 10665234     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1550-7408.2003.tb00264.x     Document Type: Article

References (31)

1. Altschul, S. F., Madden, T. L., Schaffer, A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. 1997. Gapped BLAST und PS1-BLAST: a new generation of protein database search programs. Nucl. Acids Res., 25:3389-3402.
2. Benevolenskaya, E. V., Kogan, G. L., Tulin, A. V., Philipp, D. & Gvozdev, V. A. 1997. Segmented gene conversion as a mechanism of correction of 18S rRNA pseudogene located outside of rDNA cluster in D. melanogaster. J. Mol. Evol., 44:646-651.
3. Birnboim, H. C. 1983. A rapid alkaline extraction method for the isolation of plasmid DNA. Methods Enzymol., 100:243-255.
4. Carlos, A. A., Baillie, B. K., Kawachi, M. & Maruyama, T. 1999. Phylogenetic position of Symbiodinium (Dinophyceae) isolates from Tridacnids (Bivalvia), Cardiids (Bivalvia), a sponge (Porifera), a soft coral (Anthozoa), and a free-living strain. J. Phycol., 35:1054-1062.
5. Carlos, A. A., Baillie, B. K. & Maruyama, T. 2000. Diversity of dinoflagellate symbionts (zooxanthellae) in a host individual. Mar. Ecol. Prog. Ser., 195:93-100.
6. Coffroth, M. A., Lasker, H. R., Diamond, M. E., Bruenn, J. A. & Bermingham, E. 1992. DNA fingerprinting of a gorgonian coral: a method for detecting clonal structure in a vegetative species. Mar. Biol., 114:317-325.
7. Dams, E., Hendriks, L., van de Peer, Y., Neefs, J. M., Smits, G., Vandenbempt, I. & De Wachter, R. 1988. Compilation of small ribosomal subunit RNA sequences. Nuc. Acids Res., 16(Suppl.):r87-173.
8. Daugbjerg, N., Hansen, G., Larsen, J. & Moestrup, Ø. 2000. Phylogeny of some of the major genera of dinoflagellates based on ultrastructure and partial LSU rDNA sequence data, including the erection of three new genera of unarmoured dinoflagellates. Phycologia, 39:302-317.
9. Davies, P. S. 1993. Endosymbiosis in marine cnidarians. In: John, D. M., Hawkins, S. J. & Price, J. H. (ed.), Plant-Animal Interactions in the Marine Benthos. Clarendon Press, Oxford. 23:511-540.
10. Fensome, R. A., MacRae, R. A., Moldowan, J. M., Taylor, F. J. R. & Williams, G. L. 1996. The early Mesozoic radiation of dinoflagellates. Paleobiology, 22:329-338.
11. LaJeunesse, T. C. 2001. Investigating the biodiversity, ecology, and phylogeny of endosymbiotic dinoflagellates in the genus Symbiodinium using the ITS region: in search of a "species" level marker. J. Phycol., 37:866-880.
12. LaJeunesse, T. C. & Trench, R. K. 2000. Biogeography of two species of Symbiodiniuin (Freudenthal) inhabiting the intertidal sea anemone Anthopleura elegantissima (Brandt). Biol. Bull., 199:126-134.
13. Li, W. H., Gojobori, T. & Nei, M. 1981. Pseudogenes as a paradigm of neutral evolution. Nature, 292:237-239.
14. Loh, W., Carter, D. & Hoegh-Guldberg, O. 1998. Diversity of zooxanthellae from scleractinian corals of One Tree Island (The Great Barrier Reef). In: Greenwood, J. G. & Hall, N. J. (ed.). Proceedings of the Australian Coral Reef Society, 75th Anniversity Conference, Heron Island October 1997. University of Queenland. Brisbane. p. 87-95.
15. Rehnstam-Holm, A. S., Godhe, A. & Anderson, D. M. 2002. Molecular studies of Dinophysis (Dinophyceae) species from Sweden and North America. Phycologia, 41:348-357.
16. Rowan, R. 1998. Diversity and ecology of zooxanthellae on coral reefs. J. Phycol., 34:407-417.
17. Rowan, R. & Powers, D. A. 1991a. A molecular genetic identification of zooxanthellae and the evolution of animal-algal symbioses. Science, 251:1348-1351.
18. Rowan, R. & Powers, D. A. 1991b. Molecular genetic identification of symbiotic dinoflagellates (Zooxanthellae). Mar. Ecol. Prog. Ser., 71: 65-73.
19. Saldarriaga, J. F., Taylor, F. J. R., Keeling, P. J. & Cavalier-Smith, T. 2001. Dinoflagellate nuclear SSU rRNA phylogeny suggests multiple plastid losses and replacements. J. Mol. Evol., 53:204-213.
20. Santos, S. R., Taylor, D. J. & Coffroth, M. A. 2001. Genetic comparisons of freshly isolated vs. cultured symbiotic dinoflagellates: implications for extrapolating to the intact symbiosis. J. Phycol., 37: 900-912.
21. Santos, S. R., Taylor, D. J., Kinzie III, R. A., Sakai, K. & Coffroth, M. A. 2002b. Evolution of length variation and heteroplasmy in the chloroplast rDNA of symbiotic dinoflagellates (Symbiodinium, Dinophyta) and a novel insertion in the universal core region of the large subunit rDNA. Phycologia, 41:311-318.
22. Santos, S. R., Taylor, D. J., Kinzie III, R. A., Hidaka, M., Sakai, K. & Coffroth, M. A. 2002a. Molecular phylogeny of symbiotic dinoflagellates inferred from partial chloroplast large subunit (23S)-rDNA sequences. Mol. Phylogenet. Evol., 23:97-111.
23. Saunders, G. W., Hill, D. R. A., Sexton, J. P. & Andersen, R. A. 1997. Small-subunit ribosomal RNA sequences from selected dinoflagellates: testing classical evolutionary hypothesis with molecular systematic methods. Plant Syst. Evol., 11:237-259.
24. Scholin, C. A. & Anderson, D. M. 1994. Identification of group-specific and strain-specific markers for globally distributed Alexandrium (Dinophyceae). I. RFLP analysis of SSU rRNA
25. Scholin, C. A., Anderson, D. M. & Sogin, M. L. 1993. Two distinct small-subunit ribosomal RNA genes in the North American toxic dinoflagellate Alexandrium fundyense (Dinophyceae). J. Phycol., 29: 209-216. genes. J. Phycol., 30:744-754.
26. Scholin, C. A., Anderson, D. M. & Sogin, M. L. 1993. Two distinct small-subunit ribosomal RNA genes in the North American toxic dinoflagellate Alexandrium fundyense (Dinophyceae). J. Phycol., 29: 209-216. genes. J. Phycol., 30:744-754.
27. Taylor, D. L. 1974. Symbiotic marine algae: taxonomy and biological fitness. In: Vernberg, W. B. (ed.), Symbiosis in the Sea. University of South Carolina Press, South Carolina. p. 245-262.
28. Toller, W. W., Rowan, R. & Knowlton, N. 2001. Zooxanthellae of the Montastraea annularis species complex: patterns of distribution of four taxa of Symbiodinium on different reefs and across depths. Biol. Bull., 201:348-359.
29. Wilcox, T. P. 1998. Large-subunit ribosomal RNA systematics of symbiotic dinoflagellates: morphology does not recapitulate phylogeny. Mol. Phylogenet. Evol., 10:436-448.
30. Yeung, P. K. K., Kong, K. F., Wong, F. T. W. & Wong, J. T. Y. 1996. Sequence data for two large-subunit rRNA genes from an Asian strain of Alexandrium catenella. Appl. Environ. Microbiol., 62:4199-4201.
31. Zardoya, R., Costas, E., Lopezrodas, V., Garridopertierra, A. & Bautista, J. M. 1995. Revised dinoflagellate phylogeny inferred from molecular analysis of large-subunit ribosomal gene sequences. J. Mol. Evol., 41:637-645.