RpoA: A Useful Gene for Phylogenetic Analysis in Diatoms

Journal of Eukaryotic Microbiology

Volumn 50, Issue 6, 2003, Pages 471-475

  Fox, Martin G ^a   Sorhannus, Ulf M ^a  

^a EDINBORO UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Diatoms; Molecular phylogeny; rbcL; rpoA; SSU rRNA

Indexed keywords

DNA DIRECTED RNA POLYMERASE; PRIMER DNA; RIBOSOME RNA; RNA POLYMERASE ALPHA SUBUNIT;

PHYLOGENETICS;

ARTICLE; CHEMISTRY; CLASSIFICATION; DIATOM; ENZYMOLOGY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

BASE SEQUENCE; DIATOMS; DNA PRIMERS; DNA-DIRECTED RNA POLYMERASES; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL;

ALGAE; BACILLARIOPHYTA;

EID: 0346336037     PISSN: 10665234     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1550-7408.2003.tb00273.x     Document Type: Article

References (27)

1. Beszteri, B., Acs, E., Makk, J., Kovacs, G., Marialigeti, K. & Kiss, K. T. 2001. Phylogeny of six naviculoid diatoms based on 18S rRNA sequences. Int. J. Syst. Evol. Microbiol., 51:1581-1586.
2. Chesnick, J. M., Kooistra, W. H. C. F., Wellbrock, U. & Medlin, L. K. 1997. Ribosomal RNA analysis indicates a benthic pennate diatom ancestry for endosymbionts of the dinoflagellates Peridinium foliaceum and Peridinium balticum (Pyrrophyta). J. Eukaryot. Microbiol., 44:314-320.
3. Daugbjerg, N. & Andersen, R. A. 1997. A molecular phylogeny of the heterokont algae based on analyses of chloroplast-encoded rbcL sequence data. J. Phycol., 33:1031-1041.
4. Ehara, M., Inagaki, Y., Watanabe, K. I. & Ohama, T. 2000. Phylogenetic analysis of diatoms cox I genes and implications of a fluctuating GC content on mitochondrial genetic code evolution. Curr. Genet., 37:29-33.
5. Farris, J. S. 1969. A successive approximations approach to character weighting. Syst. Zool., 18:374-385.
6. Farris, J. S. 1989. The retention index and rescaled consistency index. Cladistics, 5:417-419.
7. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39:783-791.
8. Hajos, M. & Stradner, H. 1975. Late Cretaceous Archaeomonadaceae, Diatomaceae, and Silicoflagellate from the South Pacific Ocean, Deep Sea Drilling Project Leg 29, Site 275. In: Kennett, J. P., Houtz, R. E., et al. (ed.), Initial Reports of the Deep-Sea Drilling Project 29. United States Government Printing Office, Washington, p. 913-1109.
9. Harwood, D. M. 1988. Upper Cretaceous and Lower Paleocene diatom and silicoflagellate biostratigraphy of Seymour Island, eastern Antarctic Peninsula. Geol. Soc. Am. Bull., 169:55-129.
10. Huelsenbeck, J. P. & Ronquist, F. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics, 17:754-755.
11. Lundholm, N., Daugbjerg, N. & Moestrup, Ø. 2002. Phylogeny of the Bacillariaceae with emphasis on the genus Pseudo-nitzschia (Bacillariophyceae) based on partial LSU rRDNA. Eur. J. Phycol., 37:115-134.
12. Medlin, L. K., Williams, D. M. & Sims, P. M. 1993. The evolution of the diatoms (Bacillariophyta). I. Origin of the group and assessment of the monophyly of its major divisions. Eur. J. Phycol., 28:261-275.
13. Medlin, L. K., Kooistra, W. H. C. F., Gersonde, R. & Wellbrock, U. 1996. Evolution of the diatoms (Bacillariophyta). II. Nuclear-encoded small-subunit rRNA sequence comparisons confirm a paraphyletic origin for the centric diatoms. Mol. Bio. Evol., 13:67-75.
14. Medlin, L. K., Kooistra, W. H. C. F. & Schmid, A-M. 2000. A review of the evolution of the diatoms - a total approach using molecules, morphology and geology. In: Witkowski, A. & Sieminska, J. (ed.), The Origin and Early Evolution of the Diatoms: Fossil, Molecular and Biogeographical Approaches. W. Szafer Institute of Botany, Polish Academy of Sciences, Cracow. p. 13-35.
15. Olmstead, R. G. & Palmer, J. D. 1994. Chloroplast DNA systematics: a review of methods and data analysis. Am. J. Bot., 81:1205-1224.
16. Page, R. D. M. 1996. TREEVIEW: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci., 12:357-358.
17. Posada, D. & Crandall, K. A. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics, 14:817-818
18. Round, F. E., Crawford, R. M. & Mann, D. G. 1990. The Diatoms: Biology and Morphology of the Genera. Cambridge University Press, Cambridge. 747 p.
19. Sambrook, J., Fritsch, E. & Maniatis. T. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor University Press.
20. Saitou, N. & Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4:406-426.
21. Simonsen, R. 1979. The diatoms system: ideas on phylogeny. Bacillaria, 2:9-71.
22. Sorhannus, U., Gasse, F., Perasso, R. & Baroin-Tourancheau, A. 1995. A preliminary phylogeny of diatoms based on 28S ribosomal RNA sequence data. Phycologia, 34:65-73.
23. Strelnikova, N. I. 1974. Diatomei Pozdeno Mela. Academia Nauk SSSR, Moscow. Vii. 204 p.
24. Swofford, D. L. 2002. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4.0b10. Sinauer Associates, Sunderland.
25. Thompson, J. D., Higgins. D. G. & Gibson, T. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl. Acids Res., 22:4673-4680.
26. Van Der Auwera, G. & De Wachter, R. 1998. Structure of the large subunit rDNA from a diatom, and comparison between small and large subunit ribosomal RNA for studying stramenopile evolution. J. Eukaryot. Microbiol., 45:521-527.
27. Xia, X. 2000. DAMBE: Data Analysis in Molecular Biology and Evolution. Department of Ecology and Biodiversity. University of Hong Kong.