1887

Abstract

Phylogenetic analysis of small and large subunits of rDNA genes suggested that Foraminifera originated early in the evolution of eukaryotes, preceding the origin of other rhizopodial protists. This view was recently challenged by the analysis of actin and ubiquitin protein sequences, which revealed a close relationship between Foraminifera and Cercozoa, an assemblage of various filose amoebae and amoeboflagellates that branch in the so-called crown of the SSU rDNA tree of eukaryotes. To further test this hypothesis, we sequenced a fragment of the largest subunit of the RNA polymerase II (RPB1) from five foraminiferans, two cercozoans and the testate filosean . Analysis of our data confirms a close relationship between Foraminifera and Cercozoa and points to as the closest relative of Foraminifera.

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2003-11-01
2024-03-28
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References

  1. Archibald J. M., Longet D., Pawlowski J., Keeling P. J. 2003; A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol Biol Evol 20:62–66 [CrossRef]
    [Google Scholar]
  2. Arnold Z. M. 1972; Observations on the biology of the protozoan Gromia oviformis Dujardin. Univ Calif Publ Zool100
    [Google Scholar]
  3. Baldauf S. L., Roger A. J., Wenk-Siefert I., Doolittle W. F. 2000; A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972–977 [CrossRef]
    [Google Scholar]
  4. Berney C., Pawlowski J. 2003; Revised small subunit rRNA analysis provides further evidence that Foraminifera are related to Cercozoa. J Mol Evol 57:1–8 [CrossRef]
    [Google Scholar]
  5. Bhattacharya D., Helmchen T., Melkonian M. 1995; Molecular evolutionary analyses of nuclear-encoded small subunit ribosomal RNA identify an independent rhizopod lineage containing the Euglyphina and the Chlorarachniophyta. J Eukaryot Microbiol 42:65–69 [CrossRef]
    [Google Scholar]
  6. Bovee E. C. 1985; Class Filosea Leidy, 1879. In An Illustrated Guide to the Protozoa pp 228–245Edited by Lee J. J., Hutner S. H., Bovee E. C. Lawrence, KS: Society of Protozoologists;
    [Google Scholar]
  7. Bruno W. J., Socci N. D., Halpern A. L. 2000; Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol 17:189–197 [CrossRef]
    [Google Scholar]
  8. Bulman S. R., Kühn S. F., Marshall J. W., Schnepf E. 2001; A phylogenetic analysis of the SSU rDNA from members of the Plasmodiophorida and Phagomyxida. Protist 152:43–51 [CrossRef]
    [Google Scholar]
  9. Burki F., Berney C., Pawlowski J. 2002; Phylogenetic position of Gromia oviformis Dujardin inferred from nuclear-encoded small subunit ribosomal DNA. Protist 153:251–260 [CrossRef]
    [Google Scholar]
  10. Cavalier-Smith T. 1998; A revised six-kingdom of life. Biol Rev Camb Philos Soc 73:203–266 [CrossRef]
    [Google Scholar]
  11. Cavalier-Smith T. 2000; Flagellate megaevolution: the basis for Eukaryote diversification. In The Flagellates: Unity, Diversity and Evolution pp 361–390Edited by Leadbeater B. S. C., Green J. C. London: Taylor & Francis;
    [Google Scholar]
  12. Cavalier-Smith T., Chao E. E. 1996/7; Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid Amoebae. Arch Protistenkd 147:227–236
    [Google Scholar]
  13. Cramer P., Bushnell D. A., Kornberg R. D. 2001; Structural basis of transcription: RNA polymerase II at 2·8 angstrom resolution. Science 292:1863–1876 [CrossRef]
    [Google Scholar]
  14. Dacks J. B., Marinets A., Ford Doolittle W., Cavalier-Smith T., Logsdon J. M. Jr 2002; Analyses of RNA polymerase II genes from free-living protists: phylogeny, long branch attraction, and the eukaryotic big bang. Mol Biol Evol 19:830–840 [CrossRef]
    [Google Scholar]
  15. Fast N. M., Kissinger J. C., Roos D. S., Keeling P. J. 2001; Nuclear-encoded, plastid-targeted genes suggest a common origin for apicomplexa and dinoflagellates plastids. Mol Biol Evol 18:418–426 [CrossRef]
    [Google Scholar]
  16. Felsenstein J. 1993 phylip (Phylogeny Inference Package) Department of Genetics, University of Washington; Seattle, USA:
    [Google Scholar]
  17. Harper J. T., Keeling P. J. 2003 Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids Mol Biol Evol MBE Advance Access; http://dx.doi.org/10.1093/molbev/msg195
    [Google Scholar]
  18. Hedley R. H. 1958; Confusion between Gromia oviformis and Allogromia ovoidea . Nature 182:1391–1392 [CrossRef]
    [Google Scholar]
  19. Hirt R. P., Logsdon J. M. Jr, Healy B., Dorey M. W., Doolittle W. F., Embley T. M. 1999; Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci U S A 96:580–585 [CrossRef]
    [Google Scholar]
  20. Keeling P. J. 2001; Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home? Mol Biol Evol 18. 1551–1557 [CrossRef]
  21. Keeling P. J., Fast N. M. 2002; Microsporidia: biology and evolution of highly reduced intracellular parasites. Annu Rev Microbiol 56:93–116 [CrossRef]
    [Google Scholar]
  22. Keeling P. J., Deane J. A., McFadden G. I. 1998; The phylogenetic position of alpha- and beta-tubulins from the Chlorarachnion host and Cercomonas (Cercozoa). J Eukaryot Microbiol 45:561–570 [CrossRef]
    [Google Scholar]
  23. Keeling P. J., Deane J. A., Hink-Schauer C., Douglas S. E., Maier U.-G., McFadden G. I. 1999; The secondary endosymbiont of the cryptomonad Guillardia theta contains alpha-, beta-, and gamma-tubulin genes. Mol Biol Evol 16:1308–1313 [CrossRef]
    [Google Scholar]
  24. Klenk H.-P., Zillig W., Lanzendörfer M., Grampp B., Palm P. 1995; Location of protist lineages in a phylogenetic tree inferred from sequences of DNA-dependent RNA polymerases. Arch Protistenkd 145:221–230 [CrossRef]
    [Google Scholar]
  25. Kühn S., Lange M., Medlin L. K. 2000; Phylogenetic position of Cryothecomonas inferred from nuclear-encoded small subunit ribosomal RNA. Protist 151:337–345 [CrossRef]
    [Google Scholar]
  26. Meisterfeld R., Holzmann M., Pawlowski J. 2001; Morphological and molecular characterization of a new terrestrial allogromiid species: Edaphoallogromia australica gen. et spec. nov. (Foraminifera) from Northern Queensland (Australia). Protist 152185–192 [CrossRef]
    [Google Scholar]
  27. Patterson D. J., Simpson A. G. B., Rogerson A. 2000; Amoebae of uncertain affinities. In An Illustrated Guide to the Protozoa , 2nd edn. pp 804–827Edited by Lee J. J., Leedale G. F., Bradbury P. Lawrence, KS: Society of Protozoologists;
    [Google Scholar]
  28. Pawlowski J., Bolivar I., Guiard-Maffia J., Gouy M. 1994; Phylogenetic position of the Foraminifera inferred from LSU rRNA gene sequences. Mol Biol Evol 11:929–938
    [Google Scholar]
  29. Pawlowski J., Bolivar I., Fahrni J. F., Cavalier-Smith T., Gouy M. 1996; Early origin of Foraminifera suggested by SSU rRNA gene sequences. Mol Biol Evol 13:445–450 [CrossRef]
    [Google Scholar]
  30. Pawlowski J., Bolivar I., Fahrni J. F., de Vargas C., Gouy M., Zaninetti L. 1997; Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record. Mol Biol Evol 14:498–505 [CrossRef]
    [Google Scholar]
  31. Pawlowski J., Bolivar I., Fahrni J. F., de Vargas C., Bowser S. S. 1999; Molecular evidence that Reticulomyxa filosa is a freshwater naked foraminifer. J Eukaryot Microbiol 46:612–617 [CrossRef]
    [Google Scholar]
  32. Philippe H., Adoutte A. 1998; The molecular phylogeny of eukaryotes: solid facts and uncertainties. In Evolutionary Relationships Among Protozoa pp 25–56Edited by Coombs H., Vickerman K., Sleigh M. A., Warren A. London: Chapman & Hall;
    [Google Scholar]
  33. Sogin M. 1997; History assignment: when was the mitochondrion founded?. Curr Opin Genet Dev 7:792–799 [CrossRef]
    [Google Scholar]
  34. Stiller J. W., Hall B. D. 1997; The origin of red algae: implications for plastid evolution. Proc Natl Acad Sci U S A 94:4520–4525 [CrossRef]
    [Google Scholar]
  35. Stiller J. W., Hall B. D. 2002; Evolution of the RNA polymerase II C-terminal domain. Proc Natl Acad Sci U S A 99:6091–6096 [CrossRef]
    [Google Scholar]
  36. Stiller J. W., Riley J., Hall B. D. 2001; Are red algae plants? A critical evaluation of three key molecular data sets. J Mol Evol 52:527–539 [CrossRef]
    [Google Scholar]
  37. Strimmer K., von Haeseler A. 1996; Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964–969 [CrossRef]
    [Google Scholar]
  38. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
    [Google Scholar]
  39. Wylezich C., Meisterfeld R., Meisterfeld S., Schlegel M. 2002; Phylogenetic analyses of small subunit ribosomal RNA coding regions reveal a monophyletic lineage of euglyphid testate amoebae (Order Euglyphida). J Eukaryot Microbiol 49:108–118 [CrossRef]
    [Google Scholar]
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