Journal of Molecular Evolution

, Volume 32, Issue 1, pp 53–63 | Cite as

A molecular phylogeny of dinoflagellate protists (Pyrrhophyta) inferred from the sequence of 24S rRNA divergent domains D1 and D8

  • Guy Lenaers
  • Christopher Scholin
  • Yvonne Bhaud
  • Danielle Saint-Hilaire
  • Michel Herzog


The sequence of two divergent domains (D1 and D8) from dinoflagellate 24S large subunit rRNA was determined by primer extension using total RNA as template. Nucleotide sequence alignments over 401 bases have been analyzed in order to investigate phylogenetic relationships within this highly divergent and taxonomically controversial group of protists of the division Pyrrhophyta. Data are provided confirming that dinoflagellates represent a monophyletic group. For 11 out of the 13 investigated laboratory grown species, an additional domain (D2) could not be completely sequenced by reverse transcription because of a hidden break located near its 3′-terminus. Two sets of sequence alignments were used to infer dinoflagellate phylogeny. The first [199 nucleotides (nt)] included conservative sequences flanking the D1 and D8 divergent domains. It was used to reconstruct a broad evolutionary tree for the dinoflagellates, which was rooted usingTetrahymena thermophila as the outgroup. To confirm the tree topology, and mainly the branchings leading to closely related species, a second alignment (401 nt) was considered, which included the D1 and D8 variable sequences in addition to the more conserved flanking regions. Species that showed sequence similarities with other species lower than 60% on average (Knuc values higher than 0.550) were removed from this analysis. A coherent and convincing evolutionary pattern was obtained for the dinoflagellates, also confirmed by the position of the hidden break within the D2 domain, which appears to be group specific. The reconstructed phylogeny indicates that the early emergence ofOxyrrhis marina preceded that of most Peridiniales, a large order of thecate species, whereas the unarmored Gymnodiniales appeared more recently, along with members of the Prorocentrales characterized by two thecal plates. In addition, the emergence of heterotrophic species preceded that of photosynthetic species. These results provide new perspectives on proposed evolutionary trees for the dinoflagellates based on morphology, biology, and fossil records.

Key words

Dinoflagellates Molecular phylogeny Large subunit RNA Divergent domains Direct RNA sequencing 


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  1. Ausubel FM, Brent R, Kingston RE, Moore DD, Siedman JG, Smith JA, Struhl K (1987) Current protocols in molecular biology, vol. 1. Wiley Interscience, New YorkGoogle Scholar
  2. Baroin A, Perasso R, Qu LH, Brugerolle G, Bachellerie JP, Adoutte A (1988) Partial phylogeny of the unicellular eukaryotes based on rapid sequencing of a portion of 28S ribosomal RNA. Proc Natl Acad Sci USA 85:3474–3478Google Scholar
  3. Bischoff H, Bold H (1963) Phycological studies IV. Some soil algae from Enchanted Rock and related algal species. University of Texas Publications, no. 6318Google Scholar
  4. Bujak J, Williams G (1981) The evolution of dinoflagellates. Can J Bot 59:2077–2087Google Scholar
  5. Campbell DA, Kubo K, Clark CG, Boothroyd JC (1987) Precise identification of cleavage sites involved in the unusual processing of trypanosome ribosomal RNA. J Mol Biol 196:113–124CrossRefPubMedGoogle Scholar
  6. Cedergren R, Gray MW, Abel Y, Sankoff D (1988) The evolutionary relationships among known life forms. J Mol Evol 28:98–112PubMedGoogle Scholar
  7. de Lanversin G, Jacq B (1983) Séquence de la région de coupure centrale du précurseur de l'ARN ribosomique 26S de drosophile. CR Acad Sci Ser III 296:1041–1044Google Scholar
  8. de Lanversin G, Jacq B (1989) Sequence and secondary structure of the central domain ofDrosophila 26S rRNA: a universal model for the central domain of the large rRNA containing the region in which the central break may happen. J Mol Evol 28:403–417PubMedGoogle Scholar
  9. Dodge JD (1984) Dinoflagellate taxonomy. In: Spector DL (ed) Dinoflagellates. Academic Press, New York, pp. 17–42Google Scholar
  10. Dörhöfer G, Davies E (1980) Evolution of archeopyle and tabulation in rhaetogonyaulacinean dinoflagellate cysts. R Ont Mus Life Sci Misc Publ, pp 1–91Google Scholar
  11. Eaton G (1980) Nomenclature and homology in peridinialean dinoflagellate patterns. Palaeontology 23:667–688Google Scholar
  12. Eckenrode VK, Arnold J, Meagher RB (1985) Comparison of the nucleotide sequence of soybean 18S rRNA with the sequences of other small-subunit rRNAs. J. Mol Evol 21:259–269Google Scholar
  13. Engberg J, Nielsen H, Lenaers G, Murayama O, Fujitani H, Higashinakagawa T (1990) Comparison of primary and secondary 26S ribosomal RNA structures in twoTetrahymena species: evidence for a strong evolutionary and structural constraint in expansion segments. J Mol Evol 30:514–521PubMedGoogle Scholar
  14. Fitch WM (1981) A non-sequential method for constructing trees and hierarchical classifications. J Mol Evol 18:30–37CrossRefPubMedGoogle Scholar
  15. Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155:279–284PubMedGoogle Scholar
  16. Gill LL, Hardman N, Chappell L, Qu LH, Nicoloso M, Bachellerie JP (1988) Phylogeny onOnchocerca volvulus and related species deduced from rRNA sequence comparison. Mol Biochem Parasitol 28:69–76PubMedGoogle Scholar
  17. Goodman DK (1987) Dinoflagellate cysts in ancient and modern sediments. In: Taylor JFR (ed) The biology of dinoflagellates. Bot Monog 21:649–722Google Scholar
  18. Gouy M, Li WH (1989a) Phylogenetic analysis based on ribosomal RNA sequences supports the archaebacterial tree rather than the eocyte tree. Nature 339:145–149CrossRefPubMedGoogle Scholar
  19. Gouy M, Li WH (1989b) Molecular phylogeny of the kingdoms Animalia, Plantae, and Fungi. Mol Biol Evol 6:109–122PubMedGoogle Scholar
  20. Guillard R, Ryther J (1963) Studies on marine planktonic diatoms. I.Cyclotella nana Husted andDetonula confervacea Cleve. Gran. Can J Microbiol 8:229–239Google Scholar
  21. Gutell RR, Fox EF (1988) A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res 16(suppl):r175-r269PubMedGoogle Scholar
  22. Hassouna N, Michot B, Bachellerie JP (1984) The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes. Nucleic Acids Res 12:3563–3583PubMedGoogle Scholar
  23. Herzog M, Soyer MO (1981) Distinctive features of dinoflagellate chromatin. Absence of nucleosomes in a primitive speciesProrocentrum micans. Eur J Cell Biol 23:295–302PubMedGoogle Scholar
  24. Kimura M (1968) Evolutionary rate at the molecular level. Nature 217:624–626PubMedGoogle Scholar
  25. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  26. Lane D, Pace B, Olsen G, Sthal D, Sogin M, Pace N (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955–6959PubMedGoogle Scholar
  27. Leffers H, Kjems J, Ostergaard L, Larsen N, Garret R (1987) Evolutionary relationships amongst archaebacteria. A comparative study of 23S ribosomal RNAs of a sulphur-dependant extreme thermophile, an extreme halophile and a thermophilic methanogen. J Mol Biol 195:43–61PubMedGoogle Scholar
  28. Lenaers G, Nielsen H, Engberg J, Herzog M (1988) The secondary structure of large subunit rRNA divergent domains, a marker for protist evolution. BioSystems 21:215–222CrossRefPubMedGoogle Scholar
  29. Lanaers G, Maroteaux L, Michot B, Herzog M (1989) Dinoflagellates in evolution. A molecular phylogenetic analysis of large-subunit ribosomal RNA. J Mol Evol 29(1):40–51PubMedGoogle Scholar
  30. Loeblich AR (1976) Dinoflagellate evolution: speculation and evidence. J Protozool 23:13–28PubMedGoogle Scholar
  31. Loeblich AR (1984) Dinoflagellate evolution. In: Spector DL (ed) Dinoflagellates. Academic, New York, pp 481–522Google Scholar
  32. Maniatis T, Fritsch E, Sambrook J (1982) Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, p 545Google Scholar
  33. Michot B, Bachellerie JP (1987) Comparisons of large subunit rRNAs reveal some eukaryote specific elements of secondary structure. Biochemie 69:11–23CrossRefGoogle Scholar
  34. Michot B, Hassouna N, Bachellerie JP (1984) Secondary structure of mouse 28S rRNA and general models for the folding of the large RNA in eukaryotes. Nucleic Acids Res 12:4259–4279PubMedGoogle Scholar
  35. Morrill LC, Loeblich AR (1981) A survey of body scales in dinoflagellates and a revision ofCachonina andHeterocapsa. J Phycol 16(suppl):29Google Scholar
  36. Mouches C, Pauplin Y, Agarwal M, Lemieux L, Herzog M, Abadon M, Beyssat-Arnaouty V, Hyrien O, de Saint Vincent BR, Georghiou GP, Pasteur N (1990) Characterization of amplification core and esterase B1 gene responsible for insecticide resistance inCulex. Proc Natl Acad Sci USA 87:2574–2578PubMedGoogle Scholar
  37. Perasso R, Baroin A, Qu LH, Bachellerie JP, Adoutte A (1989) Origin of the algae. Nature 339:142–144CrossRefPubMedGoogle Scholar
  38. Provasoli L (1963) Growing marine seaweeds. Proc Int Seaweed Symp 4:9–17Google Scholar
  39. Qu LH, Michot B, Bachellerie JP (1983) Improved methods for structure probing in large RNAs: a rapid heterologous sequencing approach is coupled to the direct mapping of nuclease accessible sites. Implication to the 5′ terminal domains of eukaryotic 28S rRNA. Nucleic Acids Res 17:5903–5920Google Scholar
  40. Qu LH, Hardman N, Gill LL, Chappell L, Nicoloso M, Bachellerie JP (1986) Phylogeny of helminths determined by rRNA sequence comparison. Mol Biochem Parasitol 20:93–99PubMedGoogle Scholar
  41. 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 28:113–124PubMedGoogle Scholar
  42. Rizzo PJ (1987) Biochemistry of the dinoflagellate nucleus. In: Taylor FJR (ed) The biology of dinoflagellates. Bot Monogr 21:143–173Google Scholar
  43. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  44. Sournia A (1984) Classification et nomenclature de divers dinoflagellés marins (classe des Dinophyceae). Phycologia 23: 345–355Google Scholar
  45. Sournia A (1986) Dinophyceae. In: Sournia A (ed) Atlas du phytoplancton marin, vol 1. Edition du CNRS, Paris, 219 pGoogle Scholar
  46. Spencer DF, Collings JC, Schnare MN, Gray MW (1987) Multiple spacer sequence in the nuclear large subunit ribosomal RNA gene ofCrithidia fasciculata. EMBO J 6:1063–1071Google Scholar
  47. Starr R (1964) The culture collection of algae at Indiana University. Am J Bot 51:1013–1044Google Scholar
  48. Studier JA, Keppler KJ (1988) A note on the neighbor-joining algorithm of Saitou and Nei. Mol Biol Evol 6:729–731Google Scholar
  49. Taylor F (1980) On dinoflagellate evolution. Biosystems 13: 65–108CrossRefPubMedGoogle Scholar
  50. Taylor F (1987) Taxonomy and classification. In: Taylor F (ed) The biology of dinoflagellates. Bot Monogr 21:723–731Google Scholar
  51. Tuttle R, Loeblich A (1975) An optimal growth medium for the dinoflagellateCryptecodinium cohnii. Phycologia 14(1): 1–8Google Scholar
  52. Vernet G, Sala-Rovira M, Maeder M, Jacques F, Herzog M (1990) Electrophoretic and DNA-binding properties of the major basic nuclear proteins from the histone-less eukaryoteCrypthecodinium cohnii (Pyrrhophyta). Biochim Biophys Acta 1048:281–289PubMedGoogle Scholar

Copyright information

© Springer-Verlag New York Inc. 1991

Authors and Affiliations

  • Guy Lenaers
    • 1
  • Christopher Scholin
    • 2
  • Yvonne Bhaud
    • 1
  • Danielle Saint-Hilaire
    • 1
  • Michel Herzog
    • 1
  1. 1.Département de Biologie Cellulaire et Moléculaire, Laboratoire AragoUniversité de Paris VI, CNRS UA 117Banyuls-sur-MerFrance
  2. 2.Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleUSA

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