Cryptomonad nuclear and nucleomorph 18s rrna phylogeny

European Journal of Phycology

Volumn 31, Issue 4, 1996, Pages 315-328

  Cavalier Smith, T ^a   Couch, J A ^a,c   Thorsteinsen, K E ^a   Gilson, P ^b   Deane, J A ^b   McFadden, G I ^b   Hill, D R A ^b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Chromista; Endosymbiosis; Geminigera; Komma caudata; Nucleomorphs; Plastid origins; Rhinomonas pauca; Rhodomonas abbreviata; Rrna phylogeny; Storeatula major

Indexed keywords

ABBREVIATA; ALGAE; CAUDATA; CHILOMONAS; CHLORARACHNION; CHROMISTA; CHROOMONAS; CRYPTOMONAS; CRYPTOPHYTA; GEMINIGERA; GONIOMONAS; GUILLARDIA; HANUSIA PHI; HAPTOPHYCEAE; KOMMA; KOMMA CAUDATA; RHINOMONAS; RHINOMONAS PAUCA; RHODOMONAS ABBREVIATA; RHODOPHYTA; STOREATULA; STOREATULA MAJOR; STRAMENOCHROMA;

EID: 0002394924     PISSN: 09670262     EISSN: 14694433     Source Type: Journal    
DOI: 10.1080/09670269600651541     Document Type: Article

References (89)

1. Bhattacharya, D. & MEDLIN, L. (1995). The phylogeny of plastids: a review based on comparisons of small-subunit ribosomal RNA coding regions. J. Phycol, 31: 489-498.
2. Bhattacharya, D. Helmchen, T. Bibeau, C. & Melkonian, M. (1995). Comparisons of nuclear-encoded small-subunit ribosomal RNAs reveal the evolutionary position of the Glaucocystophyta. Mol. Biol. Evol, 12: 415-420.
3. Bird, C.J. & MCLACHLAN, J.L. (1992). Seaweed flora of the Maritimes. 1. Rhodophyta: The Red Algae. Biopress, Bristol.
4. Cavalier-Smith, T. (1982). The origins of plastids. Biol. J. Linn. Soc. 17:289-306.
5. CAVALIER-SMITH, T. (1986). The kingdom Chromista: origin and systematics. In Progress in Phycological Research vol. 3 (Round, F. & Chapman, D.J. editors), 309-347. Biopress, Bristol.
6. CAVALIER-SMITH, T. (1989). The kingdom Chromista. In The Chromophyte Algae: Problems and Perspectives (Green, J.C. Leadbetter, B.S.C. & Diver, W.L. editors), 381-407. Clarendon Press, Oxford.
7. CAVALIER-SMITH, T. (1993a). Kingdom Protozoa and its 18 phyla. Microbiol. Rev. 57: 953-994.
8. CAVALIER-SMITH, T. (1993b). Evolution of the eukaryotic genome. In The Eukaryotic Genome (Broda, P. Oliver, S.G. & Sims, P. editors), 333-385. Cambridge University Press, Cambridge.
9. Cavalier-Smith, T. (1994). Origin and relationships of Haptophyta. In The Haptophyte Algae (Green, J.C. & Leadbeatter, B.S.C. editors), 413-435. Clarendon Press, Oxford.
10. CAVALIER-SMITH, T. (1995). Membrane heredity, symbiogenesis, and the multiple origins of algae. In Biodiversity and Evolution (Arai, R. Kato, M. & Doi, Y. editors), 75-114. National Science Museum, Tokyo.
11. CAVALIER-SMITH, T, ALLSOPP, M.T.E.P. & CHAO, E.E. (1994). Chimeric conundra: are nucleomorphs and chromists monophyletic or polyphy-letic? Proc. Natl Acad. Sci. U.S.A. 91: 11368-11372.
12. Cavalier-Smith, T. Chao, E.E. & Allsopp, M.T.E.P. (1995). Ribosomal RNA evidence for chloroplast loss within Heterokonta: pedinellid relationships and a revised classification of ochristan algae. Arch. Protistenk. 145:209-220.
13. Cavalier-Smith, T. Chao, E.E. Thompson, C.E. & Hourihane, S.L. (1996). Oikomonas, a distinctive zooflagellate related to chrysomonads. Arch. Protistenk. 146: 273-279.
14. CHESNICK, J.M. KUGRENS, P. & CATTOLICO, R.A. (1991). The utility of mitochondrial DNA restriction fragment length polymorphisms in cryptomonad phylogenetic assessment. Mol. Mar. Biol. Biotech. 1: 18-26.
15. DOUGLAS, S.E. MURPHY, C.A. SPENCER, D.F. & GRAY, M.W. (1991). Cryptomonad algae are evolutionary chimaeras of two phylogenetically distinct unicellular eukaryotes. Nature, 350: 148-151.
16. Elwood, H.J. Olsen, G.J. & Sogin, M.L. (1985). The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol Biol. Evol, 2: 399-410.
17. Eschbach, S. Hofmann, C.J.B. Maier, U.-G. Sitte, P. & Hansmann, P. (1991). A eukaryotic genome of 660 kb: electrophoretic karyotype of nucleomorph and cell nucleus of the cryptomonad alga, Pyrenomonas salina. Nucleic Acids Res. 19: 1779-1781.
18. Eschbach, S. Wolters, J. & Sitte, P. (1991k). Primary and secondary structure of the nuclear small subunit ribosomal RNA of the cryptomonad Pyrenomonas salina as inferred from the gene sequence: evolutionary implications. J. Mol. Evol, 32: 247-252.
19. Felsenstein, J. (1978). Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool, 27: 401-410.
20. Felsenstein, J. (1993). PHYLIP version 3.5.1. University of Washington, Seattle.
21. FELSENSTEIN, J. & CHURCHILL, G.A. (1996). A hidden Markov model approach to variation among sites in rate of evolution. Mol Biol Evol, 13: 93-104.
22. GILLOTT, M.A. & GIBBS, S.P. (1980). The cryptomonad nucleomorph: its ultrastructure and evolutionary significance. J. Phycol, 16: 558-568.
23. GILSON, P.R. & MCFADDEN, G.I. (1995). The chlorarachniophyte: a cell with two different nuclei and two different telomeres. Chromosoma, 103: 635-641.
24. GLAZER, A.N. & APPELL, G.S. (1977). A common evolutionary origin for the biliproteins of cyanobacteria, Rhodophyta, and Cryptophyta. Fed. Eur. Microbiol. Soc. Microbiol Lett. 1: 113-116.
25. Gleeson, T. & Hillier, L. (1991). A trace display and editing program for data from fluorescence-based sequencing machines. Nucleic Acids Res. 19: 6481-6483.
26. GREENWOOD, A.D. (1974). The Cryptophyta in relation to phylogeny and photosynthesis. Abstracts of the Eight International Congress of Electron Microscopy, Canberra, pp. 566-567.
27. GREENWOOD, A.D. GRIFFITHS, H.B. & SANTORE, U.J. (1977). Chloroplasts and cell compartments in Cryptophyceae. Br. Phycol. J. 12: 119.
28. HANSMANN, P. & ESCHBACH, S. (1990). Isolation and preliminary characterization of the nucleus and the nucleomorph of a cryptomonad, Pyrenomonas salina. Eur. J. Cell Biol, 52: 373-373.
29. Hansmann, P. Falk, H. SCHEER, U. & SITTE, P. (1986). Ultrastructural localization of DNA in two Cryptomonas species by use of a monoclonal DNA antibody. Eur. J, Cell Biol. 52: 373-378.
30. Hill, D.R.A. (1991a). A revised circumscription of Cryptomonas (Cryptophyceae) based on examination of Australian strains. Phycologia, 30:170-188.
31. Hill, D.R.A. (1991b). Chroomonas and other blue-green cryptomonads. J. Phycol, 27: 133-145.
32. Hill, D.R.A. & Rowan, K.S. (1989). The biliproteins of the Cryptophyceae. Phycologia, 28: 455-463.
33. Hill, D.R.A. & Wetherbee, R. (1986). Proteomonas sulcata gen. et sp. nov. (Cryptophyceae), a cryptomonad with two morphologically distinct and alternating forms. Phycologia, 25: 521-543.
34. Hill, D.R.A. & WETHERBEE, R. (1988). The structure and taxonomy of Rhinomonas pauca gen. et sp. nov. (Cryptophyceae). Phycologia, 27: 355-365.
35. Hill, D.R.A. & Wetherbee, R. (1989). A reappraisal of the genus Rhodomonas (Cryptophyceae). Phycologia, 28: 143-158.
36. Hill, D.R.A. & Wetherbee, R. (1990). Guillardia theta gen. et sp. nov. (Cryptophyceae). Can. J. Bot. 68: 1873-1876.
37. IIN, L. & NEI, M. (1990). Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol. Biol. Evol, 7: 82-102.
38. Klaveness, D. (1985). Classical and modern criteria for determining species of Cryptophyceae. Bull Plankton Soc. Japan, 32: 111-128.
39. KLAVENESS, D. (1988). Ecology of the Cryptomonadida: a first review. In Growth and Reproductive Strategies of Freshwater Phytoplanlcton (Sandgren, C.S. editor), 105-133. Cambridge University Press, Cambridge.
40. KUHNER, M.K. & FELSENSTEIN, J. (1994). A simulation comparison of phylo-geny algorithms under equal and unequal evolutionary rates. Mol. Biol Evol, 11: 459-468.
41. Lbblanc, C. Boyen, C. & Goer, S.L. (1995). Organisation of the plastid genome from the rhodophyte Chrondrus crispus (Gigartinales); sequence and phylogeny of the 16S rRNA gene. Eur. J. Phycol, 30: 133-140.
42. Ludwig, M. & Gibbs, S.P. (1985). DNA is present in the nucleomorph of cryptomonads: further evidence that the chloroplast evolved from a eukaryotic endosymbiont. Protoplasma, 12 7: 9-20.
43. LUDWIG, M. & GIBBS, S.P. (1989). Localization of phycoerythrin at the luminal surface of the thylakoid membrane in Rhodomonas lens. J. Cell Biol, 108: 875-884.
44. MAIER, U.-G. HOFMANN, C.J.B. ESCHBACH, S. WOLTERS, J. & IGLOI, G. (1991). Demonstration of nucleomorph-encoded eukaryotic small subunit ribo-somal RNA in cryptomonads. Mol. Gen. Genet. 230: 155-60.
45. MARGULIS, L. & SCHWARTZ, K.V. (1988). Five Kingdoms, 2nd edn. Freeman, New York.
46. MARTIN, W. SOMMERVILLE, C.C. & LOISEAUX-DE GOER, S. (1992). Molecular phylogenies of plastid origins and algal evolution. J. Mol Evol, 35: 385-404.
47. MCFADDEN, G.I. (1993). Second-hand chloroplasts: evolution of cryptomonad algae. Adv. Boi. Res. 19: 189-230.
48. McFadden, G.L & Gilson, P.R. (1995). Something borrowed, something green: lateral transfer of chloroplasts by secondary endosymbiosis. Trends Ecol. Evol, 10: 12-17.
49. MCFADDEN, G.I. GILSON, P.R. & HILL, D.R.A. (1994a). Goniomonas: rRNA sequences indicate that this phagotrophic flagellate is a close relative of the host component of cryptomonads. Eur. J. Phycol, 29: 29-32.
50. McFadden, G.I. Gilson, P.R. & Douglas, S.E. (1994b). The photosynthetic endosymbiont in cryptomonad cells produces both chloroplast and cytoplasmic-type ribosomes. J Cell Sci. 107: 649-657.
51. MCFADDEN, G.L, GILSON, P.R. HOFMANN, C.J.B. ADCOCK, G.J. & MAIER, U.-G. (1994c). Evidence that an amoeba acquired a chloroplast by retaining part of an engulfed eukaryotic alga. Proc. Natl. Acad. Sci. U.S.A. 91: 3690-3694.
52. MCFADDEN, G.I. GILSON, P.R. & WALLER, R.F. (1995). Molecular phylogeny of chlorarachniophytes based on plastid rRNA and rbcL sequences. Arch. Protistenk. 145: 231-239.
53. MCKERRACHER, L. & Gibbs, S.P. (1982). Cell and nucleomorph division in the alga Cryptomonas. Can. J. Bot. 60: 2440-2452.
54. MEDLIN, L. ELWOOD, H.J. STICKEL, S. & SOGIN, M.L. (1988). The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene, 71: 491-498.
55. MORRALL, S. & GREENWOOD, A.D. (1982). Ultrastructure of nucleomorph division in species of the Cryptophyceae and its evolutionary implications. J Cell Sci. 54: 311-318.
56. MORSE, D. SALOIS, P. MARKOVIC, P. & HASTINGS, J.W. (1995). A nuclear-encoded form II RuBisCO in dinoflagellates. Science, 268: 1622-1624.
57. NEI, M. (1991). The relative efficiency of different methods of phylogenetic reconstruction. In Phylogenetic Analyses of DNA Sequences (Miyamoto, M.M. & Cracraft, J. editors), 90-128. Oxford University Press, Oxford.
58. NELISSEN, B. VAN DE PEER, Y. WILMOTTE, A. & DE WACHTER, R. (1995). An early origin of plastids within the cyanobacterial divergence is suggested by evolutionary trees based on complete 16S rRNA sequences. Mol Biol. Evol, 12: 1166-1173.
59. NOVARINO, G. (1991a). Observations on Rhinomonas reticulata comb. nov. and R. reticulata var. eleniana var. nov. (Cryptophyceae), with comments on the genera Pyrenomonas and Rhodomonas. Nord. J. Bot. 11: 243-252.
60. NOVARINO, G. (1991b). Observations on some new and interesting Cryptophyceae. Nord. J. Bot. 11: 599-611.
61. Novarino, G. & Lucas, I.A.N. (1993a). Some proposals for a new classification system of the Cryptophyceae. Bot. J. Linn. Soc. Ill: 3-21.
62. NOVARINO, G. & LUCAS, I.A.N. (1993b). A comparison of some morphological characters in Chroomonas ligulata sp. nov. and C. placoidea sp. nov. (Cryptophyceae). Nord. J. Bot. 13: 585-591.
63. NOVARINO, G. & LUCAS, I.A.N. (1995). A zoological classification system of cryptomonads. Acta Protozool, 34: 173-180.
64. NOVARINO, G. LUCAS, I.A.N. & MORRALL, S. (1994). Observations on the genus Plagioselmis (Cryptophyceae). Cryptogamie, Algol, 15: 87-107
65. OLSEN, G.J. (1987). Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harbor Symp. Quant. Biol. 52: 825-837.
66. OLSEN, G.L. MATSUDA, H. HAGSTROM, R. & OVERBEEK, R. (1994). FastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comp. Appl. Bios. 10: 41-48.
67. PALMER, J.D. (1995). Rubisco rules fall; gene transfer triumphs. BioEssays, 17: 1005-1008.
68. PALMER, J.D. (1996). Rubisco surprises in dinoflagellates. Plant Cell, 8: 343-345.
69. RAGAN, M.A. & GUTELL, R.R. (1995). Are red algae plants? Bot. J. Linn. Soc. 118: 81-105.
70. RAGAN, M.A. BIRD, C.J. RICE, E.L. GUTELL, R.R. MURPHY, C.A. & SINGH, R.K. (1994). A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene. Proc. Natl Acad. Sci. U.S.A. 91: 7276-7280.
71. ROCHAIX, J.-D. MAYFIELD, S. GOLDSCHMIDTCLERMONT, M. & ERICKSON, J. (1988). Molecular biology of Chlamydomonas. In Plant Molecular Biology (C. H. Shaw, editor), 253-275. Oxford University Press, Oxford.
72. ROWAN, R. WHITNEY, S.M. FOWLER, A. & YELLOWLEES, D. (1996). Rubisco in marine symbiotic dinoflagellates: form II enzymes in eukaryotic oxygenic phototrophs encoded by a nuclear multigene family. Plant Cell, 8: 555-564.
73. SANTORE, U.J. (1982a). Comparative ultrastructure of two members of the Cryptophyceae assigned to the genus Chroomonas: with comments on their taxonomy. Arch. Protistenk. 125: 5-29.
74. SANTORE, U.J. (1982b). The distribution of the nucleomorph in the Cryptophyceae. Cell Biol. Int. Rep. 6: 1055-1063.
75. SANTORE, U.J. (1984). Some aspects of the taxonomy in the Cryptophyceae. New Phytol, 98: 627-646.
76. SANTORE, U.J. (1985). A cytological survey of the genus Cryptomonas (Cryptophyceae) with comments on its taxonomy. Arch. Protistenk. 130: 1-52.
77. SANTORE, U.J. (1986). The ultrastructure of Pyrenomonas heteromorpha comb, nov. (Cryptophyceae). Bot. Mar. 29: 75-82.
78. SANTORE, U.J. (1987). A cytological survey of the genus Chroomonas? with comments on the taxonomy of this natural group of the Cryptophyceae. Arch. Protistenk. 134: 83-114.
79. SANTORE, U.J. & LEEDALE, G.F. (1985). Cryptomonadida. In An Illustrated Guide to the Protozoa (Lee, J.J. Hutner, S.H. & Bovee, B.C. editors), 19-22. Society of Protozoologists, Lawrence, Kansas.
80. SEPSENWOL, S. (1973). Leucoplast of the cryptomonad Chilomonas paramecium: evidence for presence of a true plastid in a colorless flagellate. Exp. Cell Res. 76: 395-409.
81. SITTE, P. (1993). Symbiogenetic evolution of complex cells and complex plastids. Eur. J. ProtistoL, 29: 131-143.
82. SMITH, S. WOESE, C.R. GILBERT, W. GILLEVET, P.M. (1994). The genetic data environment and expandable GUI for multiple sequence analysis. Comp. App. Biosci. 10: 671-675.
83. SWOFFORD, D.L. & OLSEN, G.J. (1990). Phylogeny reconstruction. In Molecular Systematics (Hillis, D.M. & Moritz, C. editors), 411-501. Sinauer, Sunderland, Mass.
84. VAN DE PEER, Y. NEEFS, J.-M. DE Rijk, P. DE WACHTER, R. (1993). Evolution of eukaryotes as deduced from small ribosomal subunit RNA sequences. Biochem. System. Ecol, 21: 43-55.
85. VAN DE PEER, Y. RENSING, S.A. MAIER, U.-G. & DE WACHTER, R. (1996). Substitution rate calibration of small subunit rRNA identifies chlorar-achniophyte endosymbionts as remnants of green algae. Proc. Natl. Acad. Sci. U.S.A. 93: 4467-4471.
86. WHATLEY, J.M. JOHN, P. & WHATLEY, F.R. (1979). From extracellular to intracellular: the establishment of mitochondria and chloroplasts. Proc. R. Soc. Lond. B, 204: 165-187.
87. WHITNEY, S.M. SHAW, D.C. & YELLOWLEES, D. (1995). Evidence that some dinoflagellates contain a ribulose-l,5-bisphosphate carboxylase-oxygenase related to that of the alpha proteobacteria. Proc. Natl. Acad. Sci. U.S.A. 259: 271-275.
88. WJNNEPENNINCKX, B. BACKELJAU, T. MACKEY, L. BROOKS, J.M. DE WACHTER, R.D. KUMAR, S. & GAREY, J.R. (1995). 18S rRNA data indicate that Aschelminthes are polyphyletic in origin and consist of at least three distinct clades. Mol. Biol. Evol. 12: 1132-1137.
89. WOESE, C.R. (1987). Bacterial evolution. Microbiol. Rev. 51: 221-271.