Phylogeny of ultra-rapidly evolving dinoflagellate chloroplast genes: A possible common origin for sporozoan and dinoflagellate plastids

Journal of Molecular Evolution

Volumn 51, Issue 1, 2000, Pages 26-40

  Zhang, Zhaoduo ^a   Green, Beverley R ^a   Cavalier Smith, Thomas ^a,b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Alveolates; Chloroplast; Chromist; Dinoflagellate; Mutation pressure; Phylogeny; PsbA; Red alga; Ribosomal RNA; Sporozoa

Indexed keywords

ARTICLE; CHLOROPLAST; DINOFLAGELLATE; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOME; NONHUMAN; PHYLOGENY; PLASTID; RED ALGA;

ALGAE; ALVEOLATA; AMPHIDINIUM CARTERAE; APICOMPLEXA; CILIOPHORA; DINOPHYCEAE; HETEROCAPSA NIEI; HETEROCAPSA PYGMAEA; HETEROCAPSA ROTUNDATA; HETEROCAPSA TRIQUETRA; INVERTEBRATA; PROTOCERATIUM RETICULATUM; PROTOZOA; RHODOPHYTA; SCRIPPSIELLA TROCHOIDEA; SPOROZOA; THORACOSPHAERA HEIMII;

EID: 0033929166     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002390010064     Document Type: Article

References (61)

1. Ayala FJ (1999) Molecular clock mirages. BioEssays 21:71-75
2. Blanchard JL, Hicks JS (1999) The non-photosynthetic plastid in malarial parasites and other apicomplexans is derived from outside the green plastid lineage. J Eukaryot Microbiol 46:367-375
3. Boer PH, Gray MW (1988) Scrambled ribosomal RNA gene pieces in Chlamydomonas reinhardtii mitochondrial DNA. Cell 55:399-411
4. Cavalier-Smith T (1982) The origins of plastids. Biol J Linn Soc 17: 289-306
5. Cavalier-Smith T (1991) Cell diversification in heterotrophic flagellates. In: Patterson DJ, Larsen J (eds) The biology of free living heterotrophic flagellates. Oxford University Press, Oxford. pp 113-131
6. Cavalier-Smith T (1993a) Kingdom Protozoa and its 18 phyla. Microbiol Rev 57:953-994
7. Cavalier-Smith T (1993b) Evolution of the eukaryotic genome. In: Broda P, Oliver SG, Sims P (eds) The eukaryotic genome. Cambridge University Press, Cambridge. pp 333-385
8. Cavalier-Smith T (1998) A revised six-kingdom system of life. Biol Rev 73:203-266
9. Cavalier-Smith T (1999) Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J Eukaryot Microbiol 46:347-366
10. Cavalier-Smith T (2000) Membrane heredity and early chloroplast evolution. Tr Pl Sci 5:174-182
11. Chesnick JM, Kooistra WH, Wellbrock U, Medlin LK (1997) Ribosomal RNA analysis indicates a benthic pennate diatom ancestry for the endosymbionts of the dinoflagellates Peridinium foliaceum and Peridinium balticum (Pyrrhophyta). J Euk Microbiol 44:314-320
12. Delwiche CF (1999) Tracing the thread of plastid diversity through the tapestry of life. Am Nat 154:S164-S177
13. Dodge JD (1975) A survey of chloroplast ultrastructure in Dinophyceae. Phycologia 14:253-263
14. Douglas SE, Murphy CA, Spencer DF, Gray MW (1991) Cryptomonad algae are evolutionary chimeras of two phylogenetically distinct unicellular eukaryotes. Nature 350:148-151
15. Feagin JE (1992) The 6-kb element of Plasmodium falciparum encodes mitochondrial cytochrome genes. Mol Biochem Parasitol 52:145-148
16. Felsenslein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401-410
17. Felsenstein J (1993) Phylip (phylogeny inference package) version 3.57c. Distributed by the author, Department of Genetics, University of Washington, Seattle, WA
18. Gajadhar AA, Marquardt WC, Hall R, Gunderson J, Ariztia-Carmona EV, Sogin ML (1991) Ribosomal RNA sequences of Sarcocystis muris, Theileria annulata and Crypthecodinium cohnii reveal evolutionary relationships among apicomplexans, dinoflagellates and ciliates. Mol Biochem Parasitol 45:147-154
19. Gibbs SP (1981) The chloroplasts of some groups of algae may have evolved from endosymbiotic eukaryotic algae. Ann NY Acad Sci 361:193-207
20. Gunderson JH, Goss SH, Coats DW (1999) The phylogenetic position of Amoebophrya sp. infecting Gymnodinium sanguineum. J Eukaryot Microbiol 46:194-197
21. Hillis DM, Huelsenbeck JP, Cunningham CW (1994) Application and accuracy of molecular phylogenies. Science 264:671-677
22. Inagaki Y, Ehara M, Watanabe KI, Hayashi-Ishimaru Y, Ohama T (1998) Directionally evolving genetic code: the UGA codon from stop to tryptophan in mitochondria. J Mol Evol 47:378-384
23. Jeffrey SW et al. (1975) Chloroplast pigment patterns in dinoflagellates. J Phycol 111:374-384
24. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
25. Köhler S, Delwiche CF, Denny PW, Tilney LG, Webster P, Wilson RJ, Palmer JD, Roos DS ( 1997) A plastid of probable green algal origin in apicomplexan parasites. Science 275:336-342
26. Lockhart PJ, Steel MA, Hendy MD, Penny D (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol 11:605-612
27. Lockhart PJ, Larkum AWD, Steel MA, Waddell PJ, Penny D (1996) Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc Natl Acad Sci USA 93: 1930-1934
28. Martin W, Stoebe B, Goremykin V, Hansmann S, Hasegawa M, Kowallik KV (1998) Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393:162-165
29. Maslov DA, Avila HA, Lake JA, Simpson L (1994) Evolution of RNA editing in kinetoplastid protozoa. Nature 368:694
30. McFadden GI, Waller RF (1997) Plastids in parasites of humans. BioEssays 19:1033-1040
31. McFadden GI, Gilson PR, Hofmann CJ, Adcock GJ, Maier UG (1994) Evidence that an amoeba acquired a chloroplast by retaining part of an engulfed eukaryotic alga. Proc Natl Acad Sci USA 91:3690-3694
32. Medlin LK, Cooper A, Hill C, Wrieden S, Wellbrock U (1995) Phylogenetic position of the Chromista plastids based on small subunit rRNA coding regions. Curr Genet 28:560-565
33. Norman JE, Gray MW (1997) The cytochrome oxidase subunit 1 gene (coxl) from the dinoflagellate, Crypthecodinium cohnii. FEBS Lett 413:333-338
34. Olsen GJ (1987) Earliest phylogenetic branching: comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harbor Symp Quant Biol 52:825-837
35. Olsen GJ, Matsuda H, Hagstrom R, Overbeek R (1994) fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comp App Biosci 10:41-48
36. Palmer JD (1985) Comparative organization of chloroplast genomes. Ann Rev Genet 19:325-354
37. Palmer JD (1992) Green ancestry of malarial parasites? Curr Biol 2: 318-320
38. Palmer JD, Delwiche CF (1998) The origin and evolution of plastids and their genomes. In: Soltis DE, Soltis PS, Doyle JJ (eds) Molecular systematics of plants II. Kluwer, Norwall, MA, pp 375-409
39. Philippe H, Laurent J (1999) How good are deep phylogenetic trees? Curr Opin Genet Dev 8:616-623
40. Pritchard AE, Seilhamer JJ, Mahalingam R, Sable CL, Venuti SE (1990) Nucleotide sequence of the mitochondrial genome of Paramecium. Nucleic Acids Res 18:173-180
41. Reece KS, Siddall ME, Burreson EM, Graves JE (1997) Phylogenetic analysis of Perkinsus based on actin gene sequences. J Parasitol 83:417-423
42. Reith M (1995) Molecular biology of rhodophyte and chromophyte plastids. Ann Rev Plant Physiol Plant Mol Biol 46:549-575
43. Saunders GW, Hill DRA, Sexton JP, Andersen RA (1997) Small-subunit ribosomal RNA sequences from selected dinoflagellates: testing classical evolutionary hypotheses with molecular systematic methods. Plant Syst Evol [Suppl] 11:237-259
44. Schnepf E, Elbrächter M (1988) Cryptophycean-like double membrane-bound chloroplast in the dinoflagellate, Dinophysis Ehrenb: evolutionary phylogenetic and toxicological implications. Botanica Acta 101:196-203
45. Smith SW, Overbeek R, Woese CR, Gilbert W, Gillevet PM (1994) The genetic data environment an expandable GUI for multiple sequence analysis. Comp App Biosci 10:671-675
46. Stoebe B, Kowallik KV (1999) Gene-cluster analysis in chloroplast genomics. Trends Genet 15:344-347
47. Strimmer K, von Haeseler A (1996) Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964-969
48. Sugiura M (1995) The chloroplast genome. Essays Biochem 30:49-57
49. Swofford DL (1999) Phylogenetic analysis using parsimony (and other methods) (PAUP* 4.0b) (test version). Sinauer, Sunderland (Massachusetts)
50. Takishita K, Uchida A (1999) Molecular cloning and nucleotide sequence analysis of psbA from the dinoflagellates: origin of the dinoflagellate plastid. Phycol Res 47:207-216
51. Tengs T, Dahlberg OJ, Shalchian-Tabrizi K, Delwiche C, Klaveness D, Rudi K, Jakobsen KS (2000) Dinoflagellates of tertiary origin - the haptophyte origin of 19′' hexanoyl-fucoxanthin containing chloroplasts. Mol Biol Evol (in press)
52. Tunnel M, Otis C, Lemieux C (1999a) The complete chloroplast DNA sequence of the green alga Nephroselmis olivarea: insights into the architecture of ancestral chloroplast genomes. Proc Natl Acad Sci USA 96:10248-10253
53. Turmel M, Lemieux C, Burger G, Lang BF, Otis C, Plante I, Gray MW (1999b) The complete mitochondrial DNA sequences of Nephroselmis olivocea and Pedinomonas minor: two radically different evolutionary patterns within green algae. Plant Cell 11:1717-1729
54. Van de Peer Y, de Wachter R (1994) TREECON for windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comp Appl Biosci 10:569-570
55. Van de Peer Y, Van de Auwera G, De Wachter R (1996) The evolution of stramenopiles and alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA. J Mol Evol 42:201-210
56. Watanabe MM, Suda S, Inouye I, Sawaguchi T, Chihara M (1990) Lepidodinium viride gen sp. nov. (Gymnodiniales, Dinophyta), a green dinoflagellate with chlorophyll a-and b-containing endosymbiont. J Phycol 26:741-751
57. Williamson DH, Gardner MJ, Preiser P, More DJ, Rangachari K, Wilson RJM (1994) The evolutionary origin of the 35 kb circular DNA of Plasmodium falciparum: new evidence supports a possible rhodophyte ancestry. Mol Gen Genet 243:249-252
58. Wilson RJM, Denny PW, Preiser PR, Rangachari K, Roberts K, Roy A, Whyte A, Strath M, Moore DJ, Moore PW, Williamson DH (1996) Complete gene map of the plastid like DNA of the malaria parasite Plasmodium falciparum. J Mol Biol 261:155-172
59. Yang Z (1996) Among-site rate variation and its impact on phylogenetic analyses. Tree 11:367-372
60. Zhang Z, Green BR, Cavalier-Smith T (1999) Single gene circles in clinoflagellate chloroplast genomes. Nature 400:155-159
61. Zhu G, Marchewka MJ, Keithly JS (2000) Cryptosporidium parvum appears to lack a plastid genome. Microbiology 146:315-321