Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae

Protist

Volumn 150, Issue 1, 1999, Pages 71-84

  Andersen, Robert A ^a   Van Peer, Yves De ^b,d   Potter, Daniel ^a,e   Sexton, Julianne P ^a   Kawachi, Masanobu ^c,f   LaJeunesse, Todd ^a,g  

^a BIGELOW LABORATORY FOR OCEAN SCIENCES   (United States)

^b UNIVERSITY OF ANTWERP   (Belgium)

^c MARINE BIOTECHNOLOGY INSTITUTE   (Japan)

^d UNIVERSITY OF KONSTANZ   (Germany)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f NATIONAL INSTITUTE FOR ENVIRONMENTAL STUDIES   (Japan)

^g UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE SEQUENCE; PHYLOGENETIC ANALYSIS; RIBOSOMAL RNA; SEQUENCE ALIGNMENT; TAXONOMY; ULTRASTRUCTURE;

ALGAE; CHRYSOPHYCEAE; EUKARYOTA; EUSTIGMATOPHYCEAE; OCHROMONAS TUBERCULATA; PARAPHYSOMONADACEAE; PROTOZOA; SYNURALES;

EID: 0033103941     PISSN: 14344610     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1434-4610(99)70010-6     Document Type: Article

References (110)

1. Agardh CA (1824) Systema algarum. Lund. 312 pp
2. Andersen RA (1982) A light and electron microscopical investigation of Ochromonas sphaerocystis Matvienko (Chrysophyceae): The statospore, vegetative cell and its peripheral vesicles. Phycologia 21:390-398
3. Andersen RA (1985) The flagellar apparatus of the golden alga Synura uvella: four absolute orientations. Protoplasma 128: 94-106
4. Andersen RA (1986) Some new observations on Saccochrysis piriformis Korsh. emend. Andersen (Chrysophyceae). In Kristiansen J, Andersen RA (eds) Chrysophytes: Aspects and Problems. Cambridge Univ. Press, NY pp 107-117
5. Andersen RA (1987) The Synurophyceae classis nov., a new class of algae. Am J Bot 74:337-353
6. Andersen RA (1989a) Absolute orientation of the flagellar apparatus of Hibberdia magna comb. nov. (Chrysophyceae). Nord J Bot 8: 653-669
7. Andersen RA (1989b) The Synurophyceae and their relationship to other golden algae. In Kristiansen J, Cronberg G, Geissler U [eds], Chrysophytes:Developments and Perspectives. Nova Hedwigia Beiheft 95:1-26
8. Andersen RA (1990) The three-dimensional structure of the flagellar apparatus of Chrysosphaerella brevispina (Chrysophyceae) as viewed by high voltage electron microscopy stereo pairs. Phycologia 29:86-97
9. Andersen RA (1991) The cytoskeleton of chromophyte algae. Protoplasma 164:143-159
10. 2 in the Chrysophyceae. J Phycol 19:289-294
11. Andersen RA, Wetherbee R (1992) Microtubules of the flagellar apparatus are active in prey capture of the chrysophycean alga Epipyxis pulchra. Protoplasma 166:1-7
12. Andersen RA, Morton SL, Sexton JP (1997) CCMP - Provasoli-Guillard National Center for Culture of Marine Phytoplankton - List of Strains. J. Phycol. (suppl.) 33 (6): 1-75
13. Andersen RA, Brett RW, Potter D, Sexton JP (1998a) Phylogeny of the Eustigmatophyceae based upon the 18S rRNA gene, with emphasis on Nannochloropsis. Protist149:61-74
14. Andersen RA, Saunders GW, Paskind MP, Sexton JP (1993) Ultrastructure and 18S rRNA gene sequence for Pelagomonas ca/c/o/afa gen. et sp. nov. and the description of a new algal class, the Pelagophyceae classis nov. J. Phycol. 29:701-715
15. Andersen RA, Potter D, Bidigare RR, Latasa M, Rowan K, O'Kelly CJ (1998b) Characterization and phylogenetic position of the enigmatic golden alga Phaeothamnion confervicola: ultrastructure, pigment composition and partial SSU rDNA sequence. J. Phycol. 34: 286-298
16. Andrews HT (1970) Morphology and taxonomy of the euryhaline chrysophyte, Sphaeridothrix compressa. J Phycol 6:133-136
17. Bailey JC, Bidigare RR, Christensen SJ, Andersen RA (1998) Phaeothamniophyceae classis nova: a new lineage of chromophytes based upon photsynthetic pigments, nbcL sequence analysis and ultrastructure. Protist 149: 245-263
18. Beech PL, Wetherbee R (1990) The flagellar apparatus of Mallomonas splendens (Synurophyceae) at interphase and its development during the cell cycle. J Phycol 26:95-111
19. Bhattacharya D, Medlin L, Wainright PO, Ariztia EV, Bibeau C, Stickel SK, Sogin ML (1992) Algae containing chlorophylls a + c are paraphyletic: molecular evolutionary analysis of the Chromphyta. Evolution 46: 1801-1817
20. Bouck GB, Brown DL (1973) Microtubule biogenesis and cell shape in Ochromonas. I. The distribution of cytoplasmic and mitotic microtubules. J Cell Biol 56: 340-359
21. Bourrelly P (1957) Recherches sur les Chrysophycées. Morphologie, Phylogénie, Systématique. Rev. Algol. Mém. Hors. Sér. 1:1-412
22. Bourrelly P (1965) La classification des Chrysophycées: ses problèmes. Rev Algol N.S. 9:56-60
23. Bourrelly P (1968) Les Algues d'Eau Douce. II. Les Algues jaunes et brunes. Société Nouvelle des Éditions Boubée, Paris 438 pp
24. Bourrelly P (1981) Les Algues d'Eau Douce. II. Les Algues jaunes et brunes. Société Nouvelle des Éditions Boubée, (Réimpression revue et augmentée), Paris 517pp
25. Caron DA, Lim EL, Dennett MR, Gast RJ, Kosman C, DeLong, EF (1999) Molecular phylogenetic analysis of the heterotrophic chrysophyte genus Paraphysomonas, and the design of rRNA-targeted oligonucleotide probes for two species. J Phycol 35: (in press)
26. Cavalier-Smith T, Chao EE, Allsopp MTEP (1995) Ribosomal RNA evidence for chloroplast loss within Net-erokonta: pedinellid relationships and a revised classification of ochristan algae. Arch Protistenkd 145: 209-220
27. Cavalier-Smith T, Chao EE, Thomson CE, Hourihane SL (1996) Oikomonas, a distinctive zooflagellate related to chrysomonads. Arch Protistenkd 146: 273-279
28. Cienkowsky L (1870) Über Palmellaceen und einige Flagellaten. Arch. Mikroskop. Anat. 7:421-438
29. Christensen T (1962) Alger. In Böcher TW, Lange MC, Sorensen T (eds) Botanik, Bd. 2. Systematisk Botanik Nr. 2. Munksgaard, Copenhagen, pp 1-178
30. Daugbjerg N, Andersen RA(1997a) Phylogenetic analyses of the rbcL sequences from haptophytes and heterokont algae suggest their chloroplasts are unrelated. Mol BiolEvol 14:1242-1251
31. Daugbjerg N, Andersen RA (1997b) A molecular phylogeny of the heterokont algae based on analyses of chloroplast-encoded rbcL sequence data. J Phycol 33:1031-1041
32. Dop AJ (1978) Systematics and morphology of Chrysochaete brittanica (Godward) Rosenberg and Phaeoplaca thallosa Chodat (Chrysophyceae). Acta Bot Neerl 27: 35-60
33. Dop AJ, Van Oers F (1979) On the taxonomic position of Phaeobotrys solitaria Ettl (Chrysophyceae). Acta Bot Neerl 26:459-466
34. Dop AJ, Vroman M (1976) Observations on some interesting freshwater algae from The Netherlands. Acta Bot Neerl 25: 321-328
35. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11-15
36. Ehrenberg CG (1834) Dritter Beitrag zur Erkenntinis grosser Organisation in der Richtung des kleinsten Raumes. Abhandl Königl Akad Wiss Berlin (1833): 145-336
37. Ehrenberg CG (1838) Die Infusionsthierchen als vollkommene Organismen. Voss, Leipzig
38. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-91
39. Felsenstein J (1994) Phylogeny Inference Package (PHYLIP). Version 3.6. Distributed by the author, Department of Genetics, University of Washington, Seattle
40. Fritsch FE (1935) The Structure and Reproduction of the Algae. Vol 1, Cambridge Univ. Press, Cambridge
41. Fujiwara S, Swada M, Minaka N, Kawachi M, Inouye I (1994) Molecular analysis of rbcL in the Prymnesiophyta. J Phycol 30: 863-871
42. Herth W, Zugenmaier, P (1979) The lorica of Dinobryon. J Ultrastr Res 69: 262-272
43. Herth W, Kuppel A, Schnepf, E (1977) Chitinous fibrils in the lorica of the flagellate chrysophyte Poterioochromonas stipitata (syn. Ochromonas malhamensis). J Cell Biol 73: 311-321
44. Hibberd DJ (1970) Observations on the cytology and ultrastructure of Ochromonas tuberculatus sp. nov. (Chrysophyceae), with special reference to discobolocysts. Br Phycol J 5:119-143
45. Hibberd DJ (1971) Observations on the cytology and ultrastructure of Chrysamoeba radians Klebs (Chrysophyceae). Br Phycol J 6:207-223
46. Hibberd DJ (1975) Observations on the ultrastructure of the choanoflagellate Codosiga botrytis (Ehr.) SavilleKent with special reference to the flagellar apparatus. J Cell Sei 17:191-219
47. Hibberd DJ (1976) The ultrastructure and taxonomy of the Chrysophyceae and Prymnesiophyceae (Haptophyceae): a survey with some new observations of the ultrastructure of the Chrysophyceae. Bot J Linn Soc 72: 55-80
48. Hibberd DJ (1977) The cytology and ultrastructure of Chrysonebula holmesii Lund (Chrysophyceae), with special reference to the flagellar apparatus. Br Phycol J 12:369-383
49. Milliard DK, Asmund B (1963) Studies on Chrysophyceae from some ponds and lakes in Alaska. II. Notes on the genera Dinobryon, Hyalobryon and Epipyxis with descriptions of new species. Hydrobiologia 22: 331-397
50. Hoffman LR, Vesk M, Pickett-Heaps JD (1986) The cytology and ultrastructure of zoospores of Hydrurus foetidus (Chrysophyceae). Nord J Bot 6:105-122
51. Juris S (1977) Contributions to the knowledge of the algae of Slovakia. I. Act Rer Nat Mus Nat Slov Bratislava 23:91-102
52. Kent WS (1880-82) A Manual of the Infusoria. Bogue, London
53. Klebs G (1893a) Flagellatenstudien. I. Zeitschr Wiss Zool 55: 265-351
54. Klebs G (1893b) Flagellatenstudien. II. Zeitschr Wiss Zool 55: 353-445
55. Lavau S, Saunders GW, Wetherbee R (1997) A phylogenetic analysis of the Synurophyceae using molecular data and scale case morphology. J Phycol 33:135-151
56. Leipe DD, Tong SM, Goggin CL, Slemenda SB, Pieniazek NJ, Sogin ML (1996) 16S-like rDNA sequences from Developayella elegans, Labyrinthuloides haliotidis and Proteromonas lacertae confirm that the stramenopiles are a primarily heterotrophic group. Europ J Protistol 32: 449-458
57. Leipe DD, Wainright PO, Gunderson JH, Porter D, Patterson DJ, Valois F, Himmerich S, Sogin ML (1994) The stramenopiles from a molecular perspective: 16S-like rRNA sequences from Labyrinthuloides minuta and Cafeteria roenbergensis. Phycologia 33:369-377
58. Medlin LK, Kooistra WHCF, Potter D, Saunders GW, Andersen RA 1997. Phylogenetic relationships of the 'golden algae' (haptophytes, heterokont chromophytes) and their chloroplasts. PI Syst Evol (Suppl.) 11:187-219
59. Mesquita JF, Santos MF (1976) Études cytologiques sur les algues jaunes (Chrysophyceae). I. Ultrastructure de Chrysocapsa epiphytica Lund. Bol Soc Brot 50: 63-98
60. Meyer RL (1986) A proposed phylogenetic sequence for the loricate rhizopodial Chrysophyceae. In Kristiansen J, Andersen RA (eds) Chrysophytes: Aspects and Problems. Cambridge Univ Press, NY pp 75-85
61. Mignot JP (1977) Étude ultrastructurale d'un flagellé du genre Spumella Cienk. (= Heterochromonas Pascher = Monas O. F. Müller), Chrysomonadine leucoplastidiée. Protistologica 13: 219-231
62. Mignot JP, Brugerolle G (1982) Scale formation in chrysomonad flagellates. J Ultrastr Res 81:13-26
63. Moestrup Ø (1995) Current status of chrysophyte 'splinter groups': synurophytes, pedinellids, silicoflagellates. In Sandgren CD, Smol JP, Kristiansen J (eds) Chrysophyte Algae: ecology, phylogeny and development. Cambridge Univ Press, NY pp 75-91
64. Moestrup Ø, Andersen RA (1991) The organization of heterotrophic heterokonts. In Patterson DJ, Larsen J [eds.] The Biology of Free-Living Heterotrophic Flagellates. Systematics Association Special Publication No 45, Clarendon Press, London, pp. 333-360
65. Müller OF (1773) Vermium terrestrium et fluviatilium, vol. 1 (1). Hauniae et Lipsiae (Copenhagen and Leipzig)
66. Müller OF (1786) Animalcula Infusoria Fluviatilia et Marina. Hauniae (Copenhagen)
67. O'Kelly CJ (1989) The evolutionary origin of the brown algae: information from studies of motile cell ultrastructure. In Green JC, Leadbeater BSC, Diver WL (eds) The Chromophyte Algae: Problems and Perspectives. Systematics Association Special Volume No. 38, Clarendon Press, Oxford, pp. 255-78
68. O'Kelly CJ, Wujek DE (1995) Status of the Chrysamoebales (Chrysophyceae): observations on Chrysamoeba pyrenoidifera, Rhizochromulina marina and Lagynion delicatulum. In Sandgren CD, Smol JP, Kristiansen J (eds) Chrysophyte Algae: ecology, phylogeny and development. Cambridge Univ Press, NY pp 361-372
69. Owen HA, Mattox KR, Stewart KD (1990a) Fine structure of the flagellar apparatus of Dinobryon cylindricum (Chrysophyceae). J Phycol 26:131-141
70. Owen HA, Stewart KD, Mattox KR (1990b) Fine structure of the flagellar apparatus of Uroglena americana (Chrysophyceae). J Phycol 26:142-149
71. Parke M, Manton l, Clarke B (1955) Studies on marine flagellates. II. Three new species of Chrysochromulina. J Mar Biol Assoc UK 34: 579-609
72. Parke M, Manton I, Clarke B (1956) Studies on marine flagellates. III. Three further species of Chrysochromulina. J Mar Biol Assoc UK 35: 387-414
73. Pascher A (1910) Der Grossteich bei Hirschberg in Nord-Böhmen. Int Rev Ges Hydrobiol Hydrogr, Monogr Abhandl 1:1-66
74. Pascher A (1912) Ueber Rhizopoden- und Palmellastadien bei Flagellaten (Chrysomonaden), nebst einer Uebersicht über die braunen Flagellaten. Arch Protistenkd 25:153-200
75. Pascher A (1913) Chrysomonadinae. In Pascher A (ed) Die Süsswasser-Flora Deutschlands, Österreichs und der Schweiz. G Fischer, Jena 2: 7-95
76. Pascher A (1914) Über Flagellaten und Algen. Ber Deutsch Bot Ges 32:136-160
77. Pascher A (1925) Die braune Algenreihe der Chrysophyceen. Arch Protistenkd 52:489-564
78. Pascher A (1931) Systematische Übersicht über die mit Flagellaten in Zusammenhang stehenden Algenreihen und Versuch einer Einreihung dieser Algenstämme in die Stämme des Pflanzenreiches. Bot. Centralb. Bein. 48:317-332
79. Peters MC, Andersen RA (1993a) The fine structure and scale formation of Chrysolepidomonas dendrolepidota gen. et sp. nov. (Chrysolepidomonadaceae fam. nov., Chrysophyceae). J Phycol 29:469-475
80. Peters MC, Andersen RA (1993b) The flagellar apparatus of Chrysolepidomonas dendrolepidota (Chrysophyceae), a single-celled monad covered with organic scales. J Phycol 29: 476-485
81. Pipes LD, Tyler PA, Leedale GF (1989) Chrysonephele palustris gen. et sp. nov. (Chrysophyceae), a new colonial chrysophyte from Tasmania. Nova Hedwigia Beiheft 95:81-97
82. Potter D, Saunders GW, Andersen R A (1997b) Phylogenetic relationships of the Raphidophyceae and Xanthophyceae as inferred from nucleotide sequences of the 18S ribosomal RNA gene. Amer J Bot 84: 966-972
83. Potter D, LaJeunesse TC, Saunders GW, Andersen RA (1997a) Convergent evolution masks-extensive biodiversity among marine coccoid picoplankton. Biodiversity and Conservation 6: 99-107
84. Preisig HR (1989) The flagellar base ultrastructure and phylogeny of chromophytes. In Green JC, Leadbeater BSC, Diver WL (eds) The Chromophyte Algae: Problems and Perspectives. Systematics Association Special Volume No. 38, Clarendon Press, Oxford, pp. 167-87
85. Preisig HR (1995) A modern concept of chrysophyte classification. In Sandgren CD, Smol JP, Kristiansen J (eds) Chrysophyte Algae: Ecology, Phylogeny and Development. Cambridge Univ Press, Cambridge, pp 46-74
86. Preisig HR, Hibberd DJ (1982a) Ultrastructure and taxonomy of Paraphysomonas (Chrysophyceae) and related genera (1). Nord J Bot 2: 397-420
87. Preisig HR, Hibberd DJ (1982b) Ultrastructure and taxonomy of Paraphysomonas (Chrysophyceae) and related genera (2). Nord J Bot 2: 601-638
88. Preisig HR, Hibberd DJ (1983) Ultrastructure and taxonomy of Paraphysomonas (Chrysophyceae) and related genera (3). Nord J Bot 3: 695-723
89. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425
90. Saunders GW, Potter D, Andersen RA (1997) Phylogenetic affinities of the Sarcinochrysidales and Chrysomeridales (Heterokonta) based on analyses of molecular and combined data. J Phycol 33:310-318
91. Saunders GW, Potter D, Paskind, MP, Andersen RA (1995) Cladistic analyses of combined traditional and molecular data sets reveal an algal lineage. Proc Natl Acad Sei USA 92: 244-248
92. Schnepf E, Deichgräber G (1969) Über die Feinstruktur von Synura petersenii unter besonderer Berücksichtigung der Morphogenese ihrer Kieselschuppen. Protoplasma 68: 85-106
93. Schnepf E, Deichgräber G, Röderer G, Herth W (1977) The flagellar root apparatus, the microtubular system and associated organelles in the chrysophycean flagellate Poterioochromonas malhamensis Peterfi (syn. Poteriochromonas stipitata Scherffel and Ochromonas malhamensis Pringsheim). Protoplasma 92:87-107
94. Senn G (1900) Flagellata. In Engler A, Prantl K (eds) Die natürlichen Pflanzenfamilien, Teil 1, Abt. 2, W Engelmann, Leipzig, pp 93-188
95. Suva PC (1980) Names of classes and families of living algae. Regnum Vegetabile 103:1-156
96. nd Ed. McGraw-Hill, NY
97. Starmach K (1985) Chrysophyceae und Haptophyceae. In Ettl H, Gerloff J, Heynig H, Mollenhauer D (eds) Süsswasserflora von Mitteleuropa. Gustav Fischer Verlag, Stuttgart, pp 1-515
98. Stein F von (1878) Der Organismus der Infusionsthiere nach eigenen Forschungen in systematischer Reihenfolge bearbeitet. III. Abt. 1. W Engelmann, Leipzig
99. Stein JR (1963) A Chromulina (Chrysophyceae) from snow. Can J Bot 41:1367-1370
100. Stokes AC (1885) Notes on some apparently undescribed forms of freshwater infusoria. No. 2. Amer J Sei 29:313-328
101. Stokes AC (1886) Notices of new fresh-water infusoria. Proc Amer Philos Soc 23: 562-568
102. Van de Peer Y, De Wachter R (1997) Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comput Applic Biosci 13: 227-230
103. Van de Peer Y, Van der 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
104. Van de Peer Y, Caers A, De Rijk P, De Wachter R (1998) Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res 26:179-182
105. Vysotskii AV (1887) Mastigophora i Rhizopoda, hajdennyja v Vejsovom i Repnom ozerach. Trudy Obsc Isp Prir Imp Kark'kovsk Univ 21:119-140
106. Wetherbee R, Andersen RA (1992) Flagella play an active role in prey selection and capture in chrysophycean algae: direct observations of Epipyxis pulchra using image enhanced light microscopy. Protoplasma 166: 8-20
107. Woronin A (1880) Chromophyton rosanoffii. Bot Z 38: 625-631,641-648
108. Wujek DE (1968) Presence of a second flagellum in Chrysosphaerella multispina. J Phycol 4:167-168
109. Zhang X, Inouye I, Chihara M (1990a) An unusual short flagellum in Mallomonas guttata (Synurophyceae, Chrysophyta). Bot Mag Tokyo 103:97-101
110. Zhang X, Inouye I, Chihara M (1990b) Taxonomy and ultrastructure of a freshwater scaly flagellate Mallomonas tonsurata var. etortisetifera var. nov. (Synurophyceae, Chromophyta). Phycologia 29: 65-73