| [1] | Cavalier-Smith T (2004) Only six kingdoms of life. P Roy Soc Lond B Bio 271: 1251–1262.
|
| [2] | Leander BS, Keeling PJ (2003) Morphostasis in alveolate evolution. Trends in Ecol Evol 18: 395–402.
|
| [3] | Moore RB, Oborník M, Janou？kovec J, Chrudimsky T, Vancová M, et al. (2008) A photosynthetic alveolate closely related to apicomplexan parasites. Nature 451: 959–963.
|
| [4] | Oborník M, Janou？kovec J, Chrudimsky T, Luke？ J (2009) Evolution of the apicoplast and its hosts: From heterotrophy to autotrophy and back again. Int J Parasitol 39: 1–12.
|
| [5] | Janou？kovec J, Horák A, Oborník M, Lukes J, Keeling PJ (2010) A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. PNAS 107: 10949–10954.
|
| [6] | Botté CZ, Yamaryo-Botté Z, Janou？kovec J, Rupasinghe T, Keeling PJ, et al. (2011) Identification of Plant-like Galactolipids in Chromera velia, a Photosynthetic Relative of Malaria Parasites. J Biol Chem 286: 29893–29903.
|
| [7] | Taylor MFJR, Hoppenrath M, Saldarriaga JF (2008) Dinoflagellate diversity and distribution. Biodivers Conserv 17: 407–418.
|
| [8] | Lin S, Zhang H, Spencer DF, Norman JE, Gray MW (2002) Widespread and extensive editing of mitochondrial mRNAs in dinoflagellates. J Mol Biol 320: 727–39.
|
| [9] | Jackson CJ, Norman JE, Schnare MN, Gray MW, Keeling PJ, et al. (2007) Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria. BMC Biol 5: 41.
|
| [10] | Slamovits CH, Saidarriaga JF, Larocque A, Keeling PJ (2007) The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial Genomes. J Mol Biol 372: 356–368.
|
| [11] | Waller RF, Jackson CJ (2009) Dinoflagellate mitochondrial genomes: stretching the rules of molecular biology. Bioessays 31: 237–245.
|
| [12] | Zhang ZD, Green BR, Cavalier-Smith T (1999) Single gene circles in dinoflagellate chloroplast genomes. Nature 400: 155–9.
|
| [13] | Green BR (2004) The chloroplast genome of dinoflagellates – a reduced instruction set? Protist 155: 23–31.
|
| [14] | Lin S (2011) Genomic understanding of dinoflagellates. Res Microbiol 162: 551–569.
|
| [15] | Zhang H, Hou Y, Miranda L, Campbell DA, Sturm NR, et al. (2007) Spliced leader RNA trans-splicing in dinoflagellate. PNAS 104: 4618–4623.
|
| [16] | Lidie KB, van Dolah FM (2007) Spliced leader RNA-mediated trans-splicing in a dinoflagellate, Karenia brevis. J Euk Microbiol 54: 427–435.
|
| [17] | Zhang H, Campbell DA, Sturm NR, Lin S (2009) Dinoflagellate spliced leader RNA genes display a variety of sequences and genomic arrangements. Mol Biol Evol 26: 1757–1771.
|
| [18] | Stoeck T, Zuendorf A, Breiner H-W, Behnke A (2007) A molecular approach to identify active microbes in environmental eukaryote clone libraries. Microbial Ecol 53: 328–339.
|
| [19] | Massana R, Karniol B, Pommier T, Bodaker I, Beja O (2008) Metagenomic retrieval of a ribosomal DNA repeat array from an uncultured marine alveolate. Environ Microbiol 10: 1335–1343.
|
| [20] | Alexander E, Stock A, Breiner H-W, Behnke A, Bunge J, et al. (2009) Microbial eukaryotes in the hypersaline anoxic L’Atalante deep-sea basin. Environ Microbiol. 11: 360–381.
|
| [21] | Lopez-Garcia P, Rodriguez-Valera F, Pedros-Alio C, Moreira D (2001) Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409: 603–607.
|
| [22] | Stoeck T, Epstein SS (2003) Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl Environ Microbiol 69: 2657–2663.
|
| [23] | Stoeck T, Taylor G, Epstein SS (2003) Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean sea). Appl Environ Microbiol 69: 5656–5663.
|
| [24] | Groisillier A, Massana R, Valentin K, Vaulotl D, Guilloul L (2006) Genetic diversity and habitats of two enigmatic marine alveolate lineages. Aquat Microb Ecol 42: 277–291.
|
| [25] | Lovejoy C, Massana R, Pedros-Alio C (2006) Diversity and distribution of marine microbial eukaryotes in the Arctic Ocean and adjacent seas. Appl Environ Microbiol 72: 3085–3095.
|
| [26] | Lopez-Garcia P, Vereshchaka A, Moreira D (2007) Eukaryotic diversity associated with carbonates and fluid-seawater interface in Lost City hydrothermal field. Environ Microbiol 9: 546–554.
|
| [27] | Cuvelier ML, Ortiz A, Kim E, Moehlig H, Richardson DE, et al. (2008) Widespread distribution of a unique marine protistan lineage. Environ Microbiol 10: 1621–1634.
|
| [28] | Massana R, Pedros-Alio C (2008) Unveiling new microbial eukaryotes in the surface ocean. Curr Opin Microbiology 11: 213–218.
|
| [29] | Brown MV, Philip GK, Bunge JA, Smith MC, Bissett A, et al. (2009) Microbial community structure in the North Pacific ocean. ISME J 3: 1374–1386.
|
| [30] | Stoeck T, Behnke A, Christen R, Amaral-Zettler L, Rodriguez-Mora MJ, et al. (2009) Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biol. 7: 72.
|
| [31] | Stern RF, Horák A, Andrew RL, Coffroth M-A, Andersen RA, et al. (2010) Environmental barcoding reveals massive dinoflagellate diversity in marine environments. PLoS ONE 5: e13991.
|
| [32] | Silberman J, Collins A, Gershwin L, Johnson P, Roger A (2004) Ellobiopsids of the genus Thalassomyces are alveolates. J Eukaryot Microbiol 51: 246–252.
|
| [33] | Skovgaard A, Massana R, Balagué V, Saiz E (2005) Phylogenetic position of the copepod-infesting parasite Syndinium turbo (Dinoflagellata, Syndinea). Protist 156: 413–423.
|
| [34] | Harada A, Ohtsuka S, Horiguchi T (2007) Species of the parasitic genus Duboscquella are members of the enigmatic Marine Alveolate Group I. Protist. pp. 337–347.
|
| [35] | Guillou L, Viprey M, Chambouvet A, Welsh RM, Kirkham AR, et al. (2008) Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ Microbiol 10: 3349–3365.
|
| [36] | Kim S, Park MG, Kim K-Y, Kim C-H, Yih W, et al. (2008) Genetic diversity of parasitic dinoflagellates in the genus Amoebophrya and its relationship to parasite biology and biogeography. J Eukaryot Microbiol 55: 1–8.
|
| [37] | Skovgaard A, Daugbjerg N (2008) Identity and systematic position of Paradinium poucheti and other Paradinium-like parasites of marine copepods based on morphology and nuclear-encoded SSU rDNA. Protist 159: 401–413.
|
| [38] | Gomez F, Lopez-Garcia P, Nowaczyk A, Moreira D (2009) The crustacean parasites Ellobiopsis Caullery, 1910 and Thalassomyces Niezabitowski, 1913 form a monophyletic divergent clade within the Alveolata. Syst Parasitol 74: 65–74.
|
| [39] | Skovgaard A, Meneses I, Angelico MM (2009) Identifying the lethal fish egg parasite Ichthyodinium chabelardi as a member of Marine Alveolate Group I. Environ Microbiol 11: 2030–2041.
|
| [40] | Cachon J, Cachon M (1987) Parasitic dinoflagellates. In: Taylor F, editor. pp. 571–610. Oxford, UK: Blackwell Scientific Publications.
|
| [41] | Janson S, Gisselson L, Salomon P, Graneli E (2000) Evidence for multiple species within the endoparasitic dinoflagellate Amoebophrya ceratii as based on 18S rRNA gene-sequence analysis. Parasitol Res 86: 929–933.
|
| [42] | Gunderson J, Goss S, Coats D (1999) The phylogenetic position of Amoebophrya sp infecting Gymnodinium sanguineum. J Eukaryot Microbiol 46: 194–197.
|
| [43] | Saldarriaga J, Taylor MFJR, Cavalier-Smith T, Menden-Deuer S, Keeling PJ (2004) Molecular data and the evolutionary history of dinoflagellates. Eur J Protistol 40: 85–111.
|
| [44] | Gestal C, Novoa B, Posada D, Figueras A, Azevedo C (2006) Perkinsoide chabelardi n. gen., a protozoan parasite with an intermediate evolutionary position: possible cause of the decrease of sardine fisheries? Environ Microbiol 8: 1105–1114.
|
| [45] | Yuasa K, Kamaishi T, Mori K, Hutapea JH, Permana GN, et al. (2007) Infection by a protozoan endoparasite of the genus Ichthyodinium in embryos and yolk-sac larvae of yellowfin tuna Thunnus albacares. Fish Pathol 42: 59–66.
|
| [46] | Coats DW, Bachvaroff TR, Delwiche CF (2012) Revision of the Family Duboscquellidae with Description of Euduboscquella crenulata n. gen., n. sp. (Dinoflagellata, Syndinea), an Intracellular Parasite of the Ciliate Favella panamensis Kofoid & Campbell. J Euk Microbiol 59: 1–11.
|
| [47] | Leander BS, Hoppenrath M (2008) Ultrastructure of a novel tube-forming, intracellular parasite of dinoflagellates: Parvilucifera prorocentri sp. nov. (Alveolata, Myzozoa). Eur J Protistol. 44: 55–70.
|
| [48] | Taylor MFJR (1980) On dinoflagellate evolution. Biosystems 13: 65–108.
|
| [49] | Taylor MFJR (2004) Illumination or confusion? Dinoflagellate molecular phylogenetic data viewed from a primarily morphological standpoint. Phycol Res 52: 308–338.
|
| [50] | Appleton PL, Vickerman K (1998) In vitro cultivation and developmental cycle in culture of a parasitic dinoflagellate (Hematodinium sp.) associated with mortality of the Norway lobster (Nephrops norvegicus) in British waters. Parasitology 116: 115–130.
|
| [51] | Fritz L, Nass M (1992) Development of the Endoparasitic Dinoflagellate Amoebophyra-Ceratii Within Host Dinoflagellate Species. J Phycol 28: 312–320.
|
| [52] | Maranda L (2001) Infection of Prorocentrum minimum (Dinophyceae) by the parasite Amoebophrya sp. (Dinoflagellea). J Phycol 37: 245–248.
|
| [53] | Miller JJ, Delwiche CF, Coats DW (2011) Ultrastructure of Amoebophrya sp. and its Changes during the Course of Infection. Protist. Accessed 2012 January 31.
|
| [54] | Leander B, Keeling P (2004) Early evolutionary history of dinoflagellates and apicomplexans (Alveolata) as inferred from hsp90 and actin phylogenies. J Phycol 40: 341–350.
|
| [55] | Takishita K, Kakizoe N, Yoshida T, Maruyama T (2010) Molecular evidence that phylogenetically diverged ciliates are active in microbial mats of deep-sea cold-Seep sediment. J Eukaryot Microbiol 57: 76–86.
|
| [56] | Shimodaira H (2004) Approximately unbiased tests of regions using multistep-multiscale bootstrap resampling. Annals of Statistics, 32, 2616–2641.
|
| [57] | Patterson DJ, Simpson AGB (1996) Heterotrophic flagellates from coastal marine and hypersaline sediments in Western Australia. Eur J Protistol 32: 423–448.
|
| [58] | Myl’nikov AP (2009) Ultrastructure and phylogeny of colpodellids (Colpodellida, Alveolata). Biol Bulletin 36: 582–590.
|
| [59] | Al-Qassab S, Lee WJ, Murray S, Simpson AGB, Patterson DJ (2002) Flagellates from stromatolites and surrounding sediments in Shark Bay, Western Australia. Acta Protozool 41: 91–144.
|
| [60] | Janssen PH (2009) Dormant microbes: scouting ahead or plodding along? Nature 458: 831–831.
|
| [61] | Mangot J-F, Debroas D, Domaizon I (2011) Perkinsozoa, a well-known marine protozoan flagellate parasite group, newly identified in lacustrine systems: a review. Hydrobiologia 659: 37–48.
|
| [62] | Saldarriaga JF, McEwan ML, Fast NM, Taylor MFJR, Keeling PJ (2003) Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage. Int J Sys Evol Microbiol. 53: 355–365.
|
| [63] | Clarke K, Pennick N (1972) Flagellar scales in Oxyrrhis marina Dujardin. Br Phycol J 7: 357–360.
|
| [64] | Gomez F, Moreira D, Lopez-Garcia P (2010) Molecular Phylogeny of Noctilucoid Dinoflagellates (Noctilucales, Dinophyceae). Protist 161: 466–478.
|
| [65] | Hoppenrath M, Leander BS (2010) Dinoflagellate Phylogeny as Inferred from Heat Shock Protein 90 and Ribosomal Gene Sequences. PLoS ONE 5: e13220.
|
| [66] | Leadbeater BSC (1971) Intracellular origin of flagellar hairs in dinoflagellate Woloszynskia micra Leadbeater & Dodge. J Cell Sci 9: 443–451.
|
| [67] | Dodge J (1971) Fine structure of Pyrrophyta. Bot Rev. 37: 481–508.
|
| [68] | Dodge J, Crawford RM (1971) Fine structure of the dinoflagellate Oxyrrhis marina II. The flagellar system. Protistologica 7: 399–409.
|
| [69] | Leander BS, Hoppenrath M (2008) Ultrastructure of a novel tube-forming, intracellular parasite of dinoflagellates: Parvilucifera prorocentri sp. nov. (Alveolata, Myzozoa). Eur J Protistol. 44: 55–70.
|
| [70] | Cavalier-Smith T. Chao EE (2004) Protalveolate phylogeny and systematics and the origins of Sporozoa and dinoflagellates (Phylum Myzozoa nom. nov.) Eur J Protistol. 40: 185–212.
|
| [71] | Myl’nikova ZM, Mylnikov AP (2009) The morphology of predatory flagellate Colpodella pseudoedax Mylnikov et Mylnikov, 2007 (Colpodellida, Alveolata). Inland Wat Biol 2: 199–204.
|
| [72] | Brugerolle G (2002) Colpodella vorax: ultrastructure, predation, life-cycle mitosis, and phylogenetic relationships. Eur J Protistol 38: 113–125.
|
| [73] | Garces E, Hoppenrath M (2010) Ultrastructure of the intracellular parasite Parvilucifera sinerae (Alveolata, Myzozoa) infecting the marine toxic planktonic dinoflagellate Alexandrium minutum (Dinophyceae). Harmful Algae 10: 64–70.
|
| [74] | Noren F, Moestrup ？, Rehnstam-Holm A (1999) Parvilucifera infectans Noren et Moestrup gen. et sp nov (Perkinsozoa phylum nov.): a parasitic flagellate capable of killing toxic microalgae. Eur J Protistol 35: 233–254.
|
| [75] | Clarke K, Pennick N (1976) The occurrence of body scales in Oxyrrhis marina Dujardin. Br Phycol J 11: 345–348.
|
| [76] | Morrill L, Loeblich AR III (1981) A survey for body scales in dinoflagellates and a revision of Cachonina and Heterocapsa (Pyrrhophyta) J Plankton Res 3: 53.
|
| [77] | Watanabe MM, Suda S, Inouye I, Sawaguchi T, Chihara M (1990) Lepidodinium viride gen. et sp. nov. (Gymnodiniales, Dinophyta), a green dinoflagellate with a chlorophyll a- and b- containing endosymbiont. J Phycol 26: 741–751.
|
| [78] | Hansen G, Botes L, De Salas M (2007) Ultrastructure and large subunit rDNA sequences of Lepidodinium viride reveal a close relationship to Lepidodinium chlorophorum comb. nov. ( = Gymnodinium chlorophorum). Phycol Res 55: 25–41.
|
| [79] | Tamura M, Takano Y, Horiguchi T (2009) Discovery of a novel type of body scale in the marine dinoflagellate, Amphidinium cupulatisquama sp. nov. (Dinophyceae). Phycol Res 57: 304–312.
|
| [80] | Kato K, Moriyama A, Itoh T, Yamamoto M, Horio T, et al. (2000) Dynamic changes in microtubule organization during division of the primitive dinoflagellate Oxyrrhis marina. Biol Cell 92: 583–594.
|
| [81] | Pfiester LA, Anderson DM (1987) Dinoflagellate reproduction. In: Taylor MFJR, editor. pp. 611–648. Oxford, UK: Blackwell Scientific Publication.
|
| [82] | Azevedo C (1989) Fine structure of Perkinsus atlanticus n. sp. (Apicomplexa, Perkinsea) parasite of the clam Ruditapes decussatus from Portugal. J Parasitol 75: 627–635.
|
| [83] | Perkins FO (1996) The structure of Perkinsus marinus (Mackin, Owen and Collier, 1950) Levine, 1978 with comments on taxonomy and phylogeny of Perkinsus spp. J Shellfish Res 15: 67–87.
|
| [84] | Perkins FO (1976) Zoospores of the oyster pathogen, Dermocystidium marinum. I. Fine structure of the conoid and other sporozoan-like organelles. J Parasitol 62: 959–974.
|
| [85] | Foissner W, Foissner I (1984) First record of an ectoparasitic flagellate on ciliates: An ultrastructural investigation of the morphology and the mode of attachment of Spiromonas gonderi nov. spec. (Zoomastigophora, Spiromonadidae) invading the pelicle of ciliates of the genus Colpoda (Ciliophora, Colpodidae). Protistologica 20: 635–648.
|
| [86] | Roberts KR, Timpano P, Montegut AE (1987) The apical pore fibrous complex - a new cytological feature of some dinoflagellates. Protoplasma 137: 65–69.
|
| [87] | Hansen G, Moestrup ？ (1998) Fine-structural characterization of Alexandrium catenella (Dinophyceae) with special emphasis on the flagellar apparatus. Eur J Phycol 33: 281–291.
|
| [88] | Perkins FO (1976) Dermocystidium marinum Infection in oysters. Mar Fish Rev 38: 19–21.
|
| [89] | Boothroyd JC, Dubremetz J-F (2008) Kiss and spit: the dual roles of Toxoplasma rhoptries. Nat Rev Microbiol 6: 79–88.
|
| [90] | Keller MD, Selvin RC, Claus W, Guillard RRL (1987) Media for the culture of oceanic ultraphytoplankton. J. Phycol. 23: 633–638.
|
| [91] | Tippit DH, Pickett-Heaps JD (1977) Mitosis in the pennate diatom Surirella ovalis. J Cell Biol 73: 705–727.
|
| [92] | Reynolds ES (1963) Use of lead citrate at high pH as an electron-opaque stain inelectron microscopy. J Cell Biol 17: 208–212.
|
| [93] | Okamoto N, Chantangsi C, Horák A, Leander BS, Keeling PJ (2009) Molecular phylogeny and description of the novel katablepharid Roombia truncata gen. et sp. nov., and establishment of the Hacrobia taxon nov. PLoS ONE. pp e7080.
|
| [94] | Kim E, Simpson AGB, Graham LE (2006) Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes. Mol Biol Evol 23: 2455–2466.
|
| [95] | Katoh T (2008) Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinform 9: 212.
|
| [96] | Katoh T (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286–298.
|
| [97] | Gouy M, Guindon S, Gascuel O (2010) SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27: 221–224.
|
| [98] | Stamatakis A (2006) RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models. Bioinformatics 22(21): 2688–2690.
|
| [99] | Lartillot N, Lepage T, Blanquart S (2009) PhyloBayes 3. a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioimform 25: 2286–2288.
|
| [100] | Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 1246–1247.
|
