Molecular diversity of the syndinean genus euduboscquella based on single-cell PCR analysis

Applied and Environmental Microbiology

Volumn 78, Issue 2, 2012, Pages 334-345

  Bachvaroff, Tsvetan R ^a   Kim, Sunju ^a   Guillou, Laure ^b   Delwiche, Charles F ^c   Coats, D Wayne ^a  

^a SMITHSONIAN ENVIRONMENTAL RESEARCH CENTER   (United States)

^b STATION BIOLOGIQUE DE ROSCOFF   (France)

^c UNIVERSITY OF MARYLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLONE LIBRARY; DATA SETS; INTERNAL TRANSCRIBED SPACERS; MOLECULAR DIVERSITY; NORTHERN HEMISPHERES; PARASITE-; PCR ANALYSIS; POLYMORPHIC SITES; SMALL SUBUNITS;

CLONE CELLS; CLONING; TREES (MATHEMATICS);

RNA;

FRESH WATER;

CLADISTICS; COMPARATIVE STUDY; DATA SET; DINOFLAGELLATE; GENE EXPRESSION; HOST SPECIFICITY; MARINE ENVIRONMENT; MOLECULAR ANALYSIS; NORTHERN HEMISPHERE; PARASITE; PHYLOGENY; POLYMERASE CHAIN REACTION; SPECIES DIVERSITY;

ALVEOLATA; ARTICLE; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION;

ALVEOLATA; CLUSTER ANALYSIS; FRESH WATER; GENETIC VARIATION; GENOTYPE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

CILIOPHORA; DINOPHYCEAE; TINTINNIDA; TINTINNOPSIS;

EID: 84862907622     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.06678-11     Document Type: Article

References (50)

1. Agatha S, Riedel-Lorjé JC. 2006. Redescription of Tintinnopsis cylindrica Daday, 1887 (Ciliophora, Spirotricha) and unification of tintinnid terminology. Acta Protozool. 45:137-151.
2. Agatha S, Strüder-Kypke M. 2007. Phylogeny of the order Choreotrichida (Ciliophora, Spirotricha, Oligotrichea) as inferred from morphology, ultrastructure, ontogenesis, and SSrRNA gene sequences. Eur. J. Protistol. 43: 37-63.
3. Berney C, Fahrni J, Pawlowski J. 2004. How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys. BMC Biol. 2:13.
4. Cachon J. 1964. Contribution à l'étude des péridiniens parasites. Cytologie, cycles évolutifs. Ann. Sci. Nat. Zool. 6:1-158.
5. Cachon J, Cachon M. 1987. Parasitic dinoflagellates, p 571-610. In Taylor FJR (ed), The biology of dinoflagellates, vol 21. Blackwell Scientific Publications, Oxford, United Kingdom.
6. Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
7. Chambouvet A, Morin P, Marie D, Guillou L. 2008. Control of toxic marine dinoflagellate blooms by serial parasitic killers. Science 322: 1254-1257.
8. Chatton E. 1920. Les peridiniens parasites. Morphologie, reproduction, ethologie. Arch. Zool. Exp. Gen. 59:1-475.
9. Coats DW. 1988. Duboscquella cachoni n. sp., a parasitic dinoflagellate lethal to its tintinine host Eutintinnus pectinis. J. Protozool. 35:607-617.
10. Coats DW. 1999. Parasitic life styles of marine dinoflagellates. J. Eukaryot. Microbiol. 46:402-409.
11. Coats DW, Kim S, Bachvaroff TR, Handy SM, Delwiche CF. 2010. Tintinnophagus acutus n. g., n. sp. (Phylum Dinoflagellata), an ectoparasite of the ciliate Tintinnopsis cylindrica Daday 1887, and its relationship to Duboscquodinium collini Grassse 1952. J. Eukaryot. Microbiol. 57: 468-482.
12. Coats DW, Park MG. 2002. Parasitism of photosynthetic dinoflagellates by three strains of Amoebophyra (Dinophyta): parasite survival, infectivity, generation time, and host specificity J. Phycol. 38:520-528.
13. Coats DW, Bachvaroff TR, Delwiche CF. 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 and Campbell, 1929. J. Eukaryot. Microbiol., in press.
14. Coleman AW, Vacquier VD. 2002. Exploring the phylogenetic utility of ITS sequences for animals: a test case for abalone (Haliotis). J. Mol. Evol. 54:246-257.
15. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
16. Fensome RA, et al. 1993.A classification of living and fossil dinoflagellates. Micropaleontology special publication no. 7. American Museum of Natural History, New York, NY.
17. Gottschling M, Plötner J. 2004. Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoflagellates. Nucleic Acids Res. 32: 307-315.
18. Guillou L, et al. 2008. Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ. Microbiol. 10:3349-3365.
19. Gunderson JH, Goss SH, Coats DW. 1999. The phylogenetic position of Amoebophrya sp. infecting Gymnodinium sanguineum. J. Eukaryot. Microbiol. 46:194-197.
20. Gunderson JH, John SA, Boman WC, Coats DW. 2002. Multiple strains of the parasitic dinoflagellate Amoebophrya exist in Chesapeake Bay. J. Eukaryot. Microbiol. 49:469-474.
21. Harada A, Ohtsuka S, Horiguchi T. 2007. Species of the parasitic genus Duboscquella are members of the enigmatic marine alveolate group I. Protist 158:337-347.
22. Hoppenrath M, Leander BS. 2010. Dinoflagellate phylogeny as inferred from heat shock protein 90 and ribosomal gene sequences. PLoS One 5:e13220.
23. Janson S, Gisselson L-Å, Salomon PS, Granéli 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.
24. Keller A, et al. 2009. 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene 430:50-57.
25. Kim S. 2006. Patterns in host range for two strains of Amoebophrya (Dinophyta) infecting thecate dinoflagellates: Amoebphrya spp. ex Alexandrium affine and ex Gonyaulax polygramma. J. Phycol. 42:1170-1173.
26. Kim S, 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.
27. Kim SY, Yang EJ, Gong J, Joong KC. 2010. Redescription of Favella ehrenbergii (Claparéde and Lachmann, 1858) Jörgensen, 1924 (Ciliophora: Choreotrichia), with phylogenetic analyses based on small subunit rRNA gene sequences. J. Eukaryot. Microbiol. 57:460-467.
28. Kofoid CA, Campbell AS. 1929. A conspectus on the marine and freshwater Ciliata belonging to the suborder Tintinnoinea, with descriptions of new species principally from the Agassiz expedition to the eastern tropical Pacific 1904-1905. Univ. Cal. Publ. Zool. 34:1-403.
29. Lahr DJ, Nguyen TB, Barbero E, Katz LA. 2010. Evolution of the actin gene family in testate lobose amoebae (Arcellinida) is characterized by two distinct clades of paralogs and recent independent expansions. Mol. Biol. Evol. 28:223-236.
30. Larkin M, et al. 2007. ClustalWand Clustal X version 2.0. Bioinformatics 23:2947-2948.
31. Li Z, et al. 2009. Phylogenetic investigation on five genera of tintinnid ciliates (Ciliophora, Choreotrichia), based on the small subunit ribosomal RNA gene sequences. Prog. Nat. Sci. 19:1097-1101.
32. Logares R, et al. 2007. Phenotypically different microalgal morphospecies with identical ribosomal DNA: a case of rapid adaptive evolution? Microb. Ecol. 53:549-561.
33. Maddison WP, Maddison PR. 2002. MacClade version 4: analysis of phylogeny and character evolution. Sinauer Associates, Sunderland, MA.
34. Moon-van der Staay S, De Wachter R, Vaulot D. 2001. Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409:607-610.
35. Morgan DR, Soltis DE. 1995. Phylogenetic relationships among members of Saxifragaceae sensu lato based on rbcL sequence data. Ann. Mo. Bot. Gard. 80:631-660.
36. Ryazanova TV, Eliselkina MG, Kukhlevsky AD, Kharlamenko VI. 2010. Hematodinium sp. infection of red Paralithodes camtschaticus and blue Paralithodes platypus king crabs from the Sea of Okhotsk, Russia. J. Invertebr. Pathol. 105:329-334.
37. Saldarriaga JF, Taylor FJ, Keeling PJ, Cavalier-Smith T. 2001. Dinoflagellate nuclear SSU rRNA phylogeny suggests multiple plastid losses and replacements. J. Mol. Evol. 53:204-213.
38. Salomon PS, Janson S, Granéli E. 2003. Multiple species of the dinophagous dinoflagellate genus Amoebophrya infect the same host species. Environ. Microbiol. 5:1046-1052.
39. Scholin CA, Anderson DM. 1993. The existence of two distinct smallsubunit rRNA genes in the toxic dinoflagellate Alexandrium fundyense. J. Phycol. 29:209-216.
40. Shalchian-Tabrizi K, et al. 2006. Heterotachy processes in rhodophytederived second hand plastid genes: implications for addressing the origin and evolution of dinoflagellate plastids. Mol. Biol. Evol. 23:1504-1515.
41. Skovgaard A, Massana R, Balague V, Saiz E. 2005. Phylogenetic position of the copepod-infesting parasite Syndinium turbo (Dinoflagellata, Syndinea). Protist 156:413-423.
42. Skovgaard A, Meneses I, Angélico MM. 2009. Identifying the lethal fish egg parasite Ichthyodinium chabelardi as a member of marine alveolate group I. Environ. Microbiol. 11:2030-2041.
43. Small HJ, Neil DM, Taylor AC, Atkinson RJ, Coombs GH. 2006. Molecular detection of Hematodinium spp. in Norway lobster Nephrops norvegicus and other crustaceans. Dis. Aquat. Organ. 69:185-195.
44. Snoeyenbos-West O, Salcedo T, McManus GB, Katz LA. 2002. Insights into the diversity of choreotrich and oligotrich ciliates (class: Spirotrichea) based on genealogical analyses of multiple loci. IJSEM 52:1901-1913.
45. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analysis with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
46. Strüder-Kypke M, Lynn DH. 2008. Morphological versus molecular data- phylogeny of tintinnid ciliates (Ciliophora, Choreotrichia) inferred from small subunit rRNA gene sequences. Denisia 23:417-424.
47. Strüder-Kypke M, Lynn DH. 2003. Sequence analyses of the small subunit rRNA gene confirm the paraphyly of oligotrich ciliates sensu lato and support the monophyly of the subclasses Oligotrichia and Choreotrichia (Ciliophora, Spirotrichea). J. Zool. (London) 260:87-97.
48. Suzuki N, Kurihara T, Matsuoka A. 2009. Sporogenesis of an extracellular cell chain from the spheroidal radiolarian host Haliommilla capillaceum (Haeckel), Polycystina, Protista. Mar. Micropaleontol. 72:157-164.
49. Yuasa K, 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.
50. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415.