Marine Biotechnology

, Volume 10, Issue 6, pp 692–700 | Cite as

Preparation and Analysis of an Expressed Sequence Tag Library from the Toxic Dinoflagellate Alexandrium catenella

  • Paulina Uribe
  • Daniela Fuentes
  • Jorge Valdés
  • Amir Shmaryahu
  • Alicia Zúñiga
  • David Holmes
  • Pablo D. T. Valenzuela
Original Article


Dinoflagellates of the genus Alexandrium are photosynthetic microalgae that have an extreme importance due to the impact of some toxic species on shellfish aquaculture industry. Alexandrium catenella is the species responsible for the production of paralytic shellfish poisoning in Chile and other geographical areas. We have constructed a cDNA library from midexponential cells of A. catenella grown in culture free of associated bacteria and sequenced 10,850 expressed sequence tags (ESTs) that were assembled into 1,021 contigs and 5,475 singletons for a total of 6,496 unigenes. Approximately 41.6% of the unigenes showed similarity to genes with predicted function. A significant number of unigenes showed similarity with genes from other dinoflagellates, plants, and other protists. Among the identified genes, the most expressed correspond to those coding for proteins of luminescence, carbohydrate metabolism, and photosynthesis. The sequences of 9,847 ESTs have been deposited in Gene Bank (accession numbers EX 454357–464203).


Alexandrium catenella cDNA sequencing Red tide microalgae Toxic dinoflagellate 


  1. Abrahams MV, Townsend LD (1993) Bioluminescence in dinoflagellates: A test of the burgular alarm hypothesis. Ecology 74:258–260CrossRefGoogle Scholar
  2. Altschul SF, Gish W, Miller E, Myers EW, Lipman DT (1990) Basic local alignment search tool. J Mol Biol 3:403–410Google Scholar
  3. Anderson DM, Grabher A, Herzog M (1992) Separation of coding sequences from structural DNA in the dinoflagellate Crypthecodinium cohnii. Mol Mar Biol Biotechnol 1:89–96Google Scholar
  4. Armbrust EY, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AF, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kroger N, Lau WW, Lane T, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GT, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS (2004) The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306:79–86PubMedCrossRefGoogle Scholar
  5. Bachvaroff TR, Concepcion GT, Rogers CR, Herman EM, Delwiche CH (2004) Dinoflagellate expressed sequence tag data indicate massive transfer of chloroplast genes to the nuclear genome. Protist 155:65–78PubMedCrossRefGoogle Scholar
  6. Bhaud Y, Geraud M, Ausseil J, Soyer-Gobillard MO, Moreu H (1999) Cyclic expression of a nuclear protein in a dinoflagellate. J Eukaryot Microbiol 46:259–267PubMedCrossRefGoogle Scholar
  7. Chan LL, Sit WH, Lam PK, Hsieh DP, Hodgkiss IJ, Wan JM, Ho AY, Choi NM, Wang DZ, Dudgeon D (2006) Identification and characterization of a “biomarker of toxicity” from the proteome of the paralytic shellfish toxin-producing dinoflagellate Alexandrium tamarense (Dinophyceae). Proteomics 6:654–666PubMedCrossRefGoogle Scholar
  8. Cheng X (1995) DNA modification by methyltransferases. Curr Opin Struct Biol 5:4–10PubMedCrossRefGoogle Scholar
  9. Craig EA (1989) Essential roles of 70 kDa heat inducible proteins. Bioessays 11:48–52PubMedCrossRefGoogle Scholar
  10. Easias WE, Curl HC Jr (1972) Effect of dinoflagellate bioluminescence of copepod ingestión rates. Limnol Oceanogr 17:901–906CrossRefGoogle Scholar
  11. Edner DL, Anderson DM (2006) Global transcriptional profiling of the toxic dinoflagellate Alexandrium fundyense using massively parallel signature sequencing. BMC Genomics 7:88CrossRefGoogle Scholar
  12. Giovanelli J (1987) Sulfur aminoacids of plants: an overview. Methods Enzymol 143:419–426CrossRefGoogle Scholar
  13. Guillard R (1995) Culture methods. In: Hallegraeff GM, Anderson DM, Cembella AD (eds) IOC manuals and guides: manual on harmful marine microalgae. Intergovernmental Oceanographic Commission of UNESCO, Paris, pp 45–62Google Scholar
  14. Guzmán L, Campodónico I (1975) Marea Roja en la región de Magallanes. Publ Inst Pat Ser Monogr Punta Arenas (Chile) 9:44Google Scholar
  15. Guzmán L, Campodónico I (1978) Mareas Rojas en Chile. Interciencia 3:144–151Google Scholar
  16. Hackett JD, Scheetz TE, Yoon HS, Soares MB, Bonaldo MF, Casavant TL, Bhattacharya D (2005) Insight into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics 6:80PubMedCrossRefGoogle Scholar
  17. Hallegraeff G (1993) A review of harmful algal blooms and their apparent global increase. Phycologia 32:79–99Google Scholar
  18. Hosoi-Tanabe S, Tomishima S, Nagai S, SaKo Y (2005) Identification of a gene induced in conjugation-promoted cells of toxic marine dinoflagellate Alexandrium tamarense and Alexandrium catenella using differential display analysis. FEMS Microbiol Lett 251:161–168PubMedCrossRefGoogle Scholar
  19. Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868–877PubMedCrossRefGoogle Scholar
  20. Imai I (1987) Size distribution, number and biomass of bacteria in intertidal sediments and seawater of Ohmi Bay, Japan. Bull Jpn Soc Microb Ecol 2:1–11Google Scholar
  21. Kuwae T, Hosokawa Y (1999) Determination of abundance and biovolume of bacteria in sediments by dual staining with 4_6-diamino-2-phenylindole and acridine orange: relationship to dispersion treatment and sediment characteristics. Appl Environ Microbiol 65:3407–3412PubMedGoogle Scholar
  22. Li L, Hong R, Hastings JW (1997) Three functional luciferase domains in a single polypeptide chain. Proc Natl Acad Sci U S A 94:8954–8958PubMedCrossRefGoogle Scholar
  23. Lidie KB, Ryan JC, Barbier M, Vandolah FM (2005) Gene expression in Florida Red Tide Dinoflagellate Karenia brevis: Analysis of an expressed sequence tag library and development of a DNA microarray. Mar Biotechnol 7:481–493PubMedCrossRefGoogle Scholar
  24. Lin S (2006) The smallest dinoflagellate genome is yet to be found: A comment on LaJeunesse et al. “Simbiodinium (Pyrrophyta) genome sizes (DNA content) are smallest among dinoflagellates”. J Phycol 42:746–748CrossRefGoogle Scholar
  25. Lindquist S, Craig EA (1988) The heat-shock proteins. Annu Rev Genet 22:631–677PubMedCrossRefGoogle Scholar
  26. Liscum E, Hodgson DW, Campbell TJ (2003) Blue light signaling through the cryptochromes and phototropins. So that’s what the blues is all about. Plant Physiol 133:1429–1436PubMedCrossRefGoogle Scholar
  27. Liu L, Wilson T, Hastings JW (2004) Molecular evolution of dinoflagellate luciferases, enzymes with three catalytic domains in a single polypeptide. Proc Natl Acad Sci U S A 101(47):16555–16560PubMedCrossRefGoogle Scholar
  28. Machabee S, Wall L, Morse D (1994) Expression and genomic organization of a dinoflagellate gene family. Plant Mol Biol 25:23–31PubMedCrossRefGoogle Scholar
  29. Mulder NJ, Apweiler R, Attwook TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lóperz R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Slengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C (2007) New developments in the InterPro database. Nucleic Acids Res 35:224–228CrossRefGoogle Scholar
  30. Okamoto OK, Hastings JW (2003) Novel dinoflagellate clock-related genes identified through microarrays analysis. J Phycol 39:519–526CrossRefGoogle Scholar
  31. Patron NJ, Waller RF, Archibald JH, Keeling PT (2005) Complex protein targeting to dinoflagellate plastids. J Mol Biol 348:1015–1024PubMedCrossRefGoogle Scholar
  32. Santos SR, Coffroth MA (2003) Molecular genetic evidence that dinoflagellates belonging to the genus Symbiodinium Freudenthal are haploid. Biol Bull 204:10–20PubMedCrossRefGoogle Scholar
  33. Scholin CA, Hallegraeff GM, Anderson DM (1995) Molecular evolution of the Alexandrium tamarense species complex (Dinophyceae) dispersal in the North American and west Pacific regions. Phycologia 34:472–485Google Scholar
  34. Seliger HH, Fastie WG, McElroy WD (1961) Bioluminescence in Chesapeake Bay. Science 133:699–700PubMedCrossRefGoogle Scholar
  35. Sigee DC (1984) Structural DNA and genetically active DNA in dinoflagellate chromosomes. Biosystems 16:203–210CrossRefGoogle Scholar
  36. Sineshchekov OA, Jung KH, Spudich JL (2002) Two rhodopsins mediate phototaxis to low- and high-intensity light in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 25(99):8689–8694Google Scholar
  37. Sineshchekov OA, Govorunova EG, Jung KH, Zauner S, Maier US, Spudich JL (2005) Rhodopsin-mediated photoreception in cryptophyte flagellates. Biophys J 89:4310–4319PubMedCrossRefGoogle Scholar
  38. Spector D (1984) Dinoflagellate nuclei. In: Spector DL (ed) Dinoflagellates. Academic, Orlando, pp 107–147Google Scholar
  39. Sweeney B (1987) Bioluminescence and circadian rhythms. In: Taylor FJR (ed) The biology of dinoflagellates, botanical monographs, vol 21. Blackwell Scientific, OxfordGoogle Scholar
  40. Tanikawa N, Akimoto H, Ogoh K, Chun W, Ohmiya Y (2004) Expressed sequence tag analysis of the dinoflagellate Lingulodinium polyedrum during dark phase. Photochem Photobiol 80:31–35PubMedCrossRefGoogle Scholar
  41. Taroncher-Oldenburg G, Anderson DM (2000) Identification and characterization of three differentially expressed genes, encoding S-adenosylhomocysteine hydrolase, methionine aminopeptidase, and a histone-like protein, in the toxic dinoflagellate Alexandrium fundyense. Appl Environ Microbiol 66:2105–2112PubMedCrossRefGoogle Scholar
  42. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41PubMedCrossRefGoogle Scholar
  43. The Gene Ontology Consortium (2007) The Gene Ontology project in 2008. Nucleic Acids Res 34:D322–D326CrossRefGoogle Scholar
  44. Triplett EL, Govind NS, Roman SI, Jovinem RVM, Prèzelinm BB (1993) Characterization of the sequence organization of DNA from the dinoflagellate Heterocapsa pygmaea (Glenodinium sp.). Mol Mar Biol Biotechnol 2:239–245Google Scholar
  45. Uribe P, Espejo RT (2003) Effect of associated bacterial microflora in the growth and toxin production of Alexandrium catenella. Appl Environ Microbiol 69:659–662PubMedCrossRefGoogle Scholar
  46. Weinmaster G, Roberts VJ, Lemke G (1992) Notch2: a second mammalian Notch gene. Development 116:931–941PubMedGoogle Scholar
  47. Widder EA, Case JF, Bernstein SA, MacIntyre S, Lowenstine MR, Bowlby MR, Cook DP (1993) A new large volume bioluminescence bathyphotometer with defined turbulence excitation. Deep-Sea Res 40:607–627CrossRefGoogle Scholar
  48. Wilson WH, Schroeder DC, Allen MJ, Holden MT, Parkhill J, Barrell BG, Churcher C, Hamlin N, Mungall K, Norbertczak H, Quail MA, Price C, Rabbinowitsch E, Walker D, Craigon M, Roy D, Ghazal P (2005) Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science 309:1090–1092PubMedCrossRefGoogle Scholar
  49. Zhang Z, Green BR, Cavalier-Smith T (1999) Single gene circles in dinoflagellate chloroplast genomes. Nature 400:155–159PubMedCrossRefGoogle Scholar
  50. Zhang H, Hou Y, Miranda L, Campbell DA, Sturm NR, Gaasterland T, Lin S (2007) Spliced leader RNA trans-splicing in dinoflagellates. Proc Natl Acad Sci U S A 104:4618–4623PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Paulina Uribe
    • 1
  • Daniela Fuentes
    • 1
  • Jorge Valdés
    • 2
    • 3
  • Amir Shmaryahu
    • 2
    • 3
  • Alicia Zúñiga
    • 1
  • David Holmes
    • 2
    • 3
  • Pablo D. T. Valenzuela
    • 1
    • 2
  1. 1.Fundación Ciencia para la VidaSantiagoChile
  2. 2.Instituto MIFABSantiagoChile
  3. 3.Center for Bioinformatics and Genome BiologySantiagoChile

Personalised recommendations