Preparation and analysis of an expressed sequence tag library from the toxic dinoflagellate Alexandrium catenella

Marine Biotechnology

Volumn 10, Issue 6, 2008, Pages 692-700

  Uribe, Paulina ^a   Fuentes, Daniela ^a   Valdés, Jorge ^b,c   Shmaryahu, Amir ^b,c   Zúñiga, Alicia ^a   Holmes, David ^b,c   Valenzuela, Pablo D T ^a,b  

^a Fundacion Ciencia para la Vida   (Chile)

^b UNIVERSIDAD ANDRÉS BELLO   (Chile)

^c Center for Bioinformatics and Genome Biology   (Chile)

Author keywords

Alexandrium catenella; cDNA sequencing; Red tide microalgae; Toxic dinoflagellate

Indexed keywords

ALEXANDRIUM; ALEXANDRIUM CATENELLA; CARBOHYDRATE METABOLISMS; CDNA LIBRARIES; CDNA SEQUENCING; CONTIGS; EXPRESSED SEQUENCE TAGS; GENE BANKS; GEOGRAPHICAL AREAS; MICROALGAE; PARALYTIC SHELLFISH POISONING; RED TIDE MICROALGAE; SHELLFISH AQUACULTURE INDUSTRIES; TOXIC DINOFLAGELLATE; TOXIC DINOFLAGELLATES; TOXIC SPECIES;

ALGAE; AQUACULTURE; BIOCHEMISTRY; CARBOHYDRATES; CELL CULTURE; GENES; MICROORGANISMS; OPTICAL TOMOGRAPHY; ORGANIC COMPOUNDS; PHOTOSYNTHESIS; PROGRAMMING THEORY; REAL TIME SYSTEMS;

TOXIC MATERIALS;

PROTOZOAL DNA;

DINOFLAGELLATE; GENE EXPRESSION; PARALYTIC SHELLFISH POISONING; TOXIC ORGANISM;

ANIMAL; ARTICLE; CONTIG MAPPING; DINOFLAGELLATE; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE LIBRARY; GENETIC DATABASE; GENETICS; GENOMICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ANIMALS; CONTIG MAPPING; DATABASES, GENETIC; DINOFLAGELLIDA; DNA, PROTOZOAN; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; GENOMICS; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA;

ALEXANDRIUM; ALEXANDRIUM CATENELLA; BACTERIA (MICROORGANISMS); DINOPHYCEAE; PROTISTA;

EID: 55949096148     PISSN: 14362228     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10126-008-9107-8     Document Type: Article

References (50)

1. MV Abrahams LD Townsend 1993 Bioluminescence in dinoflagellates: A test of the burgular alarm hypothesis Ecology 74 258 260
2. SF Altschul W Gish E Miller EW Myers DT Lipman 1990 Basic local alignment search tool J Mol Biol 3 403 410
3. DM Anderson A Grabher M Herzog 1992 Separation of coding sequences from structural DNA in the dinoflagellate Crypthecodinium cohnii Mol Mar Biol Biotechnol 1 89 96
4. EY Armbrust JA Berges C Bowler BR Green D Martinez NH Putnam S Zhou AF Allen KE Apt M Bechner MA Brzezinski BK Chaal A Chiovitti AK Davis MS Demarest JC Detter T Glavina D Goodstein MZ Hadi U Hellsten M Hildebrand BD Jenkins J Jurka VV Kapitonov N Kroger WW Lau T Lane FW Larimer JC Lippmeier S Lucas M Medina A Montsant M Obornik MS Parker B Palenik GT Pazour PM Richardson TA Rynearson MA Saito DC Schwartz K Thamatrakoln K Valentin A Vardi FP Wilkerson DS Rokhsar 2004 The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism Science 306 79 86
5. TR Bachvaroff GT Concepcion CR Rogers EM Herman CH Delwiche 2004 Dinoflagellate expressed sequence tag data indicate massive transfer of chloroplast genes to the nuclear genome Protist 155 65 78
6. Y Bhaud M Geraud J Ausseil MO Soyer-Gobillard H Moreu 1999 Cyclic expression of a nuclear protein in a dinoflagellate J Eukaryot Microbiol 46 259 267
7. LL Chan WH Sit PK Lam DP Hsieh IJ Hodgkiss JM Wan AY Ho NM Choi DZ Wang D Dudgeon 2006 Identification and characterization of a "biomarker of toxicity" from the proteome of the paralytic shellfish toxin-producing dinoflagellate Alexandrium tamarense (Dinophyceae) Proteomics 6 654 666
8. X Cheng 1995 DNA modification by methyltransferases Curr Opin Struct Biol 5 4 10
9. EA Craig 1989 Essential roles of 70 kDa heat inducible proteins Bioessays 11 48 52
10. WE Easias HC Curl Jr 1972 Effect of dinoflagellate bioluminescence of copepod ingestión rates Limnol Oceanogr 17 901 906
11. DL Edner DM Anderson 2006 Global transcriptional profiling of the toxic dinoflagellate Alexandrium fundyense using massively parallel signature sequencing BMC Genomics 7 88
12. J Giovanelli 1987 Sulfur aminoacids of plants: an overview Methods Enzymol 143 419 426
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 45-62
14. L Guzmán I Campodónico 1975 Marea Roja en la región de Magallanes Publ Inst Pat Ser Monogr Punta Arenas (Chile) 9 44
15. L Guzmán I Campodónico 1978 Mareas Rojas en Chile Interciencia 3 144 151
16. JD Hackett TE Scheetz HS Yoon MB Soares MF Bonaldo TL Casavant D Bhattacharya 2005 Insight into a dinoflagellate genome through expressed sequence tag analysis BMC Genomics 6 80
17. G Hallegraeff 1993 A review of harmful algal blooms and their apparent global increase Phycologia 32 79 99
18. S Hosoi-Tanabe S Tomishima S Nagai Y SaKo 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 251 161 168
19. X Huang A Madan 1999 CAP3: A DNA sequence assembly program Genome Res 9 868 877
20. I Imai 1987 Size distribution, number and biomass of bacteria in intertidal sediments and seawater of Ohmi Bay, Japan Bull Jpn Soc Microb Ecol 2 1 11
21. T Kuwae Y Hosokawa 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 3412
22. L Li R Hong JW Hastings 1997 Three functional luciferase domains in a single polypeptide chain Proc Natl Acad Sci U S A 94 8954 8958
23. KB Lidie JC Ryan M Barbier FM Vandolah 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 7 481 493
24. S Lin 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 42 746 748
25. S Lindquist EA Craig 1988 The heat-shock proteins Annu Rev Genet 22 631 677
26. E Liscum DW Hodgson TJ Campbell 2003 Blue light signaling through the cryptochromes and phototropins. So that's what the blues is all about Plant Physiol 133 1429 1436
27. L Liu T Wilson JW Hastings 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 16560
28. S Machabee L Wall D Morse 1994 Expression and genomic organization of a dinoflagellate gene family Plant Mol Biol 25 23 31
29. NJ Mulder R Apweiler TK Attwook A Bairoch A Bateman D Binns P Bork V Buillard L Cerutti R Copley E Courcelle U Das L Daugherty M Dibley R Finn W Fleischmann J Gough D Haft N Hulo S Hunter D Kahn A Kanapin A Kejariwal A Labarga PS Langendijk-Genevaux D Lonsdale R Lóperz I Letunic M Madera J Maslen C McAnulla J McDowall J Mistry A Mitchell AN Nikolskaya S Orchard C Orengo R Petryszak JD Slengut CJ Sigrist PD Thomas F Valentin D Wilson CH Wu C Yeats 2007 New developments in the InterPro database Nucleic Acids Res 35 224 228
30. OK Okamoto JW Hastings 2003 Novel dinoflagellate clock-related genes identified through microarrays analysis J Phycol 39 519 526
31. NJ Patron RF Waller JH Archibald PT Keeling 2005 Complex protein targeting to dinoflagellate plastids J Mol Biol 348 1015 1024
32. SR Santos MA Coffroth 2003 Molecular genetic evidence that dinoflagellates belonging to the genus Symbiodinium Freudenthal are haploid Biol Bull 204 10 20
33. CA Scholin GM Hallegraeff DM Anderson 1995 Molecular evolution of the Alexandrium tamarense species complex (Dinophyceae) dispersal in the North American and west Pacific regions Phycologia 34 472 485
34. HH Seliger WG Fastie WD McElroy 1961 Bioluminescence in Chesapeake Bay Science 133 699 700
35. DC Sigee 1984 Structural DNA and genetically active DNA in dinoflagellate chromosomes Biosystems 16 203 210
36. OA Sineshchekov KH Jung JL Spudich 2002 Two rhodopsins mediate phototaxis to low- and high-intensity light in Chlamydomonas reinhardtii Proc Natl Acad Sci U S A 25 99 8689 8694
37. OA Sineshchekov EG Govorunova KH Jung S Zauner US Maier JL Spudich 2005 Rhodopsin-mediated photoreception in cryptophyte flagellates Biophys J 89 4310 4319
38. Spector D (1984) Dinoflagellate nuclei. In: Spector DL (ed) Dinoflagellates. Academic, Orlando, pp 107-147
39. Sweeney B (1987) Bioluminescence and circadian rhythms. In: Taylor FJR (ed) The biology of dinoflagellates, botanical monographs, vol 21. Blackwell Scientific, Oxford
40. N Tanikawa H Akimoto K Ogoh W Chun Y Ohmiya 2004 Expressed sequence tag analysis of the dinoflagellate Lingulodinium polyedrum during dark phase Photochem Photobiol 80 31 35
41. G Taroncher-Oldenburg DM Anderson 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 2112
42. RL Tatusov ND Fedorova JD Jackson AR Jacobs B Kiryutin EV Koonin DM Krylov R Mazumder SL Mekhedov AN Nikolskaya BS Rao S Smirnov AV Sverdlov S Vasudevan YI Wolf JJ Yin DA Natale 2003 The COG database: an updated version includes eukaryotes BMC Bioinformatics 4 41
43. The Gene Ontology Consortium 2007 The Gene Ontology project in 2008 Nucleic Acids Res 34 D322 D326
44. EL Triplett NS Govind SI Roman RVM Jovinem BB Prèzelinm 1993 Characterization of the sequence organization of DNA from the dinoflagellate Heterocapsa pygmaea (Glenodinium sp.) Mol Mar Biol Biotechnol 2 239 245
45. P Uribe RT Espejo 2003 Effect of associated bacterial microflora in the growth and toxin production of Alexandrium catenella Appl Environ Microbiol 69 659 662
46. G Weinmaster VJ Roberts G Lemke 1992 Notch2: a second mammalian Notch gene Development 116 931 941
47. EA Widder JF Case SA Bernstein S MacIntyre MR Lowenstine MR Bowlby DP Cook 1993 A new large volume bioluminescence bathyphotometer with defined turbulence excitation Deep-Sea Res 40 607 627
48. WH Wilson DC Schroeder MJ Allen MT Holden J Parkhill BG Barrell C Churcher N Hamlin K Mungall H Norbertczak MA Quail C Price E Rabbinowitsch D Walker M Craigon D Roy P Ghazal 2005 Complete genome sequence and lytic phase transcription profile of a Coccolithovirus Science 309 1090 1092
49. Z Zhang BR Green T Cavalier-Smith 1999 Single gene circles in dinoflagellate chloroplast genomes Nature 400 155 159
50. H Zhang Y Hou L Miranda DA Campbell NR Sturm T Gaasterland S Lin 2007 Spliced leader RNA trans-splicing in dinoflagellates Proc Natl Acad Sci U S A 104 4618 4623