Comprehensive EST analysis of Atlantic halibut (Hippoglossus hippoglossus), a commercially relevant aquaculture species

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Douglas, Susan E ^a   Knickle, Leah C ^a   Kimball, Jennifer ^a   Reith, Michael E ^a  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; CONTIG; MICROSATELLITE DNA;

ANIMAL TISSUE; AQUACULTURE; ARTICLE; DNA LIBRARY; DNA MICROARRAY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; FISH; GENE EXPRESSION; GENE MAPPING; GILL; HIPPOGLOSSUS HIPPOGLOSSUS; INTESTINE; KIDNEY; LARVAL STAGE; LIVER; MICROARRAY ANALYSIS; MICROSATELLITE MARKER; NONHUMAN; NUCLEOTIDE SEQUENCE; OVARY; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; SKIN; SPLEEN; TESTIS; UNINDEXED SEQUENCE; ANIMAL; BIOLOGICAL MODEL; CONTIG MAPPING; FLOUNDER; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC MARKER; GENETICS; GENOME; GENOMICS; METHODOLOGY; TISSUE DISTRIBUTION;

HIPPOGLOSSUS HIPPOGLOSSUS;

ANIMALS; CONTIG MAPPING; EXPRESSED SEQUENCE TAGS; FLOUNDER; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC MARKERS; GENOME; GENOMICS; MICROSATELLITE REPEATS; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TISSUE DISTRIBUTION;

EID: 34447527051     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-144     Document Type: Article

References (46)

1. Worm B Barbier EB Beaumont N Duffy JE Folke C Halpern BS Jackson JBC Lotze HK Micheli F Palumbi SR Sala E Selkoe KA Stachowicz JJ Watson R Impacts of biodiversity loss on ocean ecosystem services Science 2006 314 787-790 10.1126/science.1132294 17082450
2. Hendry CI Martin-Robichaud DJ Benfey TJ Hormonal sex reversal of Atlantic halibut (Hippoglossus hippoglossus L.) Aquaculture 2003 219 769-781 10.1016/S0044-8486(02)00344-7
3. Gara B Shields RJ McEvoy L Feeding strategies to achieve correct metamorphosis of Atlantic halibut, Hippoglossus hippoglossus L., using enriched Artemia Aquaculture Research 1998 29 935-948 10.1046/ j.1365-2109.1998.29120935.x
4. Hamre K Opstad I Espe M Solbakken J Hemre G-I Pittman K Nutrient composition and metamorphosis success of Atlantic halibut (Hippoglossus hippoglossus, L.) larvae fed natural zooplankton or Artemia Aquaculture Nutrition 2002 8 139-148 10.1046/j.1365-2095.2002.00201.x
5. Okada N Takagi Y Seikai T Tanaka M Tagawa M Asymmetrical development of bones and soft tissues during eye migration of metamorphosing Japanese flounder, Paralichthys olivaceus Cell Tissue Research 2001 304 59-66 10.1007/s004410100353 11383887
6. Naess T Lie O A sensitive period during first feeding for the determination of pigmentation pattern in Atlantic halibut, Hippoglossus hippoglossus L., juveniles: The role of diet Aquaculture Research 1998 29 925-934 10.1046/j.1365-2109.1998.29120925.x
7. Venizelos A Benetti D Pigment abnormalities in flatfish Aquaculture 1999 176 181-188 10.1016/S0044-8486(99)00060-5
8. Saele O Solbakken JS Watanabe K Hamre K Pittman K The effect of diet on ossification and eye migration in Atlantic halibut larvae (Hippoglossus hippoglossus L.) Aquaculture 2003 220 683-696 10.1016/ S0044-8486(02)00584-7
9. Adams MD Kelley JM Gocayne JD Dubnick M Polymeropoulos MH Xiao H Merril CR Wu A Olde B Moreno RF Complementary DNA sequencing: Expressed sequence tags and human genome project Science 1991 252 1651-1656 10.1126/science.2047873 2047873
10. Marra MA Hillier L Waterston RH Expressed sequence tags - ESTablishing bridges between genomes Trends in Genetics 1998 14 4-7 10.1016/ S0168-9525(97)01355-3 9448457
11. Serapion J Kucuktas H Feng J Liu Z Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus) Marine Biotechnology 2004 6 364-377 10.1007/ s10126-003-0039-z 15136916
12. Diatchenko L Lau Y-FC Campbell AP Chenchik A Moqadam F Huang B Lukyanov S Lukyanov K Gurskaya N Sverdlov ED Siebert PD Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries Proceedings of the National Academy of Science of the USA 1996 93 6025-6030 10.1073/pnas.93.12.6025
13. Nam B-H Yamamoto E Hirono I Aoki T A survey of expressed genes in the leukocytes of Japanese flounder, Paralichthys olivaceus, infected with Hirame rhabdovirus Developmental and Comparative Immunology 2000 24 13-24 10.1016/S0145-305X(99)00058-0
14. Kono T Sakai M The analysis of expressed genes in the kidney of Japanese flounder, Paralichthys olivaceus, injected with the immunostimulant peptidoglycan Fish and Shellfish Immunology 2001 11 357-366 10.1006/ fsim.2000.0314
15. Davey GC Caplice NC Martin SA Powell R A survey of genes in the Atlantic salmon (Salmo salar) as identified by expressed sequence tags Gene 2001 263 121-130 10.1016/S0378-1119(00)00587-4 11223250
16. Aoki T Hirono I Kim M-G Katagiri T Tokuda Y Toyohara H Yamamota E Identification of viral induced genes in Ig+ leucocytes of Japanese flounder Paralichthys olivaceus, by differential hybridisation with subtracted and un-subtracted cDNA probes Fish and Shellfish Immunology 2000 10 623-630 10.1006/fsim.2000.0279
17. Aoki T Nam B-H Hirono I Yamamota E Sequences of 596 cDNA clones (565,977 bp) of Japanese flounder (Paralichthys olivaceus) leukocytes infected with Hirame rhabdovirus Marine Biotechnology 1999 1 477-488 10525682 10.1007/PL00011804
18. Bayne CJ Gerwick L Fujiki K Nakao M Yano T Immune-relevant (including acute phase) genes identified in the livers of rainbow trout, Oncorhynchus mykiss, by means of suppression subtractive hybridization Developmental and Comparative Immunology 2001 25 205-217 10.1016/ S0145-305X(00)00057-4
19. Douglas SE Belanger JC Tsoi SCM Williams J Ewart KV Identification of differentially expressed genes involved in Atlantic salmon (Salmo salar) host-pathogen interaction using microarray technology Sixth International Marine Biotechnology Conference - Aquatic Genomics Symposium; Sept. 20-27, 2003 Tokyo, Japan. Marine Biotechnology 2003 S335-339
20. Gerwick L Steinhauer R LaPatra SE Sandell T Ortuno J Hajiseyedjavadi N Bayne CJ The acute phase response of rainbow trout (Oncorhynchus mykiss) plasma proteins to viral, bacterial and fungal inflammatory agents Fish and Shellfish Immunology 2002 12 229-242 10.1006/fsim.2001.0367
21. Kocabas AM Li P Cao D Karsi A He C Patterson A Ju Z Dunham RA Liu Z Expression profile of the channel catfish spleen: Analysis of genes involved in immune functions Marine Biotechnology 2002 4 526-536 10.1007/ s10126-002-0067-0 14961227
22. Kono T Sakai M LaPatra SE Expressed sequence tag analysis of kidney and gill tissues from rainbow trout (Oncorhynchus mykiss) infected with Infectious Hematopoietic Necrosis virus Marine Biotechnology 2000 2 493-498 11246416
23. Martin SA Blaney SC Houlihan DF Secombes CJ Transcriptome response following administration of a live bacterial vaccine in Atlantic salmon (Salmo salar) Molecular Immunology 2006 43 1900-1911 10.1016/ j.molimm.2005.10.007 16313960
24. Savan R Sakai M Analysis of expressed sequence tags (EST) obtained from common carp, Cyprinus carpio L., head kidney cells after stimulation by two mitogens, lipopolysaccharide and concanavalin-A Comparative Biochemistry and Physiology Part B 2002 131 71-82 10.1016/ S1096-4959(01)00488-2
25. Suzuki T Shin IT Kohara Y Kasahara M Transcriptome analysis of hagfish leukocytes: A framework for understanding the immune system of jawless fishes Developmental and Comparative Immunology 2004 28 993-1003 10.1016/ j.dci.2004.04.005
26. Tsoi SC Ewart KV Penny S Melville K Liebscher RS Brown LL Douglas SE Identification of immune-relevant genes from Atlantic salmon using suppression subtractive hybridization Marine Biotechnology 2004 6 199-214 10.1007/s10126-002-0101-2 15129324
27. Chini V Rimoldi S Terova G Saroglia M Rossi F Bernardini G Gornati R EST-based identification of genes expressed in the liver of adult seabass (Dicentrarchus labrax, L.) Gene 2006 376 102-106 10.1016/ j.gene.2006.02.010 16616996
28. Park KC Osborne JA Tsoi SC Brown LL Johnson SC Expressed sequence tags analysis of Atlantic halibut (Hippoglossus hippoglossus) liver, kidney and spleen tissues following vaccination against Vibrio anguillarum and Aeromonas salmonicida Fish and Shellfish Immunology 2005 18 393-415 10.1016/j.fsi.2004.10.003
29. Fernandes JM Mackenzie MG Elgar G Suzuki Y Watabe S Kinghorn JR Johnston IA A genomic approach to reveal novel genes associated with myotube formation in the model teleost, Takifugu rubripes Physiological Genomics 2005 22 327-338 10.1152/physiolgenomics.00087.2005 15928209
30. Ju Z Karsi A Kocobas A Patterson A Li P Cao D Dunham R Liu Z Transcriptome analysis of channel catfish (Ictalurus punctatus): Genes and expression profile from the brain Gene 2000 261 373-382 10.1016/ S0378-1119(00)00491-1 11167026
31. Karsi A Li P Dunham R Liu ZJ Transcriptional activities in the pituitaries of channel catfish before and after induced ovulation by injection of carp pituitary extract as revealed by expressed sequence tag analysis Journal of Molecular Endocrinology 1998 21 121-129 10.1677/ jme.0.0210121 9801455
32. Zhou L Yao B Xia W Li CJ Wang Y Shi YH Gui JF EST-based identification of genes expressed in the hypothalamus of male orange-spotted grouper (Epinephelus coioides) Aquaculture 256 129-139 10.1016/ j.aquaculture.2006.01.022
33. Magalhaes GS Junqueira-de-Azevedo IL Lopes-Ferreira M Lorenzini DM Ho PL Moura-da-Silva AM Transcriptome analysis of expressed sequence tags from the venom glands of the fish Thalassophryne nattereri Biochimie 2006 88 693-699 10.1016/j.biochi.2005.12.008 16488069
34. Gene Ontology http://www.geneontology.org/
35. Pleurogene http://www.pleurogene.ca
36. Clusters of Orthologous Genes http://www.ncbi.nlm.nih.gov/COG/
37. Kyoto Encyclopedia of Genes and Genomes http://www.genome.jp/kegg/
38. Galloway TF Bardal T Kvam SN Dahle SW Nesse G Randol M Kjorsvik E Andersen O Somite formation and expression of MyoD, myogenin and myosin in Atlantic halibut (Hippoglossus hippoglossus L.) embryos incubated at different temperatures: Transient asymmetric expression of MyoD Journal of Experimental Biology 2006 209 2432-2441 10.1242/jeb.02269 16788026
39. Murray HM Perez-Casanova JC Gallant JW Johnson SC Douglas SE Trypsinogen expression during the development of the exocrine pancreas in winter flounder (Pleuronectes americanus) Comparative Biochemistry and Physiology Part A 2004 138 53-59 10.1016/j.cbpb.2004.02.020
40. Murray HM Gallant JW Johnson SC Douglas SE Cloning and expression analysis of three digestive enzymes from Atlantic halibut during early development: Predicting gastrointestinal functionality Aquaculture 2006 252 394-408 10.1016/j.aquaculture.2005.03.030
41. Song HD Sun XJ Deng M Zhang GW Zhou Y Wu XY Sheng Y Chen Y Ruan Z Jiang CL Fan HY Zon LI Kanki JP Liu TX Look AT Chen Z Hematopoietic gene expression profile in zebrafish kidney marrow Proceedings of the National Academy of Science of the USA 2004 101 16240-16245 10.1073/ pnas.0407241101
42. Sekar V A rapid screening procedure for the identification of recombinant bacterial clones BioTechniques 5 11-13
43. Huang X Madan A CAP3: A DNA Sequence Assembly Program Genome Res 1999 9 868-877 310812 10508846 10.1101/gr.9.9.868
44. Koski LB Gray MW Lang BF Burger G AutoFACT: An Automatic Functional Annotation and Classification Tool BMC Bioinformatics 2005 6 151-161 1182349 15960857 10.1186/1471-2105-6-151
45. Groth D Lehrach H Hennig S GOblet: A platform for Gene Ontology annotation of anonymous sequence data Nucleic Acids Research 2004 32 W313-317 441544 15215401 10.1093/nar/gkh406
46. Benson G Tandem repeats finder: A program to analyze DNA sequences Nucleic Acids Research 1999 27 573-580 148217 9862982 10.1093/nar/ 27.2.573