An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar)

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Hagen Larsen, Heidi ^a   Laerdahl, Jon K ^b   Panitz, Frank ^c   Adzhubei, Alexei ^b   Høyheim, Bjørn ^a,d  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

^c DANISH INSTITUTE OF AGRICULTURAL SCIENCES   (Denmark)

^d OSLO UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; CONTIG; GENE PRODUCT;

ARTICLE; ATLANTIC SALMON; DEVELOPMENTAL STAGE; DNA LIBRARY; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GILL; INTESTINE; MARINE ENVIRONMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; OSMOREGULATION; SEQUENCE ANALYSIS; SURVIVAL; UNINDEXED SEQUENCE; ANIMAL; BIOLOGY; CLUSTER ANALYSIS; CONTIG MAPPING; DNA SEQUENCE; GENE LIBRARY; METABOLISM; MOLECULAR GENETICS; SALMON;

SALMO SALAR;

ANIMALS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; CONTIG MAPPING; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION REGULATION; GENE LIBRARY; GILLS; INTESTINES; MOLECULAR SEQUENCE DATA; SALMON; SEQUENCE ANALYSIS, DNA;

EID: 29144462664     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-171     Document Type: Article

References (22)

1. NCBI - National Center for Biotechnology Information [http://www.ncbi.nlm.nih.gov/entrez].
2. Allendorf FWaT, G. H.: Tetraploidy and the evolution of salmonid fishes. In: Evolutionary genetcs of fishes. Edited by Turner BJ. New York: Plenum Press; 1984: 1-53.
3. Ohno S, Wolf U, Atkin NB: Evolution from fish to mammals by gene duplication. Hereditas 1968, 59(1):169-187.
4. Wolfe KH: Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2001, 2(5):333-341.
5. Boeuf G: Salmonid smolting: a pre-adaptation to the oceanic environment. London: Chapman & Hall; 1993.
6. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF et al: Complementary DNA sequencing: expressed sequence tags and human genome project. Science 1991, 252(5013):1651-1656.
7. Marra MA, Hillier L, Waterston RH: Expressed sequence tags - ESTablishing bridges between genomes. Trends Genet 1998, 14(1):4-7.
8. 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(1-2):121-130.
9. Martin SA, Caplice NC, Davey GC, Powell R: EST-based identification of genes expressed in the liver of adult Atlantic salmon (Salmo salar). Biochem Biophys Res Commun 2002, 293(1):578-585.
10. Rise ML, von Schalburg KR, Brown GD, Mawer MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR et al: Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res 2004, 14(3):478-490.
11. SGP - Salmon genome project [http://www.salmongenome.no].
12. Chomczynski P, Sacchi N: Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 1987, 162(1):156-159.
13. Ewing B, Hillier L, Wendl MC, Green P: Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998, 8(3):175-185.
14. Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8(3):186-194.
15. Repeat Masker [http://ftp.genomewashington.edu/RM/RepeatMasker.html].
16. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
17. NCBI - National Center for Biotechnology Information [ftp://ftp.ncbi.nih.gov/blast/db].
18. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29.
19. Ashburner M, Lewis S: On ontologies for biologists: the Gene Ontology - untangling the web. Novartis Found Symp 2002, 247:66-80; discussion 80-63, 84-90, 244-252.
20. European Bioinformatics Institute [http://www.ebi.ac.uk/GOA].
21. European Bioinformatics Institute [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT].
22. The Gene Ontology [http://www.geneontology.org].