Home LiteratureArticle Details
PMID: 20887641 Published · ppublish English Journal Article

Sequencing the genome of the Atlantic salmon (Salmo salar).

Genome biology ·Vol. 11 ·No. 9 ·2010-00-00 ·Pages 403

Davidson WS, Koop BF, Jones SJ, Iturra P, Vidal R, Maass A, Jonassen I, Lien S, Omholt SW

Abstract

The International Collaboration to Sequence the Atlantic Salmon Genome (ICSASG) will produce a genome sequence that identifies and physically maps all genes in the Atlantic salmon genome and acts as a reference sequence for other salmonids.

MeSH Terms
Animals Base Sequence Chromosome Mapping Databases, Genetic Genetic Linkage Genetic Markers Genome Genomic Library Genomics Phylogeny Salmo salar/genetics Sequence Analysis, DNA
Chemicals
Genetic Markers
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Davidson William S
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby BC, V5A 1S6, Canada. wdavidso@sfu.ca
Koop Ben F
Jones Steven J M
Iturra Patricia
Vidal Rodrigo
Maass Alejandro
Jonassen Inge
Lien Sigbjorn
Omholt Stig W
References (60)
60 references, click to expand
  1. Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss).
    BMC Genet. 2009 Aug 18;10:46 PMID: 19689812
  2. An overview of Ensembl.
    Genome Res. 2004 May;14(5):925-8 PMID: 15078858
  3. Evolution of duplicated IgH loci in Atlantic salmon, Salmo salar.
    BMC Genomics. 2010 Sep 02;11:486 PMID: 20813058
  4. Comparative genome analysis of the primary sex-determining locus in salmonid fishes.
    Genome Res. 2003 Feb;13(2):272-80 PMID: 12566405
  5. Comparative genomics identifies candidate genes for infectious salmon anemia (ISA) resistance in Atlantic salmon (Salmo salar).
    Mar Biotechnol (NY). 2011 Apr;13(2):232-41 PMID: 20396924
  6. Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in atlantic salmon (Salmo salar L.).
    Mol Biol Evol. 2005 Apr;22(4):1067-76 PMID: 15689532
  7. Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon.
    Mol Ecol. 2005 Nov;14(13):4193-203 PMID: 16262869
  8. Expression of morphogenic genes in mature ovarian and testicular tissues: potential stem-cell niche markers and patterning factors.
    Mol Reprod Dev. 2006 Feb;73(2):142-52 PMID: 16224774
  9. The isochore organization of the human genome and its evolutionary history--a review.
    Gene. 1993 Dec 15;135(1-2):57-66 PMID: 8276279
  10. Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon).
    BMC Genomics. 2008 Nov 25;9:557 PMID: 19032764
  11. A physical map of the genome of Atlantic salmon, Salmo salar.
    Genomics. 2005 Oct;86(4):396-404 PMID: 16026963
  12. EST-based identification of genes expressed in the liver of adult Atlantic salmon (Salmo salar).
    Biochem Biophys Res Commun. 2002 Apr 26;293(1):578-85 PMID: 12054641
  13. Regulation, expression and characterization of aromatase (cyp19b1) transcripts in ovary and testis of rainbow trout (Oncorhynchus mykiss).
    Comp Biochem Physiol B Biochem Mol Biol. 2010 Feb;155(2):118-25 PMID: 19895900
  14. Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon.
    BMC Genomics. 2010 Mar 05;11:154 PMID: 20205726
  15. Landscape evolutionary genomics.
    Biol Lett. 2010 Aug 23;6(4):502-4 PMID: 20106855
  16. Eukaryotic genome size databases.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D332-8 PMID: 17090588
  17. Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics.
    Genome Res. 2004 Mar;14(3):478-90 PMID: 14962987
  18. An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar).
    BMC Genomics. 2005 Dec 01;6:171 PMID: 16321156
  19. Chromosome relationships in the genus Salmo.
    Chromosoma. 1984;90(3):229-37 PMID: 6499596
  20. Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids.
    BMC Genomics. 2007 Nov 16;8:422 PMID: 18021408
  21. Fish and chips: various methodologies demonstrate utility of a 16,006-gene salmonid microarray.
    BMC Genomics. 2005 Sep 15;6:126 PMID: 16164747
  22. A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects.
    BMC Genomics. 2005 Apr 04;6:50 PMID: 15807896
  23. BAC-based upgrading and physical integration of a genetic SNP map in Atlantic salmon.
    Anim Genet. 2010 Feb;41(1):48-54 PMID: 19917045
  24. Genomic organization of Atlantic salmon (Salmo salar) fatty acid binding protein (fabp2) genes reveals independent loss of duplicate loci in teleosts.
    Mar Genomics. 2009 Sep-Dec;2(3-4):193-200 PMID: 21798188
  25. Striking antigen recognition diversity in the Atlantic salmon T-cell receptor alpha/delta locus.
    Dev Comp Immunol. 2008;32(3):204-12 PMID: 17604101
  26. A linkage map of Atlantic salmon (Salmo salar) reveals an uncommonly large difference in recombination rate between the sexes.
    Anim Genet. 2004 Apr;35(2):81-92 PMID: 15025566
  27. Status and opportunities for genomics research with rainbow trout.
    Comp Biochem Physiol B Biochem Mol Biol. 2002 Dec;133(4):609-46 PMID: 12470823
  28. Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar).
    BMC Genomics. 2009 Oct 30;10:502 PMID: 19878547
  29. Annotated expressed sequence tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource.
    BMC Genomics. 2007 Jul 02;8:209 PMID: 17605782
  30. Identification of the sex-determining locus of Atlantic salmon (Salmo salar) on chromosome 2.
    Cytogenet Genome Res. 2006;112(1-2):152-9 PMID: 16276105
  31. Genomic organization and evolution of the vomeronasal type 2 receptor-like (OlfC) gene clusters in Atlantic salmon, Salmo salar.
    Mol Biol Evol. 2009 May;26(5):1117-25 PMID: 19221009
  32. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species.
    J Hered. 2009 Nov-Dec;100(6):659-74 PMID: 19892720
  33. A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers.
    BMC Genomics. 2008 May 15;9:223 PMID: 18482444
  34. Preservation of duplicate genes by complementary, degenerative mutations.
    Genetics. 1999 Apr;151(4):1531-45 PMID: 10101175
  35. Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome.
    BMC Genomics. 2010 Apr 30;11:279 PMID: 20433749
  36. A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray.
    J Fish Biol. 2008 Jun;72(9):2071-2094 PMID: 19125201
  37. Chromosome evolution in the Salmonidae (Pisces): an update.
    Biol Rev Camb Philos Soc. 2001 Feb;76(1):1-25 PMID: 11325050
  38. Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar).
    BMC Genomics. 2007 Jul 25;8:251 PMID: 17651474
  39. From 2R to 3R: evidence for a fish-specific genome duplication (FSGD).
    Bioessays. 2005 Sep;27(9):937-45 PMID: 16108068
  40. An ultracentrifugation analysis of two hundred fish genomes.
    Gene. 2002 Aug 7;295(2):153-62 PMID: 12354649
  41. Functional adaptive diversity of the Atlantic salmon T-cell receptor gamma locus.
    Mol Immunol. 2008 Apr;45(8):2150-7 PMID: 18241922
  42. Identification of immune-relevant genes from atlantic salmon using suppression subtractive hybridization.
    Mar Biotechnol (NY). 2004 May-Jun;6(3):199-214 PMID: 15129324
  43. Community annotation: procedures, protocols, and supporting tools.
    Genome Res. 2006 Nov;16(11):1329-33 PMID: 17065605
  44. A comprehensive survey of the genes involved in maturation and development of the rainbow trout ovary.
    Biol Reprod. 2005 Mar;72(3):687-99 PMID: 15496514
  45. Microarray analyses identify molecular biomarkers of Atlantic salmon macrophage and hematopoietic kidney response to Piscirickettsia salmonis infection.
    Physiol Genomics. 2004 Dec 15;20(1):21-35 PMID: 15454580
  46. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.
    Nature. 2004 Oct 21;431(7011):946-57 PMID: 15496914
  47. Yesterday's polyploids and the mystery of diploidization.
    Nat Rev Genet. 2001 May;2(5):333-41 PMID: 11331899
  48. Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs.
    J Mol Evol. 2006 Jun;62(6):772-84 PMID: 16752215
  49. Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes.
    Mol Biol Evol. 2004 Jun;21(6):1146-51 PMID: 15014147
  50. A microsatellite linkage map for Atlantic salmon (Salmo salar).
    Anim Genet. 2004 Apr;35(2):98-105 PMID: 15025568
  51. The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes.
    Genome. 2003 Aug;46(4):683-706 PMID: 12897876
  52. The sex determining loci and sex chromosomes in the family salmonidae.
    Sex Dev. 2009;3(2-3):78-87 PMID: 19684453
  53. Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.
    BMC Genomics. 2008 Aug 28;9:404 PMID: 18755037
  54. Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): population-level associations between markers and trait.
    BMC Genomics. 2009 Aug 07;10:368 PMID: 19664221
  55. Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates.
    Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1638-43 PMID: 14757817
  56. A salmonid EST genomic study: genes, duplications, phylogeny and microarrays.
    BMC Genomics. 2008 Nov 17;9:545 PMID: 19014685
  57. A survey of genes in the Atlantic salmon (Salmo salar) as identified by expressed sequence tags.
    Gene. 2001 Jan 24;263(1-2):121-30 PMID: 11223250
  58. Prepublication data sharing.
    Nature. 2009 Sep 10;461(7261):168-70 PMID: 19741685
  59. Isolation, characterization and comparison of Atlantic and Chinook salmon growth hormone 1 and 2.
    BMC Genomics. 2008 Nov 03;9:522 PMID: 18980692
  60. Genomic organization and characterization of two vomeronasal 1 receptor-like genes (ora1 and ora2) in Atlantic salmon Salmo salar.
    Mar Genomics. 2008 Mar;1(1):23-31 PMID: 21798150
Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
Published
2010-00-00
Epub
2010-00-30
Pages
403
Language
English
Region
England
NLM ID
100960660
PMCID
PMC2965382
Subset
IM
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com