Sequencing the genome of the Atlantic salmon (Salmo salar)

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.

• Publication year

  2010

• Venue

  Genome Biology

• Publication date

  2010-09-30

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1186/gb-2010-11-9-403PMID 20887641PMCID 2965382
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Evolutionary Genetics of Fishes

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  2009cited by this paper
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  2009cited by this paper
• Prepublication data sharing

  2009influential reference
• Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species.

  2009cited by this paper
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  2009cited by this paper
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  2008cited by this paper
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  2008cited by this paper
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  2008cited by this paper
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  2008cited by this paper
• Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection

  2008cited by this paper
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  2008cited by this paper
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  2008cited by this paper
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  2008cited by this paper
• Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon)

  2008cited by this paper
• Striking antigen recognition diversity in the Atlantic salmon T-cell receptor alpha/delta locus.

  2008cited by this paper
• Functional adaptive diversity of the Atlantic salmon T-cell receptor gamma locus.

  2008cited by this paper
• Striking antigen recognition diversity in the Atlantic salmon T-cell receptor α/δ locus

  2008cited by this paper
• Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar)

  2007cited by this paper
• Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource

  2007cited by this paper
• Biodiversity and Population Structure

  2007cited by this paper
• Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids

  2007cited by this paper
• The Atlantic salmon : genetics, conservation and management

  2007cited by this paper
• An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences

  2007cited by this paper
• Community annotation: procedures, protocols, and supporting tools.

  2006cited by this paper
• Novel Relationships Among Ten Fish Model Species Revealed Based on a Phylogenomic Analysis Using ESTs

  2006cited by this paper
• Expression of morphogenic genes in mature ovarian and testicular tissues: Potential stem‐cell niche markers and patterning factors

  2006cited by this paper
• Eukaryotic genome size databases

  2006cited by this paper
• A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects

  2005cited by this paper
• Type I microsatellite markers from Atlantic salmon (Salmo salar) expressed sequence tags

  2005cited by this paper
• A physical map of the genome of Atlantic salmon, Salmo salar.

  2005cited by this paper
• Protein domains and architectural innovation in plant-associated Proteobacteria

  2005cited by this paper
• From 2R to 3R: evidence for a fish-specific genome duplication (FSGD).

  2005cited by this paper
• Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in atlantic salmon (Salmo salar L.).

  2005cited by this paper
• Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray

  2005cited by this paper
• A Comprehensive Survey of the Genes Involved in Maturation and Development of the Rainbow Trout Ovary1

  2005cited by this paper
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  2005cited by this paper
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  2005cited by this paper
• An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar)

  2005cited by this paper
• The Ensembl core software libraries.

  2004cited by this paper
• Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates.

  2004cited by this paper
• Microarray analyses identify molecular biomarkers of Atlantic salmon macrophage and hematopoietic kidney response to Piscirickettsia salmonis infection.

  2004cited by this paper
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  2004cited by this paper
• A microsatellite linkage map for Atlantic salmon (Salmo salar).

  2004cited by this paper
• Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

  2004cited by this paper
• A linkage map of Atlantic salmon (Salmo salar) reveals an uncommonly large difference in recombination rate between the sexes.

  2004cited by this paper
• Identification of Immune-Relevant Genes from Atlantic Salmon Using Suppression Subtractive Hybridization

  2004cited by this paper
• Chromosome relationships in the genus Salmo

  2004cited by this paper
• To order or request additional

  2004cited by this paper
• An overview of Ensembl.

  2004cited by this paper
• Comparative genome analysis of the primary sex-determining locus in salmonid fishes.

  2003cited by this paper
• The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes.

  2003cited by this paper
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  2002cited by this paper
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  2002cited by this paper
• EST-based identification of genes expressed in the liver of adult Atlantic salmon (Salmo salar).

  2002cited by this paper
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  2001cited by this paper
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  2001cited by this paper
• Chromosome evolution in the Salmonidae (Pisces): an update

  2001cited by this paper
• Preservation of duplicate genes by complementary, degenerative mutations.

  1999cited by this paper
• Fishes of the World, 3rd Edition

  1994cited by this paper
• The isochore organization of the human genome and its evolutionary history--a review.

  1993cited by this paper
• A survey of

  1989cited by this paper
• THE CHROMOSOMES OF SALMONID FISHES

  1987cited by this paper
• Tetraploidy and the Evolution of Salmonid Fishes

  1984cited by this paper
• Fishes of the world.

  1978cited by this paper
• Evolution by Gene Duplication

  1970influential reference

• Commercial fish genomics: A bibliometric and visualized study

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