Genome

Salmo salar (Atlantic salmon) Atlantic salmon; highly valued in fishing and aquaculture Lineage: Eukaryota[15557]; Metazoa[7782]; Chordata[3579]; Craniata[3544]; Vertebrata[3544]; Euteleostomi[3500]; Actinopterygii[1301]; Neopterygii[1292]; Teleostei[1289]; Protacanthopterygii[35]; Salmoniformes[21]; Salmonidae[21]; Salmoninae[15]; Salmo[2]; Salmo salar[1]

The Atlantic salmon Salmo salar is a higly valued food fish. Salmonid ancestors had a tetraploid genome, and it is thought that these fish are still re-establishing diploidy. As a result, a given locus in one species may have merged into a single gene, while in another species two paralogs may still exist. Triploid salmon, found in natural populations More...or experimentally induced, may be of interest to salmon farmers, as triploid females are functionally sterile and do not experience changes in maturation that lower their market value. Less...

Summary Sequence data:  genome assemblies: 15; sequence reads: 6  (See  Genome Assembly and Annotation report) Statistics:  median total length (Mb): 2638.95  median protein count: 95302  median GC%: 43.4 NCBI Annotation Release:  102 Publications (limited to 20 most recent records) The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon. Gao G, et al. G3 (Bethesda) 2023 Aug 30 A de novo Full-Length mRNA Transcriptome Generated From Hybrid-Corrected PacBio Long-Reads Improves the Transcript Annotation and Identifies Thousands of Novel Splice Variants in Atlantic Salmon. Ramberg S, et al. Front Genet 2021 The Atlantic salmon genome provides insights into rediploidization. Lien S, et al. Nature 2016 May 12 Exploring the transcriptome of Atlantic salmon (Salmo salar) skin, a major defense organ. Micallef G, et al. Mar Biotechnol (NY) 2012 Oct Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome. Leong JS, et al. BMC Genomics 2010 Apr 30 Sequencing the genome of the Atlantic salmon (Salmo salar). Davidson WS, et al. Genome Biol 2010 More...  Representative (genome information for reference and representative genomes) Reference genome:   Salmo salar Ssal_v3.1 Submitter: National Center for Biotechnology Information Loc Type Name RefSeq INSDC Size (Mb) GC% Protein rRNA tRNA Other RNA Gene Pseudogene Chr ssa01 NC_059442.1 HG993260.1 174.5 43.3 5,883 2 212 617 3,200 147 Chr ssa02 NC_059443.1 HG993261.1 95.48 43.5 4,384 1 349 582 2,967 181 Chr ssa03 NC_059444.1 HG993262.1 105.78 43.3 4,489 2 377 599 2,987 124 Chr ssa04 NC_059445.1 HG993263.1 90.54 43.2 3,683 1 380 413 2,428 100 Chr ssa05 NC_059446.1 HG993264.1 92.79 43.7 3,855 - 56 367 2,148 125 Chr ssa06 NC_059447.1 HG993265.1 96.06 43.5 3,909 64 34 498 2,258 96 Chr ssa07 NC_059448.1 HG993266.1 68.86 43.9 2,585 - 264 276 1,622 72 Chr ssa08 NC_059449.1 HG993267.1 28.86 43.5 1,050 - 250 171 920 56 Chr ssa09 NC_059450.1 HG993268.2 161.28 43.7 5,038 3 167 581 2,989 171 Chr ssa10 NC_059451.1 HG993269.1 125.88 43.3 4,328 3 76 703 2,602 168 Chr ssa11 NC_059452.1 HG993270.2 111.87 43.5 3,673 - 44 475 2,042 107 Chr ssa12 NC_059453.1 HG993271.1 101.68 43.3 4,097 - 244 596 2,705 112 Chr ssa13 NC_059454.1 HG993272.1 114.42 43.3 4,422 1 295 464 2,521 105 Chr ssa14 NC_059455.1 HG993273.1 101.98 43.3 4,060 4 96 454 2,226 77 Chr ssa15 NC_059456.1 HG993274.1 110.67 43.5 3,979 2 86 675 2,339 89 Chr ssa16 NC_059457.1 HG993275.1 96.49 43.5 3,614 4 84 378 1,970 108 Chr ssa17 NC_059458.1 HG993276.1 87.49 44.1 3,104 3 273 358 1,994 123 Chr ssa18 NC_059459.1 HG993277.2 84.08 43.2 2,946 1 88 451 1,608 74 Chr ssa19 NC_059460.1 HG993278.1 88.11 43.2 2,864 1 48 336 1,474 79 Chr ssa20 NC_059461.1 HG993279.1 96.85 43.6 3,594 - 148 438 2,013 104 Chr ssa21 NC_059462.1 HG993280.1 59.82 43.0 1,874 - 22 149 931 55 Chr ssa22 NC_059463.1 HG993281.1 63.82 43.0 2,492 - 54 252 1,291 71 Chr ssa23 NC_059464.1 HG993282.1 52.46 43.1 1,825 - 334 305 1,409 57 Chr ssa24 NC_059465.1 HG993283.1 49.35 43.4 1,963 - 18 251 1,060 53 Chr ssa25 NC_059466.1 HG993284.1 54.39 43.3 1,790 11 22 255 1,051 87 Chr ssa26 NC_059467.1 HG993285.2 55.99 43.7 2,166 - 19 229 1,043 33 Chr ssa27 NC_059468.1 HG993286.1 45.31 43.5 1,847 - 392 186 1,363 43 Chr ssa28 NC_059469.1 HG993287.1 41.47 43.3 1,505 - 18 170 817 30 Chr ssa29 NC_059470.1 HG993288.1 43.05 43.3 1,341 - 92 152 715 30 Un - . - 257.26 43.4 2,942 4,048 1,332 2,067 10,659 1,660 Chromosomes Click on chromosome name to open Genome Data Viewer External Resources Salmon Genome Project GOLD