Genome

Oncorhynchus mykiss (rainbow trout) The rainbow trout is a freshwater fish important to sport and commercial fisheries. 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]; Oncorhynchus[7]; Oncorhynchus mykiss[1]

The rainbow trout, Oncorhynchus mykiss, is a widely studied model fish species.Rainbow trout have been widely utilized in research and are well characterized. There are numerous resources available, including clonal cell lines, BAC libraries, and genetic maps. A relatively recent tetraploid event has occurred, resulting in a high incidence of More...duplicated genes. Additional genomic sequence data will provide resources to further study this commercially valuable fish. Less...

Summary Sequence data:  genome assemblies: 8; sequence reads: 3  (See  Genome Assembly and Annotation report) Statistics:  median total length (Mb): 2250.66  median protein count: 72164  median GC%: 43.4596 NCBI Annotation Release:  101 Publications (limited to 20 most recent records) A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout. Gao G, et al. G3 (Bethesda) 2021 Apr 15 Sex-dependent dominance maintains migration supergene in rainbow trout. Pearse DE, et al. Nat Ecol Evol 2019 Dec Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics 2016 May 18 The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Berthelot C, et al. Nat Commun 2014 Apr 22 Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. Salem M, et al. BMC Genomics 2010 Oct 13 The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. Zardoya R, et al. J Mol Evol 1995 Dec More...  Representative (genome information for reference and representative genomes) Reference genome:   Oncorhynchus mykiss USDA_OmykA_1.1 Submitter: USDA/ARS Loc Type Name RefSeq INSDC Size (Mb) GC% Protein rRNA tRNA Other RNA Gene Pseudogene Chr 1 NC_048565.1 CM023219.2 95.77 43.2 3,699 - 11 428 1,798 69 Chr 2 NC_048566.1 CM023220.2 103.81 43.5 4,829 - 124 550 2,531 91 Chr 3 NC_048567.1 CM023221.2 85.31 43.4 4,015 - 17 345 1,946 87 Chr 4 NC_048568.1 CM023222.3 46.84 43.3 1,777 - 9 175 884 30 Chr 5 NC_048569.1 CM023223.2 100.8 43.4 4,460 - 24 433 2,077 64 Chr 6 NC_048570.1 CM023224.2 101.1 43.5 4,189 - 92 525 2,191 81 Chr 7 NC_048571.1 CM023225.2 90.92 43.4 4,114 6 64 346 2,030 78 Chr 8 NC_048572.1 CM023226.2 91.62 43.2 3,943 2 257 382 2,159 63 Chr 9 NC_048573.1 CM023227.2 79.46 43.4 3,612 - 404 440 2,197 66 Chr 10 NC_048574.1 CM023228.2 87.81 43.3 3,956 - 186 588 2,328 87 Chr 11 NC_048575.1 CM023229.2 86.28 43.4 3,249 2 140 307 1,679 60 Chr 12 NC_048576.1 CM023230.2 102.85 43.2 4,757 38 127 518 2,645 95 Chr 13 NC_048577.1 CM023231.2 73.33 43.6 3,975 53 21 490 2,420 86 Chr 14 NC_048578.1 CM023232.3 43.31 43.3 1,641 - 8 169 814 22 Chr 15 NC_048579.1 CM023233.2 81.57 43.8 3,111 2 505 365 1,962 51 Chr 16 NC_048580.1 CM023234.2 78.54 43.6 3,673 2 484 346 2,198 57 Chr 17 NC_048581.1 CM023235.2 95.21 43.3 4,611 - 313 669 2,980 96 Chr 18 NC_048582.1 CM023236.2 74.66 43.9 3,708 - 142 300 1,853 70 Chr 19 NC_048583.1 CM023237.2 67.24 43.4 2,829 - 465 327 1,914 46 Chr 20 NC_048584.1 CM023238.2 46.62 43.3 1,697 375 334 219 1,598 51 Chr 21 NC_048585.1 CM023239.2 64.94 44.0 2,760 - 600 363 1,976 46 Chr 22 NC_048586.1 CM023240.2 52.47 43.1 1,898 - 51 367 1,052 48 Chr 23 NC_048587.1 CM023241.2 62.88 43.2 2,100 - 81 223 1,024 39 Chr 24 NC_048588.1 CM023242.2 45.93 44.0 1,888 - 16 166 942 38 Chr 25 NC_048589.1 CM023243.3 47.54 43.5 1,724 - 4 211 911 44 Chr 26 NC_048590.1 CM023244.2 51.11 43.9 2,053 1 70 341 1,033 25 Chr 27 NC_048591.1 CM023245.2 51.56 43.9 2,098 - 17 206 1,037 46 Chr 28 NC_048592.1 CM023246.2 43.72 43.1 2,001 - 400 226 1,358 26 Chr 30 NC_050570.1 CM025857.1 46.33 43.1 1,846 - 13 314 1,048 48 Chr 31 NC_050571.1 CM025858.1 44.11 43.6 1,623 - 391 168 1,184 18 Chr 32 NC_050572.1 CM025859.1 41.84 43.6 1,845 - 16 184 890 24 Chr Y NC_048593.1 CM023247.2 47.75 43.5 1,897 111 55 428 1,421 97 MT NC_001717.1 - 0.02 46.0 13 2 22 - 37 - Un - . - 108.45 44.0 2,152 8,484 7,063 1,344 18,680 863 Chromosomes Click on chromosome name to open Genome Data Viewer External Resources AEX-BAC Resources FishBase GOLD HCGS Trout BAC Resources Rainbow Trout QTLdb Rainmap TIGR Rainbow Trout Gene Index