title: A salmonid EST genomic study: genes, duplications, phylogeny and microarrays.
abstract: BACKGROUND
  Salmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish.
  
  
  RESULTS
  298,304 expressed sequence tags (ESTs) from Atlantic salmon (69% of the total), 11,664 chinook, 10,813 sockeye, 10,051 brook trout, 10,975 grayling, 8,630 lake whitefish, and 3,624 northern pike ESTs were obtained in this study and have been deposited into the public databases. Contigs were built and putative full-length Atlantic salmon clones have been identified. A database containing ESTs, assemblies, consensus sequences, open reading frames, gene predictions and putative annotation is available. The overall similarity between Atlantic salmon ESTs and those of rainbow trout, chinook, sockeye, brook trout, grayling, lake whitefish, northern pike and rainbow smelt is 93.4, 94.2, 94.6, 94.4, 92.5, 91.7, 89.6, and 86.2% respectively. An analysis of 78 transcript sets show Salmo as a sister group to Oncorhynchus and Salvelinus within Salmoninae, and Thymallinae as a sister group to Salmoninae and Coregoninae within Salmonidae. Extensive gene duplication is consistent with a genome duplication in the common ancestor of salmonids. Using all of the available EST data, a new expanded salmonid cDNA microarray of 32,000 features was created. Cross-species hybridizations to this cDNA microarray indicate that this resource will be useful for studies of all 68 salmonid species.
  
  
  CONCLUSIONS
  An extensive collection and analysis of salmonid RNA putative transcripts indicate that Pacific salmon, Atlantic salmon and charr are 94-96% similar while the more distant whitefish, grayling, pike and smelt are 93, 92, 89 and 86% similar to salmon. The salmonid transcriptome reveals a complex history of gene duplication that is consistent with an ancestral salmonid genome duplication hypothesis. Genome resources, including a new 32 K microarray, provide valuable new tools to study salmonids.
authors.affiliation: Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W3N5, Canada. bkoop@uvic.ca
authors.forename: Ben F
authors.initials: BF
authors.lastname: Koop
authors.forename: Kristian R
authors.initials: KR
authors.lastname: von Schalburg
authors.forename: Jong
authors.initials: J
authors.lastname: Leong
authors.forename: Neil
authors.initials: N
authors.lastname: Walker
authors.forename: Ryan
authors.initials: R
authors.lastname: Lieph
authors.forename: Glenn A
authors.initials: GA
authors.lastname: Cooper
authors.forename: Adrienne
authors.initials: A
authors.lastname: Robb
authors.forename: Marianne
authors.initials: M
authors.lastname: Beetz-Sargent
authors.forename: Robert A
authors.initials: RA
authors.lastname: Holt
authors.forename: Richard
authors.initials: R
authors.lastname: Moore
authors.forename: Sonal
authors.initials: S
authors.lastname: Brahmbhatt
authors.forename: Jamie
authors.initials: J
authors.lastname: Rosner
authors.forename: Caird E
authors.initials: CE
authors.lastname: Rexroad
authors.forename: Colin R
authors.initials: CR
authors.lastname: McGowan
authors.forename: William S
authors.initials: WS
authors.lastname: Davidson
mesh_terms: D000818:Animals; D020451:Contig Mapping; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D020440:Gene Duplication; D020869:Gene Expression Profiling; D016678:Genome; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D012487:Salmonidae / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity