A Salmonid EST Genomic Study: Genes, Duplications, Phylogeny and Microarrays

Background: Salmonids are of interest because of their relatively recent genome duplication, and their extensive usein wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different speciesprovide 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, 10,813sockeye, 10,051 brook trout, 10,975 grayling, 8,630 lake whitefish, and 3,624 northern pike ESTs were obtained in thisstudy and have been deposited into the public databases. Contigs were built and putative full-length Atlantic salmonclones have been identified. A database containing ESTs, assemblies, consensus sequences, open reading frames, genepredictions and putative annotation is available. The overall similarity between Atlantic salmon ESTs and those of rainbowtrout, 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 Oncorhynchusand 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 theavailable EST data, a new expanded salmonid cDNA microarray of 32,000 features was created. Cross-specieshybridizations to this cDNA microarray indicate that this resource will be useful for studies of all 68 salmonid species.Conclusion: 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 and86% similar to salmon. The salmonid transcriptome reveals a complex history of gene duplication that is consistent withan ancestral salmonid genome duplication hypothesis. Genome resources, including a new 32 K microarray, providevaluable new tools to study salmonids.