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Open Access Highly Accessed Research article

A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

Ben F Koop16*, Kristian R von Schalburg1, Jong Leong1, Neil Walker1, Ryan Lieph1, Glenn A Cooper1, Adrienne Robb1, Marianne Beetz-Sargent1, Robert A Holt2, Richard Moore2, Sonal Brahmbhatt3, Jamie Rosner3, Caird E Rexroad4, Colin R McGowan5 and William S Davidson5

Author Affiliations

1 Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada

2 Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada

3 Prostate Centre, Vancouver, British Columbia, V6H 3Z6, Canada

4 ARS, USDA, Natl Ctr Cool & Cold Water Aquaculture, Kearneysville, WV 25430, USA

5 Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada

6 Department of Biology, University of Victoria, P.O. Box 3020, Victoria, British Columbia, V8W 3N5, Canada

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BMC Genomics 2008, 9:545  doi:10.1186/1471-2164-9-545

Published: 17 November 2008

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.

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 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.