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

Authors: KOOP, BEN - UNIVERSITY OF VICTORIA; VON SCHALBURG, KRISTIAN - UNIVERSITY OF VICTORIA; LEONG, JONG - UNIVERSITY OF VICTORIA; WALKER, NEIL - UNIVERSITY OF VICTORIA; LIEPH, RYAN - UNIVERSITY OF VICTORIA; COOPER, GLENN - UNIVERSITY OF VICTORIA; ROBB, ADRIENNE - UNIVERSITY OF VICTORIA; BEETZ-SARGENT, MARIANNE - UNIVERSITY OF VICTORIA; HOLT, ROBERT - GENOME SCIENCES CENTRE; MOORE, RICHARD - GENOME SCIENCES CENTRE; BRAHMBHATT, SONAL - PROSTATE CENTRE; ROSNER, JAMIE - PROSTATE CENTRE; MCGOWAN, COLIN - SIMON FRASER UNIVERSITY; Rexroad, Caird; DAVIDSON, WILLIAM - SIMON FRASER UNIVERSITY

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/25/2008
Publication Date: 11/17/2008
Citation: Koop, B., Von Schalburg, K., Leong, J., Walker, N., Lieph, R., Cooper, G., Robb, A., Beetz-Sargent, M., Holt, R.A., Moore, R., Brahmbhatt, S., Rosner, J., Mcgowan, C., Rexroad Iii, C.E., Davidson, W. 2008. A salmonid EST genomic study: genes, duplications, phylogeny and microarrays. Biomed Central (BMC) Genomics. 9:545.

Interpretive Summary: A great deal of knowledge of trout and salmon biology has resulted in their widespread use in scientific research, as an environmental indicator species and as a food and sport fish. Perhaps more is known about the physiology, ecology, genetics, behavior and biology of salmonids (salmon, trout, and white fish) than any other fish group. This background provides a wealth of data from an economically important and evolutionary distinct group of fishes that can help guide, and benefit from, new genomic studies. The genomic resources of salmonids are being rapidly expanded through a few large-scale genomics programs. Here we identify 354,061 new sequences representing genes from Atlantic salmon and several other salmonid and related species in order to identify species relationships and construct a new microarray tool for genetic analyses. Atlantic salmon and rainbow trout now rank 19th and 29th in terms of species representation in molecular databases, almost half of these data are presented in this study. These data provide an excellent genetic resource for physiological, ecological, biochemical, behavioral, disease and biological studies of salmonids. They also provide key materials for the characterization genes affecting traits of interest, such as disease resistance.

Technical 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 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 the much larger EST database, 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 transcripts show 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 32K microarray, provide valuable new tools.