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

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dc.contributor.authorKoop, Ben F
dc.contributor.authorVon Schalburg, Kristian R
dc.contributor.authorLeong, Jong
dc.contributor.authorWalker, Neil
dc.contributor.authorLieph, Ryan
dc.contributor.authorCooper, Glenn A
dc.contributor.authorRobb, Adrienne
dc.contributor.authorBeetz-Sargent, Marianne
dc.contributor.authorHolt, Robert A
dc.contributor.authorMoore, Richard
dc.contributor.authorBrahmbhatt, Sonal
dc.contributor.authorRosner, Jamie
dc.contributor.authorRexroad, Caird E
dc.contributor.authorMcGowan, Colin R
dc.contributor.authorDavidson, William S
dc.date.accessioned2014-07-28T23:08:59Z
dc.date.available2014-07-28T23:08:59Z
dc.date.copyright2008en_US
dc.date.issued2008-11-17
dc.descriptionBioMed Centralen_US
dc.description.abstractBackground: 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.en_US
dc.description.reviewstatusRevieweden_US
dc.description.scholarlevelFacultyen_US
dc.description.sponsorshipThis research was supported by Genome Canada and Genome British Columbia. Bioinformatics support was also provided through NSERC funds.en_US
dc.identifier.citationKoop et al.: A salmonid EST genomic study: genes, duplications, phylogeny and microarrays. BMC Genomics 2008, 9:545en_US
dc.identifier.urihttp://www.biomedcentral.com/1471-2164/9/545
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2164-9-545
dc.identifier.urihttp://hdl.handle.net/1828/5497
dc.language.isoenen_US
dc.publisherBioMed Centralen_US
dc.subjectCentre for Biomedical Research
dc.subject.departmentDepartment of Biology
dc.titleA salmonid EST genomic study: genes, duplications, phylogeny and microarraysen_US
dc.typeArticleen_US

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