title: Multi-tissue transcriptome profiles for coho salmon (Oncorhynchus kisutch), a species undergoing rediploidization following whole-genome duplication.
abstract: Salmonids are an important family of fish both from economic and basic research perspectives, and have been subjected to extensive research at whole-animal and molecular levels. Most research to date has been conducted on Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), but more recently other salmonids have become a focus of study due to their interesting life histories and because of their potential for use in commercial aquaculture. However, molecular biology and genetic analyses for these emerging species are currently hampered due to the lack of extensive genomic resources. To overcome some of these limitations, we have constructed a 43,228 sequence transcriptome from 13 tissues from coho salmon, Oncorhynchus kisutch using de novo transcriptome assembly methods. The transcriptome profiling analysis has provided data distinguishing allelic variation from paralogues that arose during the recent whole-genome duplication event in this family, thus allowing simplified analysis of gene-specific expression. Additionally, 1599 novel coho sequences have been identified through comparison with transcriptomes from two other salmonids species (Atlantic salmon and rainbow trout), and with northern pike. The transcriptome presented here will be useful for genomic analysis of coho salmon and other closely related salmonid species.
authors.affiliation: Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, 4160 Marine Drive, West Vancouver, British Columbia V7V 1N6, Canada.
authors.forename: Jin-Hyoung
authors.initials: JH
authors.lastname: Kim
authors.affiliation: Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada.
authors.forename: Jong S
authors.initials: JS
authors.lastname: Leong
authors.affiliation: Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada.
authors.forename: Ben F
authors.initials: BF
authors.lastname: Koop
authors.affiliation: Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, 4160 Marine Drive, West Vancouver, British Columbia V7V 1N6, Canada. Electronic address: Robert.Devlin@dfo-mpo.gc.ca.
authors.forename: Robert H
authors.initials: RH
authors.lastname: Devlin
mesh_terms: D000818:Animals; D020440:Gene Duplication; D005786:Gene Expression Regulation / Q000502:physiology; D016678:Genome; D017684:Oncorhynchus kisutch / Q000235:genetics*; D011003:Ploidies; D013045:Species Specificity; D059467:Transcriptome
keywords: Coho salmon; RNA sequencing; Salmonids; Transcriptome; Whole-genome duplication