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Differential gene expression between fall- and spring-run Chinook salmon assessed by long serial analysis of gene expression

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https://ir.library.oregonstate.edu/concern/articles/z603qz01g

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  • Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial analysis of gene expression (LongSAGE) and microarrays, allow gene expression to be analyzed for thousands of genes simultaneously. To investigate whether differential gene expression is observed between fall- and spring-run Chinook salmon from California's Central Valley, LongSAGE libraries were constructed. Three libraries containing between 25,512 and 29,372 sequenced tags (21 base pairs/tag) were generated using messenger RNA from the brains of adult Chinook salmon returning in fall and spring and from one ocean-caught Chinook salmon. Tags were annotated to genes using complementary DNA libraries from Atlantic salmon Salmo salar and rainbow trout O. mykiss. Differentially expressed genes, as estimated by differences in the number of sequence tags, were found in all pairwise comparisons of libraries (freshwater versus saltwater = 40 genes; fall versus spring = 11 genes; and spawning versus nonspawning = 51 genes). The gene for ependymin, an extracellular glycoprotein involved in behavioral plasticity in fish, exhibited the most differential expression among the three groupings. Reverse transcription polymerase chain reaction analysis verified the differential expression of ependymin between the fall- and spring-run samples. These LongSAGE libraries, the first reported for Chinook salmon, provide a window of the transcriptional changes during Chinook salmon return migration to freshwater and spawning and increase the amount of expressed sequence data.
  • Keywords: Oncorhynchus tshawytscha, migration, serial analysis of gene expression
  • Keywords: Oncorhynchus tshawytscha, migration, serial analysis of gene expression
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  • Bernier, J. C., Birkeland, S. R., Cipriano, M. J., McArthur, A. G., & Banks, M. A. (2008, September). Differential gene expression between fall- and spring-run Chinook salmon assessed by long serial analysis of gene expression. Transactions of the American Fisheries Society, 137(5), 1378-1388.
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  • 137
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  • This work was supported with a grant from the California Department of Water Resources awarded to M.A.B.; J.C.B. received additional funding from the North Umpqua Foundation, Roseburg, Oregon. Partial support was provided by the Marine Biological Laboratory’s Program in Global Infectious Diseases, which is funded by the Ellison Medical Foundation. Computational resources were provided by the Marine Biology Laboratory’s Josephine Bay Paul Center for Comparative Molecular Biology and Evolution through funds provided by the W. M. Keck Foundation and the G.Unger Vetlesen Foundation.
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