Differential Gene Expression between Fall‐ and Spring‐Run Chinook Salmon Assessed by Long Serial Analysis of Gene Expression

Abstract

Abstract.-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 falland 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 oceancaught 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 saltwater¼ 40 genes; fall versus spring¼ 11 genes; and spawning versus nonspawning ¼ 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.

Differential expression of olfactory genes in Atlantic salmon (Salmo salar) during the parr–smolt transformation

“…Seven MOR genes, n24 , asor , and two ependymin ‐ like genes were significantly upregulated (1.5–2.5×), and olfc13.1 and O51F2 HUMAN —a novel salmonid gene—were downregulated (0.7–0.5×) in prespawning individuals. Bernier et al () also found elevated ependymin levels in the brains of returning adult Chinook salmon. Our data confirm the downregulation of olfc13.1 and asor1 in adults, whereas ependymin levels were similar in adults and juveniles.…”

“…GST (Kudo et al, 1999) and UGT (Lazard et al, 1991) are detoxification enzymes that may be involved in neuromodulation and in termination of odor signaling by degrading/conjugating odorant molecules (Hino et al, 2009). Ependymin is a neurotrophic factor, which has long been thought of as an effector of long-term memory consolidation in fish (Bernier, Birkeland, Cipriano, McArthur, & Banks, 2008;Lado et al, 2013). It was upregulated in fall-run mature chinook salmon (O. tshawytscha) compared with spring-run and ocean-dwelling fish and was suggested to have a role in memory formation in homing salmon (Bernier et al, 2008).…”

“…Ependymin is a neurotrophic factor, which has long been thought of as an effector of long-term memory consolidation in fish (Bernier, Birkeland, Cipriano, McArthur, & Banks, 2008;Lado et al, 2013). It was upregulated in fall-run mature chinook salmon (O. tshawytscha) compared with spring-run and ocean-dwelling fish and was suggested to have a role in memory formation in homing salmon (Bernier et al, 2008). Ependymin has not been analyzed before during the PST of any species.…”

Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha

“…Comparisons of haplotype composition, overall genetic diversity, and differentiation (based on both exact tests and φ ST ) indicate more similarity to the sample of contemporary fall Chinook salmon than to those in the contemporary tributaries used for redirection, particularly to the Chinook salmon from Priest Rapids Hatchery. Genetic components have been indicated for functional life history differences, including run timing in Chinook salmon [ 108 – 111 ]. However, to our knowledge, no functional associations have been made for control region haplotypes, or for mtDNA in general, in Chinook salmon.…”

The Olfactory Transcriptome and Progression of Sexual Maturation in Homing Chum Salmon Oncorhynchus keta

“…Thereby ependymin is hypothesized to be involved in the retrieval of olfactory imprinting memory, once retained as juvenile migrating downstream from their natal stream to the ocean. Also in fall- and spring-run Chinook salmon, ependymin exhibited much higher expression levels than in an individual from the ocean [ 41 ]. Recently, ependymin (in this case the ependymin II precursor) was shown to play an important role as neural mediator in the olfactory processing of sex pheromones in the telencephalon of goldfish [ 42 ].…”