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Braden LM, Michaud D, Groman D, Byrne P, Hori TS, Fast MD. Rejection of Lepeophtheirus salmonis driven in part by chitin sensing is not impacted by seawater acclimitization in Coho salmon (Oncorhynchus kisutch). Sci Rep 2023; 13:9685. [PMID: 37322246 PMCID: PMC10272145 DOI: 10.1038/s41598-023-36632-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/07/2023] [Indexed: 06/17/2023] Open
Abstract
There is tremendous variation in life-history strategies among anadromous salmonids. Species that enter the ocean environment at small sizes (< 20 g) are likely under more physiological pressure from pathogens; however, little data is available on responses at these early stages. With this in mind, we performed salmon louse challenges with Coho salmon either immediately after seawater entry (SW; ca. 10 g) or after 30 days in SW (ca. 20 g). Irrespective of size or time in SW, parasites were rapidly rejected by the host, with > 90% of all parasites lost by 16 days post-infection (dpi). Rejection was concomitant with host epithelial granulomatous infiltrations that initially targeted the embedded frontal filament (4 dpi) and the entire parasite by 10 dpi. Illumina sequencing, followed by functional enrichment analysis, revealed a concerted defense response in the fin within 1 dpi that included multiple innate and adaptive immunity components. Strikingly, early indications of an allergic-type inflammatory response were associated with chitin sensing pathways orchestrated by early overexpression of the IgE-receptor, fcer1g. Additionally, there was profound overexpression of several classes of c-type lectin receptors, including dectin-2, mincle, and dc-sign at 1 dpi onward. These profiles and upregulation of cellular effector markers were corroborated by histopathological evaluation, revealing the simultaneous presence of mast cell/eosinophilic granular cells, sacciform cells, macrophages/histiocytes, and granulocytes in fin. At 10 dpi and concurrent with parasite expulsion, there was evidence of immunoregulation in addition to tissue remodelling pathways. At 16 dpi, the response was effectively abrogated. Simultaneous profiling of the parasite transcriptome revealed early induction of chitin metabolism and immunomodulation, toxin production and ECM degradation; however, after 7 dpi, these were replaced with overexpression of stress and immune defense genes. These data present the first evidence for Coho salmon demonstrating chitin- and sugar moiety-sensing as key drivers of salmon louse rejection.
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Affiliation(s)
- Laura M Braden
- Department of Pathology and Microbiology, Atlantic Veterinary College, Charlottetown, PE, Canada
- Department of Fish Health and Molecular Biology, AquaBounty Canada, Souris, PE, Canada
| | - Dylan Michaud
- Department of Pathology and Microbiology, Atlantic Veterinary College, Charlottetown, PE, Canada
| | - David Groman
- Aquatic Diagnostic Services, Atlantic Veterinary College, Charlottetown, PE, Canada
| | - Phil Byrne
- Department of Fisheries and Oceans Canada, Charlottetown, PE, Canada
| | | | - Mark D Fast
- Department of Pathology and Microbiology, Atlantic Veterinary College, Charlottetown, PE, Canada.
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2
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Shwe A, Krasnov A, Visnovska T, Ramberg S, Østbye TKK, Andreassen R. Differential Expression of miRNAs and Their Predicted Target Genes Indicates That Gene Expression in Atlantic Salmon Gill Is Post-Transcriptionally Regulated by miRNAs in the Parr-Smolt Transformation and Adaptation to Sea Water. Int J Mol Sci 2022; 23:ijms23158831. [PMID: 35955964 PMCID: PMC9369087 DOI: 10.3390/ijms23158831] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 12/19/2022] Open
Abstract
Smoltification (parr-smolt transformation) is a complex developmental process consisting of developmental changes that lead to remodeling of the Atlantic salmon gill. Here, the expression changes of miRNAs and mRNAs were studied by small-RNA sequencing and microarray analysis, respectively, to identify miRNAs and their predicted targets associated with smoltification and subsequent sea water adaptation (SWA). In total, 18 guide miRNAs were identified as differentially expressed (gDE miRNAs). Hierarchical clustering analysis of expression changes divided these into one cluster of 13 gDE miRNAs with decreasing expression during smoltification and SWA that included the miRNA-146, miRNA-30 and miRNA-7132 families. Another smaller cluster that showed increasing expression consisted of miR-101a-3p, miR-193b-5p, miR-499a-5p, miR-727a-3p and miR-8159-5p. The gDE miRNAs were predicted to target 747 of the genes (DE mRNAs), showing expression changes in the microarray analysis. The predicted targets included genes encoding NKA-subunits, aquaporin-subunits, cystic fibrosis transmembrane conductance regulator and the solute carrier family. Furthermore, the predicted target genes were enriched in biological processes associated with smoltification and SWA (e.g., immune system, reactive oxygen species, stress response and extracellular matrix organization). Collectively, the results indicate that remodeling of the gill involves the post-transcriptional regulation of gene expression by the characterized gDE miRNAs.
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Affiliation(s)
- Alice Shwe
- Department of Life Science and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, 0167 Oslo, Norway
| | - Aleksei Krasnov
- Nofima (Norwegian Institute of Food, Fisheries and Aquaculture Research), 1430 Ås, Norway
| | - Tina Visnovska
- Bioinformatics Core Facility, Oslo University Hospital, 0372 Oslo, Norway
| | - Sigmund Ramberg
- Department of Life Science and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, 0167 Oslo, Norway
| | - Tone-Kari K. Østbye
- Nofima (Norwegian Institute of Food, Fisheries and Aquaculture Research), 1430 Ås, Norway
| | - Rune Andreassen
- Department of Life Science and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, 0167 Oslo, Norway
- Correspondence:
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3
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Xue X, Caballero-Solares A, Hall JR, Umasuthan N, Kumar S, Jakob E, Skugor S, Hawes C, Santander J, Taylor RG, Rise ML. Transcriptome Profiling of Atlantic Salmon ( Salmo salar) Parr With Higher and Lower Pathogen Loads Following Piscirickettsia salmonis Infection. Front Immunol 2022; 12:789465. [PMID: 35035387 PMCID: PMC8758579 DOI: 10.3389/fimmu.2021.789465] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/03/2021] [Indexed: 12/29/2022] Open
Abstract
Salmonid rickettsial septicemia (SRS), caused by Piscirickettsia salmonis, is one of the most devastating diseases of salmonids. However, the transcriptomic responses of Atlantic salmon (Salmon salar) in freshwater to an EM-90-like isolate have not been explored. Here, we infected Atlantic salmon parr with an EM-90-like isolate and conducted time-course qPCR analyses of pathogen load and four biomarkers (campb, hampa, il8a, tlr5a) of innate immunity on the head kidney samples. Transcript expression of three of these genes (except hampa), as well as pathogen level, peaked at 21 days post-injection (DPI). Multivariate analyses of infected individuals at 21 DPI revealed two infection phenotypes [lower (L-SRS) and higher (H-SRS) infection level]. Five fish from each group (Control, L-SRS, and H-SRS) were selected for transcriptome profiling using a 44K salmonid microarray platform. We identified 1,636 and 3,076 differentially expressed probes (DEPs) in the L-SRS and H-SRS groups compared with the control group, respectively (FDR = 1%). Gene ontology term enrichment analyses of SRS-responsive genes revealed the activation of a large number of innate (e.g. “phagocytosis”, “defense response to bacterium”, “inflammatory response”) and adaptive (e.g. “regulation of T cell activation”, “antigen processing and presentation of exogenous antigen”) immune processes, while a small number of general physiological processes (e.g. “apoptotic process”, development and metabolism relevant) was enriched. Transcriptome results were confirmed by qPCR analyses of 42 microarray-identified transcripts. Furthermore, the comparison of individuals with differing levels of infection (H-SRS vs. L-SRS) generated insights into the biological processes possibly involved in disease resistance or susceptibility. This study demonstrated a low mortality (~30%) EM-90-like infection model and broadened the current understanding of molecular pathways underlying P. salmonis-triggered responses of Atlantic salmon, identifying biomarkers that may assist to diagnose and combat this pathogen.
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Affiliation(s)
- Xi Xue
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Jennifer R Hall
- Aquatic Research Cluster, CREAIT Network, Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Surendra Kumar
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Eva Jakob
- Cargill Innovation Centre - Colaco, Colaco, Chile
| | - Stanko Skugor
- Cargill Aqua Nutrition, Cargill, Sea Lice Research Center (SLRC), Sandnes, Norway
| | | | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Lab, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Richard G Taylor
- Cargill Animal Nutrition and Health, Elk River, MN, United States
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
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4
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Deeg CM, Kanzeparova AN, Somov AA, Esenkulova S, Di Cicco E, Kaukinen KH, Tabata A, Ming TJ, Li S, Mordecai G, Schulze A, Miller KM. Way out there: pathogens, health, and condition of overwintering salmon in the Gulf of Alaska. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Salmon are keystone species across the North Pacific, supporting ecosystems, commercial opportunities, and cultural identity. Nevertheless, many wild salmon stocks have experienced significant declines. Salmon restoration efforts focus on fresh and coastal waters, but little is known about the open ocean environment. Here we use high throughput RT-qPCR tools to provide the first report on the health, condition, and infection profile of coho, chum, pink, and sockeye salmon in the Gulf of Alaska during the 2019 winter. We found lower infectious agent number, diversity, and burden compared with coastal British Columbia in all species except coho, which exhibited elevated stock-specific infection profiles. We identified Loma sp. and Ichthyophonus hoferi as key pathogens, suggesting transmission in the open ocean. Reduced prey availability, potentially linked to change in ocean conditions due to an El Niño event, correlated with energetic deficits and immunosuppression in salmon. Immunosuppressed individuals showed higher relative infection burden and higher prevalence of opportunistic pathogens. We highlight the cumulative effects of infection and environmental stressors on overwintering salmon, establishing a baseline to document the impacts of a changing ocean on salmon.
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Affiliation(s)
- Christoph M. Deeg
- Department of Forest & Conservation Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Pacific Salmon Foundation, Vancouver, BC V6J 4S6, Canada
| | | | - Alexei A. Somov
- Pacific branch of VNIRO (“TINRO”), Vladivostok, Russia 690091
| | | | | | - Karia H. Kaukinen
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Amy Tabata
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Tobi J. Ming
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Gideon Mordecai
- Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Angela Schulze
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Kristina M. Miller
- Department of Forest & Conservation Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
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5
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Wynne R, Archer LC, Hutton SA, Harman L, Gargan P, Moran PA, Dillane E, Coughlan J, Cross TF, McGinnity P, Colgan TJ, Reed TE. Alternative migratory tactics in brown trout ( Salmo trutta) are underpinned by divergent regulation of metabolic but not neurological genes. Ecol Evol 2021; 11:8347-8362. [PMID: 34188891 PMCID: PMC8216917 DOI: 10.1002/ece3.7664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/15/2021] [Accepted: 04/18/2021] [Indexed: 12/03/2022] Open
Abstract
The occurrence of alternative morphs within populations is common, but the underlying molecular mechanisms remain poorly understood. Many animals, for example, exhibit facultative migration, where two or more alternative migratory tactics (AMTs) coexist within populations. In certain salmonid species, some individuals remain in natal rivers all their lives, while others (in particular, females) migrate to sea for a period of marine growth. Here, we performed transcriptional profiling ("RNA-seq") of the brain and liver of male and female brown trout to understand the genes and processes that differentiate between migratory and residency morphs (AMT-associated genes) and how they may differ in expression between the sexes. We found tissue-specific differences with a greater number of genes expressed differentially in the liver (n = 867 genes) compared with the brain (n = 10) between the morphs. Genes with increased expression in resident livers were enriched for Gene Ontology terms associated with metabolic processes, highlighting key molecular-genetic pathways underlying the energetic requirements associated with divergent migratory tactics. In contrast, smolt-biased genes were enriched for biological processes such as response to cytokines, suggestive of possible immune function differences between smolts and residents. Finally, we identified evidence of sex-biased gene expression for AMT-associated genes in the liver (n = 12) but not the brain. Collectively, our results provide insights into tissue-specific gene expression underlying the production of alternative life histories within and between the sexes, and point toward a key role for metabolic processes in the liver in mediating divergent physiological trajectories of migrants versus residents.
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Affiliation(s)
- Robert Wynne
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Louise C. Archer
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Stephen A. Hutton
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Luke Harman
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | | | - Peter A. Moran
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
- Present address:
Department of Ecological Science – Animal EcologyVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Eileen Dillane
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Jamie Coughlan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Thomas F. Cross
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
- Marine InstituteNewportIreland
| | - Thomas J. Colgan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
- Present address:
Institute of Organismic and Molecular EvolutionJohannes Gutenberg University MainzMainzGermany
| | - Thomas E. Reed
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
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6
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Eslamloo K, Caballero-Solares A, Inkpen SM, Emam M, Kumar S, Bouniot C, Avendaño-Herrera R, Jakob E, Rise ML. Transcriptomic Profiling of the Adaptive and Innate Immune Responses of Atlantic Salmon to Renibacterium salmoninarum Infection. Front Immunol 2020; 11:567838. [PMID: 33193341 PMCID: PMC7656060 DOI: 10.3389/fimmu.2020.567838] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 09/07/2020] [Indexed: 01/08/2023] Open
Abstract
Bacterial Kidney Disease (BKD), which is caused by a Gram-positive, intracellular bacterial pathogen (Renibacterium salmoninarum), affects salmonids including Atlantic salmon (Salmo salar). However, the transcriptome response of Atlantic salmon to BKD remained unknown before the current study. We used a 44K salmonid microarray platform to characterise the global gene expression response of Atlantic salmon to BKD. Fish (~54 g) were injected with a dose of R. salmoninarum (H-2 strain, 2 × 108 CFU per fish) or sterile medium (control), and then head kidney samples were collected at 13 days post-infection/injection (dpi). Firstly, infection levels of individuals were determined through quantifying the R. salmoninarum level by RNA-based TaqMan qPCR assays. Thereafter, based on the qPCR results for infection level, fish (n = 5) that showed no (control), higher (H-BKD), or lower (L-BKD) infection level at 13 dpi were subjected to microarray analyses. We identified 6,766 and 7,729 differentially expressed probes in the H-BKD and L-BKD groups, respectively. There were 357 probes responsive to the infection level (H-BKD vs. L-BKD). Several adaptive and innate immune processes were dysregulated in R. salmoninarum-infected Atlantic salmon. Adaptive immune pathways associated with lymphocyte differentiation and activation (e.g., lymphocyte chemotaxis, T-cell activation, and immunoglobulin secretion), as well as antigen-presenting cell functions, were shown to be differentially regulated in response to BKD. The infection level-responsive transcripts were related to several mechanisms such as the JAK-STAT signalling pathway, B-cell differentiation and interleukin-1 responses. Sixty-five microarray-identified transcripts were subjected to qPCR validation, and they showed the same fold-change direction as microarray results. The qPCR-validated transcripts studied herein play putative roles in various immune processes including pathogen recognition (e.g., tlr5), antibacterial activity (e.g., hamp and camp), regulation of immune responses (e.g., tnfrsf11b and socs1), T-/B-cell differentiation (e.g., ccl4, irf1 and ccr5), T-cell functions (e.g., rnf144a, il13ra1b and tnfrsf6b), and antigen-presenting cell functions (e.g., fcgr1). The present study revealed diverse immune mechanisms dysregulated by R. salmoninarum in Atlantic salmon, and enhanced the current understanding of Atlantic salmon response to BKD. The identified biomarker genes can be used for future studies on improving the resistance of Atlantic salmon to BKD.
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Affiliation(s)
- Khalil Eslamloo
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Sabrina M Inkpen
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mohamed Emam
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Surendra Kumar
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Ruben Avendaño-Herrera
- Facultad Ciencias de la Vida, Viña del Mar, and FONDAP Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Santiago, Chile
| | - Eva Jakob
- Cargill Innovation Center-Colaco, Calbuco, Chile
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
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7
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Cleveland BM, Gao G, Leeds TD. Transcriptomic Response to Selective Breeding for Fast Growth in Rainbow Trout (Oncorhynchus mykiss). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:539-550. [PMID: 32451652 DOI: 10.1007/s10126-020-09974-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
Genetic improvement for faster growth is a conventional approach to increase growth rates in aquaculture species; however, the genetic and physiological factors regulating growth performance in fish are not fully characterized. The objective of this study was to identify physiological mechanisms associated with faster growth rates by comparing the liver and muscle transcriptome of a rainbow trout line selectively bred for fast growth (growth line, GL) and a contemporary randomly mated control line (synthetic control, SC) from the same selective breeding program. A third genetic line from a commercial egg supplier (commercial A, CA) was also included to characterize differences in gene expression profiles between populations. Body weight of the GL at harvest was approximately 20% and 8% heavier (p < 0.05) than SC and CA, respectively. There were 145 and 36 differentially expressed genes (DEG) in liver and white muscle, respectively, between the GL and SC that were enriched for the growth hormone/insulin-like growth factor axis (GH/IGF) and PI3K-Akt, JAK-STAT, MAPK, and cAMP signal transduction pathways. A greater concentration of plasma IGF-I was detected in the GL compared with SC (p < 0.05). A unique gene profile was detected in CA, with 11 and 210 DEG in liver and white muscle; these genes associated with innate immunity, complement systems, and metabolic pathways. Collectively, these findings provide a more extensive characterization of the fast-growth phenotype in fish that furthers knowledge of the physiological basis for genetic variation in growth performance in selectively bred rainbow trout.
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Affiliation(s)
- Beth M Cleveland
- National Center for Cool and Cold Water Aquaculture, USDA/ARS, 11861 Leetown Rd, Kearneysville, WV, 25430, USA.
| | - Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, USDA/ARS, 11861 Leetown Rd, Kearneysville, WV, 25430, USA
| | - Timothy D Leeds
- National Center for Cool and Cold Water Aquaculture, USDA/ARS, 11861 Leetown Rd, Kearneysville, WV, 25430, USA
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8
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Iversen M, Mulugeta T, Gellein Blikeng B, West AC, Jørgensen EH, Rød Sandven S, Hazlerigg D. RNA profiling identifies novel, photoperiod-history dependent markers associated with enhanced saltwater performance in juvenile Atlantic salmon. PLoS One 2020; 15:e0227496. [PMID: 32267864 PMCID: PMC7141700 DOI: 10.1371/journal.pone.0227496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 12/09/2019] [Indexed: 12/20/2022] Open
Abstract
Atlantic salmon migrate to sea following completion of a developmental process known as smolting, which establishes a seawater (SW) tolerant phenotype. Smolting is stimulated by exposure to long photoperiod or continuous light (LL) following a period of exposure to short photoperiod (SP), and this leads to major changes in gill ion exchange and osmoregulatory function. Here, we performed an RNAseq experiment to discover novel genes involved in photoperiod-dependent remodeling of the gill. This revealed a novel cohort of genes whose expression rises dramatically in fish transferred to LL following SP exposure, but not in control fish maintained continuously on LL or on SP. A follow-up experiment revealed that the SP-history dependence of LL induction of gene expression varies considerably between genes. Some genes were inducible by LL exposure after only 2 weeks exposure to SP, while others required 8 weeks prior SP exposure for maximum responsiveness to LL. Since subsequent SW growth performance is also markedly improved following 8 weeks SP exposure, these photoperiodic history-dependent genes may be useful predictive markers for full smolt development.
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Affiliation(s)
- Marianne Iversen
- Department of Arctic and Marine Biology, UiT -The Arctic University of Norway, Tromsø, Norway
| | - Teshome Mulugeta
- Department of Animal and Aquaculture Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Børge Gellein Blikeng
- Department of Arctic and Marine Biology, UiT -The Arctic University of Norway, Tromsø, Norway
| | | | - Even Hjalmar Jørgensen
- Department of Arctic and Marine Biology, UiT -The Arctic University of Norway, Tromsø, Norway
| | - Simen Rød Sandven
- Centre for Integrative Genetics, Department of Animal and Aquaculture Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - David Hazlerigg
- Department of Arctic and Marine Biology, UiT -The Arctic University of Norway, Tromsø, Norway
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9
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Eslamloo K, Kumar S, Caballero-Solares A, Gnanagobal H, Santander J, Rise ML. Profiling the transcriptome response of Atlantic salmon head kidney to formalin-killed Renibacterium salmoninarum. FISH & SHELLFISH IMMUNOLOGY 2020; 98:937-949. [PMID: 31770640 DOI: 10.1016/j.fsi.2019.11.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/17/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Renibacterium salmoninarum is a Gram-positive, intracellular bacterial pathogen that causes Bacterial Kidney Disease (BKD) in Atlantic salmon (Salmo salar). The host transcriptomic response to this immune-suppressive pathogen remains poorly understood. To identify R. salmoninarum-responsive genes, Atlantic salmon were intraperitoneally injected with a low (5 × 105 cells/kg, Low-Rs) or high (5 × 107 cells/kg; High-Rs) dose of formalin-killed R. salmoninarum bacterin or phosphate-buffered saline (PBS control); head kidney samples were collected before and 24 h after injection. Using 44K microarray analysis, we identified 107 and 345 differentially expressed probes in response to R. salmoninarum bacterin (i.e. High-Rs vs. PBS control) by Significance Analysis of Microarrays (SAM) and Rank Products (RP), respectively. Twenty-two microarray-identified genes were subjected to qPCR assays, and 17 genes were confirmed as being significantly responsive to the bacterin. There was an up-regulation in expression of genes playing putative roles as immune receptors and antimicrobial effectors. Genes with putative roles as pathogen recognition (e.g. clec12b and tlr5) or immunoregulatory (e.g. tnfrsf6b and tnfrsf11b) receptors were up-regulated in response to R.salmoninarum bacterin. Also, chemokines and a chemokine receptor showed opposite regulation [up-regulation of effectors (i.e. ccl13 and ccl) and down-regulation of cxcr1] in response to the bacterin. The present study identified and validated novel biomarker genes (e.g. ctsl1, lipe, cldn4, ccny) that can be used to assess Atlantic salmon response to R. salmoninarum, and will be valuable in the development of tools to combat BKD.
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Affiliation(s)
- Khalil Eslamloo
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada.
| | - Surendra Kumar
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Hajarooba Gnanagobal
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Javier Santander
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada.
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10
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Morro B, Doherty MK, Balseiro P, Handeland SO, MacKenzie S, Sveier H, Albalat A. Plasma proteome profiling of freshwater and seawater life stages of rainbow trout (Oncorhynchus mykiss). PLoS One 2020; 15:e0227003. [PMID: 31899766 PMCID: PMC6941806 DOI: 10.1371/journal.pone.0227003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/09/2019] [Indexed: 01/18/2023] Open
Abstract
The sea-run phenotype of rainbow trout (Oncorhynchus mykiss), like other anadromous salmonids, present a juvenile stage fully adapted to life in freshwater known as parr. Development in freshwater is followed by the smolt stage, where preadaptations needed for seawater life are developed making fish ready to migrate to the ocean, after which event they become post-smolts. While these three life stages have been studied using a variety of approaches, proteomics has never been used for such purpose. The present study characterised the blood plasma proteome of parr, smolt and post-smolt rainbow trout using a gel electrophoresis liquid chromatography tandem mass spectrometry approach alone or in combination with low-abundant protein enrichment technology (combinatorial peptide ligand library). In total, 1,822 proteins were quantified, 17.95% of them being detected only in plasma post enrichment. Across all life stages, the most abundant proteins were ankyrin-2, DNA primase large subunit, actin, serum albumin, apolipoproteins, hemoglobin subunits, hemopexin-like proteins and complement C3. When comparing the different life stages, 17 proteins involved in mechanisms to cope with hyperosmotic stress and retinal changes, as well as the downregulation of nonessential processes in smolts, were significantly different between parr and smolt samples. On the other hand, 11 proteins related to increased growth in post-smolts, and also related to coping with hyperosmotic stress and to retinal changes, were significantly different between smolt and post-smolt samples. Overall, this study presents a series of proteins with the potential to complement current seawater-readiness assessment tests in rainbow trout, which can be measured non-lethally in an easily accessible biofluid. Furthermore, this study represents a first in-depth characterisation of the rainbow trout blood plasma proteome, having considered three life stages of the fish and used both fractionation alone or in combination with enrichment methods to increase protein detection.
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Affiliation(s)
- Bernat Morro
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Mary K. Doherty
- Institute of Health Research and Innovation, Centre for Health Science, University of the Highlands and Islands, Inverness, Scotland, United Kingdom
| | | | | | - Simon MacKenzie
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
- NORCE AS, Universitetet i Bergen, Bergen, Norway
| | - Harald Sveier
- Lerøy Seafood Group ASA, Universitetet i Bergen, Bergen, Norway
| | - Amaya Albalat
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
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11
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Houde ALS, Günther OP, Strohm J, Ming TJ, Li S, Kaukinen KH, Patterson DA, Farrell AP, Hinch SG, Miller KM. Discovery and validation of candidate smoltification gene expression biomarkers across multiple species and ecotypes of Pacific salmonids. CONSERVATION PHYSIOLOGY 2019; 7:coz051. [PMID: 31620289 PMCID: PMC6788492 DOI: 10.1093/conphys/coz051] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 06/27/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
Early marine survival of juvenile salmon is intimately associated with their physiological condition during smoltification and ocean entry. Smoltification (parr-smolt transformation) is a developmental process that allows salmon to acquire seawater tolerance in preparation for marine living. Traditionally, this developmental process has been monitored using gill Na+/K+-ATPase (NKA) activity or plasma hormones, but gill gene expression offers the possibility of another method. Here, we describe the discovery of candidate genes from gill tissue for staging smoltification using comparisons of microarray studies with particular focus on the commonalities between anadromous Rainbow trout and Sockeye salmon datasets, as well as a literature comparison encompassing more species. A subset of 37 candidate genes mainly from the microarray analyses was used for TaqMan quantitative PCR assay design and their expression patterns were validated using gill samples from four groups, representing three species and two ecotypes: Coho salmon, Sockeye salmon, stream-type Chinook salmon and ocean-type Chinook salmon. The best smoltification biomarkers, as measured by consistent changes across these four groups, were genes involved in ion regulation, oxygen transport and immunity. Smoltification gene expression patterns (using the top 10 biomarkers) were confirmed by significant correlations with NKA activity and were associated with changes in body brightness, caudal fin darkness and caudal peduncle length. We incorporate gene expression patterns of pre-smolt, smolt and de-smolt trials from acute seawater transfers from a companion study to develop a preliminary seawater tolerance classification model for ocean-type Chinook salmon. This work demonstrates the potential of gene expression biomarkers to stage smoltification and classify juveniles as pre-smolt, smolt or de-smolt.
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Affiliation(s)
- Aimee Lee S Houde
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
| | - Oliver P Günther
- Günther Analytics, 402-5775 Hampton Place, Vancouver, British Columbia, V6T 2G6, Canada
| | - Jeffrey Strohm
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
| | - Tobi J Ming
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
| | - David A Patterson
- School of Resource and Environmental Management, Fisheries and Oceans Canada, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Anthony P Farrell
- Department of Zoology and Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Scott G Hinch
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
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12
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Association Mapping Based on a Common-Garden Migration Experiment Reveals Candidate Genes for Migration Tendency in Brown Trout. G3-GENES GENOMES GENETICS 2019; 9:2887-2896. [PMID: 31289024 PMCID: PMC6723140 DOI: 10.1534/g3.119.400369] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A better understanding of the environmental and genetic contribution to migratory behavior and the evolution of traits linked to migration is crucial for fish conservation and fisheries management. Up to date, a few genes with unequivocal influence on the adoption of alternative migration strategies have been identified in salmonids. Here, we used a common garden set-up to measure individual migration distances of generally highly polymorphic brown trout Salmo trutta from two populations. Fish from the assumedly resident population showed clearly shorter migration distances than the fish from the assumed migratory population at the ages of 2 and 3 years. By using two alternative analytical pipelines with 22186 and 18264 SNPs obtained through RAD-sequencing, we searched for associations between individual migration distance, and both called genotypes and genotype probabilities. None of the SNPs showed statistically significant individual effects on migration after correction for multiple testing. By choosing a less stringent threshold, defined as an overlap of the top 0.1% SNPs identified by the analytical pipelines, GAPIT and Angsd, we identified eight candidate genes that are potentially linked to individual migration distance. While our results demonstrate large individual and population level differences in migration distances, the detected genetic associations were weak suggesting that migration traits likely have multigenic control.
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13
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Sutherland BJG, Prokkola JM, Audet C, Bernatchez L. Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis. G3 (BETHESDA, MD.) 2019; 9:955-968. [PMID: 30692150 PMCID: PMC6404618 DOI: 10.1534/g3.118.200910] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/21/2019] [Indexed: 12/31/2022]
Abstract
Networks of co-expressed genes produce complex phenotypes associated with functional novelty. Sex differences in gene expression levels or in the structure of gene co-expression networks can cause sexual dimorphism and may resolve sexually antagonistic selection. Here we used RNA-sequencing in the salmonid Brook Charr Salvelinus fontinalis to characterize sex-specific co-expression networks in the liver of 47 female and 53 male offspring. In both networks, modules were characterized for functional enrichment, hub gene identification, and associations with 15 growth, reproduction, and stress-related phenotypes. Modules were then evaluated for preservation in the opposite sex, and in the congener Arctic Charr Salvelinus alpinus Overall, more transcripts were assigned to a module in the female network than in the male network, which coincided with higher inter-individual gene expression and phenotype variation in the females. Most modules were preserved between sexes and species, including those involved in conserved cellular processes (e.g., translation, immune pathways). However, two sex-specific male modules were identified, and these may contribute to sexual dimorphism. To compare with the network analysis, differentially expressed transcripts were identified between the sexes, revealing a total of 16% of expressed transcripts as sex-biased. For both sexes, there was no overrepresentation of sex-biased genes or sex-specific modules on the putative sex chromosome. Sex-biased transcripts were also not overrepresented in sex-specific modules, and in fact highly male-biased transcripts were enriched in preserved modules. Comparative network analysis and differential expression analyses identified different aspects of sex differences in gene expression, and both provided new insights on the genes underlying sexual dimorphism in the salmonid Brook Charr.
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Affiliation(s)
- Ben J G Sutherland
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
| | - Jenni M Prokkola
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, UK
| | - Céline Audet
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Rimouski, QC G5L 3A1, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
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14
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Houde ALS, Schulze AD, Kaukinen KH, Strohm J, Patterson DA, Beacham TD, Farrell AP, Hinch SG, Miller KM. Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 29:32-42. [PMID: 30419481 DOI: 10.1016/j.cbd.2018.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 10/13/2018] [Indexed: 11/30/2022]
Abstract
There is a paucity of information on the physiological changes that occur over the course of salmon early marine migration. Here we aim to provide insight on juvenile Coho salmon (Oncorhynchus kisutch) physiology using the changes in gene expression (cGRASP 44K microarray) of four tissues (brain, gill, muscle, and liver) across the parr to smolt transition in freshwater and through the first eight months of ocean residence. We also examined transcriptome changes with body size as a covariate. The strongest shift in the transcriptome for brain, gill, and muscle occurred between summer and fall in the ocean, representing physiological changes that we speculate may be associated with migration preparation to feeding areas. Metabolic processes in the liver were positively associated with body length, generally consistent with enhanced feeding opportunities. However, a notable exception to this metabolic pattern was for spring post-smolts sampled soon after entry into the ocean, which showed a pattern of gene expression more likely associated with depressed feeding or recent fasting. Overall, this study has revealed life stages that may be the most critical developmentally (fall post-smolt) and for survival (spring post-smolt) in the early marine environment. These life stages may warrant further investigation.
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Affiliation(s)
- Aimee Lee S Houde
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Angela D Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Jeffrey Strohm
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - David A Patterson
- Fisheries and Oceans Canada, School of Resource and Environmental Management, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Terry D Beacham
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Anthony P Farrell
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Scott G Hinch
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada.
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15
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Braden LM, Rasmussen KJ, Purcell SL, Ellis L, Mahony A, Cho S, Whyte SK, Jones SRM, Fast MD. Acquired Protective Immunity in Atlantic Salmon Salmo salar against the Myxozoan Kudoa thyrsites Involves Induction of MHIIβ + CD83 + Antigen-Presenting Cells. Infect Immun 2018; 86:e00556-17. [PMID: 28993459 PMCID: PMC5736826 DOI: 10.1128/iai.00556-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/03/2017] [Indexed: 12/15/2022] Open
Abstract
The histozoic myxozoan parasite Kudoa thyrsites causes postmortem myoliquefaction and is responsible for economic losses to salmon aquaculture in the Pacific Northwest. Despite its importance, little is known about the host-parasite relationship, including the host response to infection. The present work sought to characterize the immune response in Atlantic salmon during infection, recovery, and reexposure to K. thyrsites After exposure to infective seawater, infected and uninfected smolts were sampled three times over 4,275 degree-days. Histological analysis revealed infection severity decreased over time in exposed fish, while in controls there was no evidence of infection. Following a secondary exposure of all fish, severity of infection in the controls was similar to that measured in exposed fish at the first sampling time but was significantly reduced in reexposed fish, suggesting the acquisition of protective immunity. Using immunohistochemistry, we detected a population of MHIIβ+ cells in infected muscle that followed a pattern of abundance concordant with parasite prevalence. Infiltration of these cells into infected myocytes preceded destruction of the plasmodium and dissemination of myxospores. Dual labeling indicated a majority of these cells were CD83+/MHIIβ+ Using reverse transcription-quantitative PCR, we detected significant induction of cellular effectors, including macrophage/dendritic cells (mhii/cd83/mcsf), B cells (igm/igt), and cytotoxic T cells (cd8/nkl), in the musculature of infected fish. These data support a role for cellular effectors such as antigen-presenting cells (monocyte/macrophage and dendritic cells) along with B and T cells in the acquired protective immune response of Atlantic salmon against K. thyrsites.
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Affiliation(s)
- Laura M Braden
- Hoplite Laboratory, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Karina J Rasmussen
- Department of Cancer and Inflammation Research, University of Southern Denmark, Odense, Denmark
| | - Sara L Purcell
- Hoplite Laboratory, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Lauren Ellis
- Hoplite Laboratory, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Amelia Mahony
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Steven Cho
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Shona K Whyte
- Hoplite Laboratory, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Simon R M Jones
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Mark D Fast
- Hoplite Laboratory, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
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16
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Teffer AK, Hinch SG, Miller KM, Patterson DA, Farrell AP, Cooke SJ, Bass AL, Szekeres P, Juanes F. Capture severity, infectious disease processes and sex influence post-release mortality of sockeye salmon bycatch. CONSERVATION PHYSIOLOGY 2017; 5:cox017. [PMID: 28852514 PMCID: PMC5569998 DOI: 10.1093/conphys/cox017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 02/17/2017] [Accepted: 03/07/2017] [Indexed: 05/21/2023]
Abstract
Bycatch is a common occurrence in heavily fished areas such as the Fraser River, British Columbia, where fisheries target returning adult Pacific salmon (Oncorhynchus spp.) en route to spawning grounds. The extent to which these encounters reduce fish survival through injury and physiological impairment depends on multiple factors including capture severity, river temperature and infectious agents. In an effort to characterize the mechanisms of post-release mortality and address fishery and managerial concerns regarding specific regulations, wild-caught Early Stuart sockeye salmon (Oncorhynchus nerka) were exposed to either mild (20 s) or severe (20 min) gillnet entanglement and then held at ecologically relevant temperatures throughout their period of river migration (mid-late July) and spawning (early August). Individuals were biopsy sampled immediately after entanglement and at death to measure indicators of stress and immunity, and the infection intensity of 44 potential pathogens. Biopsy alone increased mortality (males: 33%, females: 60%) when compared with non-biopsied controls (males: 7%, females: 15%), indicating high sensitivity to any handling during river migration, especially among females. Mortality did not occur until 5-10 days after entanglement, with severe entanglement resulting in the greatest mortality (males: 62%, females: 90%), followed by mild entanglement (males: 44%, females: 70%). Infection intensities of Flavobacterium psychrophilum and Ceratonova shasta measured at death were greater in fish that died sooner. Physiological indicators of host stress and immunity also differed depending on longevity, and indicated anaerobic metabolism, osmoregulatory failure and altered immune gene regulation in premature mortalities. Together, these results implicate latent effects of entanglement, especially among females, resulting in mortality days or weeks after release. Although any entanglement is potentially detrimental, reducing entanglement durations can improve post-release survival.
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Affiliation(s)
- Amy K. Teffer
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
- Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Scott G. Hinch
- Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kristi M. Miller
- Fisheries and Oceans Canada, Molecular Genetics Section, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - David A. Patterson
- Fisheries and Oceans Canada, Cooperative Resource Management Institute, School of Resource and Environmental Management, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Anthony P. Farrell
- Department of Zoology, Department of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Steven J. Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental Science, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Arthur L. Bass
- Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Petra Szekeres
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental Science, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Francis Juanes
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
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17
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RNA-seq reveals differential gene expression in the brains of juvenile resident and migratory smolt rainbow trout (Oncorhynchus mykiss). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 20:136-150. [DOI: 10.1016/j.cbd.2016.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 07/21/2016] [Accepted: 07/28/2016] [Indexed: 11/20/2022]
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18
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Dennenmoser S, Vamosi SM, Nolte AW, Rogers SM. Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq. Mol Ecol 2016; 26:25-42. [DOI: 10.1111/mec.13805] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 07/29/2016] [Accepted: 08/11/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Stefan Dennenmoser
- Max-Planck Institute for Evolutionary Biology; August Thienemann Strasse 2 24306 Plön Germany
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary AB Canada T2N 1N4
| | - Steven M. Vamosi
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary AB Canada T2N 1N4
| | - Arne W. Nolte
- Max-Planck Institute for Evolutionary Biology; August Thienemann Strasse 2 24306 Plön Germany
- Institute for Biology; Carl von Ossietzky University Oldenburg; Carl von Ossietzky Str. 9-11 26111 Oldenburg Germany
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary AB Canada T2N 1N4
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19
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Kim JH, Leong JS, Koop BF, Devlin RH. Multi-tissue transcriptome profiles for coho salmon (Oncorhynchus kisutch), a species undergoing rediploidization following whole-genome duplication. Mar Genomics 2015; 25:33-37. [PMID: 26614614 DOI: 10.1016/j.margen.2015.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/16/2015] [Accepted: 11/17/2015] [Indexed: 01/15/2023]
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.
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Affiliation(s)
- Jin-Hyoung Kim
- Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, 4160 Marine Drive, West Vancouver, British Columbia V7V 1N6, Canada
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, 4160 Marine Drive, West Vancouver, British Columbia V7V 1N6, Canada.
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20
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Müller A, Sutherland BJG, Koop BF, Johnson SC, Garver KA. Infectious hematopoietic necrosis virus (IHNV) persistence in Sockeye Salmon: influence on brain transcriptome and subsequent response to the viral mimic poly(I:C). BMC Genomics 2015; 16:634. [PMID: 26306576 PMCID: PMC4549833 DOI: 10.1186/s12864-015-1759-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/07/2015] [Indexed: 11/10/2022] Open
Abstract
Background Sockeye Salmon are an iconic species widely distributed throughout the North Pacific. A devastating pathogen of Sockeye Salmon is infectious hematopoietic necrosis virus (IHNV, genus Novirhabdovirus, family Rhabdoviridae). It has been postulated that IHNV is maintained in salmon populations by persisting over the life of its host and/or by residing in natural reservoirs other than its susceptible hosts. Herein we demonstrate the presence of IHNV in the brain of Sockeye Salmon that survived an experimentally-induced outbreak, suggesting the presence of viral persistence in this susceptible species. To understand the viral persistent state in Sockeye Salmon we profiled the transcriptome to evaluate the host response in asymptomatic carriers and to determine what effects (if any) IHNV exposure may have on subsequent virus challenges. Results A laboratory disease model to simulate a natural IHNV outbreak in Sockeye Salmon resulted in over a third of the population incurring acute IHN disease and mortality during the first four months after initial exposure. Nine months post IHNV exposure, despite the absence of disease and mortality, a small percentage (<4 %) of the surviving population contained IHNV in brain. Transcriptome analysis in brain of asymptomatic virus carriers and survivors without virus exhibited distinct transcriptional profiles in comparison to naïve fish. Characteristic for carriers was the up-regulation of genes involved in antibody production and antigen presentation. In both carriers and survivors a down-regulation of genes related to cholesterol biosynthesis, resembling an antiviral mechanism observed in higher vertebrates was revealed along with differences in nervous system development. Moreover, following challenge with poly(I:C), survivors and carriers displayed an elevated antiviral immune response in comparison to naïve fish. Conclusions IHN virus persistence was identified in Sockeye Salmon where it elicited a unique brain transcriptome profile suggesting an ongoing adaptive immune response. IHNV carriers remained uncompromised in mounting efficient innate antiviral responses when exposed to a viral mimic. The capacity of IHNV to reside in asymptomatic hosts supports a virus carrier hypothesis and if proven infectious, could have significant epidemiological consequences towards maintaining and spreading IHNV among susceptible host populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1759-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anita Müller
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, V9T 6N7, British Columbia, Canada.
| | - Ben J G Sutherland
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada. .,Present address: Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada.
| | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada.
| | - Stewart C Johnson
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, V9T 6N7, British Columbia, Canada.
| | - Kyle A Garver
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, V9T 6N7, British Columbia, Canada.
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21
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Baerwald MR, Meek MH, Stephens MR, Nagarajan RP, Goodbla AM, Tomalty KMH, Thorgaard GH, May B, Nichols KM. Migration-related phenotypic divergence is associated with epigenetic modifications in rainbow trout. Mol Ecol 2015; 25:1785-1800. [PMID: 25958780 DOI: 10.1111/mec.13231] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 04/30/2015] [Accepted: 05/01/2015] [Indexed: 12/11/2022]
Abstract
Migration is essential for the reproduction and survival of many animals, yet little is understood about its underlying molecular mechanisms. We used the salmonid Oncorhynchus mykiss to gain mechanistic insight into smoltification, which is a morphological, physiological and behavioural transition undertaken by juveniles in preparation for seaward migration. O. mykiss is experimentally tractable and displays intra- and interpopulation variation in migration propensity. Migratory individuals can produce nonmigratory progeny and vice versa, indicating a high degree of phenotypic plasticity. One potential way that phenotypic plasticity might be linked to variation in migration-related life history tactics is through epigenetic regulation of gene expression. To explore this, we quantitatively measured genome-scale DNA methylation in fin tissue using reduced representation bisulphite sequencing of F2 siblings produced from a cross between steelhead (migratory) and rainbow trout (nonmigratory) lines. We identified 57 differentially methylated regions (DMRs) between smolt and resident O. mykiss juveniles. DMRs were high in magnitude, with up to 62% differential methylation between life history types, and over half of the gene-associated DMRs were in transcriptional regulatory regions. Many of the DMRs encode proteins with activity relevant to migration-related transitions (e.g. circadian rhythm pathway, nervous system development, protein kinase activity). This study provides the first evidence of a relationship between epigenetic variation and life history divergence associated with migration-related traits in any species.
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Affiliation(s)
- Melinda R Baerwald
- Department of Animal Science, University of California - Davis, Davis, CA, 95616
| | - Mariah H Meek
- Department of Animal Science, University of California - Davis, Davis, CA, 95616
| | - Molly R Stephens
- School of Natural Sciences, University of California - Merced, Merced, CA, 95343
| | - Raman P Nagarajan
- GlaxoSmithKline, Cancer Epigenetics Discovery Performance Unit, Collegeville, PA 19426
| | - Alisha M Goodbla
- Department of Animal Science, University of California - Davis, Davis, CA, 95616
| | | | - Gary H Thorgaard
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164
| | - Bernie May
- Department of Animal Science, University of California - Davis, Davis, CA, 95616
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd E, Seattle, WA 98112
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22
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McKinney GJ, Hale MC, Goetz G, Gribskov M, Thrower FP, Nichols KM. Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and residentOncorhynchus mykiss. Mol Ecol 2015; 24:1792-809. [DOI: 10.1111/mec.13143] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Garrett J. McKinney
- Department of Biological Sciences; Purdue University; West Lafayette IN 47907 USA
- School of Aquatic and Fishery Sciences; University of Washington; Seattle WA 98195-5020 USA
| | - Matthew C. Hale
- Department of Biological Sciences; Purdue University; West Lafayette IN 47907 USA
| | - Giles Goetz
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; National Oceanic and Atmospheric Administration; Seattle WA 98112 USA
| | - Michael Gribskov
- Department of Biological Sciences; Purdue University; West Lafayette IN 47907 USA
| | - Frank P. Thrower
- Ted Stevens Marine Research Institute; Alaska Fisheries Science Center; National Marine Fisheries Service; National Oceanic and Atmospheric Administration; Juneau AK 99801 USA
| | - Krista M. Nichols
- Department of Biological Sciences; Purdue University; West Lafayette IN 47907 USA
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; National Oceanic and Atmospheric Administration; Seattle WA 98112 USA
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23
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Hutchings JA. Unintentional selection, unanticipated insights: introductions, stocking and the evolutionary ecology of fishes. JOURNAL OF FISH BIOLOGY 2014; 85:1907-1926. [PMID: 25469951 DOI: 10.1111/jfb.12545] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 09/19/2014] [Indexed: 06/04/2023]
Abstract
Natural environmental change has produced countless opportunities for species to disperse into and persist in habitats where they previously did not exist. Introduction and stocking programmes have facilitated similar sorts of colonization opportunities across considerably greater geographical scales and often in much shorter periods of time. Even though the mechanism of colonization differs, the result can be the same: evolutionary change in the colonizing population in response to novel selection pressures. As a consequence, some human-mediated fish transfers have unintentionally yielded novel research opportunities to study how phenotypes and genes interact with their environment and affect ecological and evolutionary change. The primary purpose here is to explore how work, directly or indirectly involved with human-mediated transfers, has unintentionally yielded novel research and research opportunities in fish ecology and evolution. Insights have produced new knowledge or altered previously held perceptions on topics such as local adaptation, rate of evolutionary change, phenotypic plasticity, alternative reproductive strategies, population structure and colonization probability. Well-documented stocking programmes, especially in terms of history, numbers and original population sources, can provide highly fertile ground for generating further insights on the ecology and evolution of fishes and of the factors likely to influence the success of conservation-based, restoration programmes.
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Affiliation(s)
- J A Hutchings
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, B3H 4R2, Canada; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P. O. Box 1066, Blindern, NO-0316 Oslo, Norway
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24
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Jeffries KM, Hinch SG, Gale MK, Clark TD, Lotto AG, Casselman MT, Li S, Rechisky EL, Porter AD, Welch DW, Miller KM. Immune response genes and pathogen presence predict migration survival in wild salmon smolts. Mol Ecol 2014; 23:5803-15. [PMID: 25354752 DOI: 10.1111/mec.12980] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 10/10/2014] [Accepted: 10/15/2014] [Indexed: 01/18/2023]
Abstract
We present the first data to link physiological responses and pathogen presence with subsequent fate during migration of wild salmonid smolts. We tagged and non-lethally sampled gill tissue from sockeye salmon (Oncorhynchus nerka) smolts as they left their nursery lake (Chilko Lake, BC, Canada) to compare gene expression profiles and freshwater pathogen loads with migration success over the first ~1150 km of their migration to the North Pacific Ocean using acoustic telemetry. Fifteen per cent of smolts were never detected again after release, and these fish had gene expression profiles consistent with an immune response to one or more viral pathogens compared with fish that survived their freshwater migration. Among the significantly upregulated genes of the fish that were never detected postrelease were MX (interferon-induced GTP-binding protein Mx) and STAT1 (signal transducer and activator of transcription 1-alpha/beta), which are characteristic of a type I interferon response to viral pathogens. The most commonly detected pathogen in the smolts leaving the nursery lake was infectious haematopoietic necrosis virus (IHNV). Collectively, these data show that some of the fish assumed to have died after leaving the nursery lake appeared to be responding to one or more viral pathogens and had elevated stress levels that could have contributed to some of the mortality shortly after release. We present the first evidence that changes in gene expression may be predictive of some of the freshwater migration mortality in wild salmonid smolts.
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Affiliation(s)
- Ken M Jeffries
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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