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Bull JK, Stanford BCM, Bokvist JK, Josephson MP, Rogers SM. Environment and genotype predict the genomic nature of domestication of salmonids as revealed by gene expression. Proc Biol Sci 2022; 289:20222124. [PMID: 36475438 PMCID: PMC9727666 DOI: 10.1098/rspb.2022.2124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Billions of salmonids are produced annually by artificial reproduction for harvest and conservation. Morphologically, behaviourally and physiologically these fish differ from wild-born fish, including in ways consistent with domestication. Unlike most studied domesticates, which diverged from wild ancestors millennia ago, salmonids offer a tractable model for early-stage domestication. Here, we review a fundamental mechanism for domestication-driven differences in early-stage domestication, differentially expressed genes (DEGs), in salmonids. We found 34 publications examining DEGs under domestication driven by environment and genotype, covering six species, over a range of life-history stages and tissues. Three trends emerged. First, domesticated genotypes have increased expression of growth hormone and related metabolic genes, with differences magnified under artificial environments with increased food. Regulatory consequences of these DEGs potentially drive overall DEG patterns. Second, immune genes are often DEGs under domestication and not simply owing to release from growth-immune trade-offs under increased food. Third, domesticated genotypes exhibit reduced gene expression plasticity, with plasticity further reduced in low-complexity environments typical of production systems. Recommendations for experimental design improvements, coupled with tissue-specific expression and emerging analytical approaches for DEGs present tractable avenues to understand the evolution of domestication in salmonids and other species.
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Affiliation(s)
- James K. Bull
- Department of Biological Sciences, University of Calgary, Alberta, Canada T2N 1N4
| | | | - Jessy K. Bokvist
- Department of Biological Sciences, University of Calgary, Alberta, Canada T2N 1N4,Fisheries and Oceans Canada, South Coast Area Office, Nanaimo, British Columbia, Canada V9T 1K3
| | - Matthew P. Josephson
- Department of Biological Sciences, University of Calgary, Alberta, Canada T2N 1N4
| | - Sean M. Rogers
- Department of Biological Sciences, University of Calgary, Alberta, Canada T2N 1N4,Bamfield Marine Sciences Centre, Bamfield, British Columbia, Canada V0R 1B0
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2
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Xiang K, Yang Q, Liu M, Yang X, Li J, Hou Z, Wen H. Crosstalk between Growth and Osmoregulation of GHRH-SST-GH-IGF Axis in Triploid Rainbow Trout ( Oncorhynchus mykiss). Int J Mol Sci 2022; 23:ijms23158691. [PMID: 35955823 PMCID: PMC9369269 DOI: 10.3390/ijms23158691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 12/04/2022] Open
Abstract
Smolting is an important development stage of salmonid, and an energy trade-off occurs between osmotic regulation and growth during smolting in rainbow trout (Oncorhynchus mykiss). Growth hormone releasing hormone, somatostatin, growth hormone and insulin-like growth factor (GHRH-SST-GH-IGF) axis exhibit pleiotropic effects in regulating growth and osmotic adaptation. Due to salmonid specific genome duplication, increased paralogs are identified in the ghrh-sst-gh-igf axis, however, their physiology in modulating osmoregulation has yet to be investigated. In this study, seven sst genes (sst1a, sst1b, sst2, sst3a, sst3b, sst5, sst6) were identified in trout. We further investigated the ghrh-sst-gh-igf axis of diploid and triploid trout in response to seawater challenge. Kidney sst (sst1b, sst2, sst5) and sstr (sstr1b1, sstr5a, sstr5b) expressions were changed (more than 2-fold increase (except for sstr5a with 1.99-fold increase) or less than 0.5-fold decrease) due to osmoregulation, suggesting a pleiotropic physiology of SSTs in modulating growth and smoltification. Triploid trout showed significantly down-regulated brain sstr1b1 and igfbp2a1 (p < 0.05), while diploid trout showed up-regulated brain igfbp1a1 (~2.61-fold, p = 0.057) and igfbp2a subtypes (~1.38-fold, p < 0.05), suggesting triploid trout exhibited a better acclimation to the seawater environment. The triploid trout showed up-regulated kidney igfbp5a subtypes (~6.62 and 7.25-fold, p = 0.099 and 0.078) and significantly down-regulated igfbp5b2 (~0.37-fold, p < 0.05), showing a conserved physiology of teleost IGFBP5a in regulating osmoregulation. The IGFBP6 subtypes are involved in energy and nutritional regulation. Distinctive igfbp6 subtypes patterns (p < 0.05) potentially indicated trout triggered energy redistribution in brain and kidney during osmoregulatory regulation. In conclusion, we showed that the GHRH-SST-GH-IGF axis exhibited pleiotropic effects in regulating growth and osmoregulatory regulation during trout smolting, which might provide new insights into seawater aquaculture of salmonid species.
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Affiliation(s)
| | | | | | | | | | - Zhishuai Hou
- Correspondence: (Z.H.); (H.W.); Tel.: +86-133-4524-7715 (Z.H.); +86-532-8203-1825 (H.W.)
| | - Haishen Wen
- Correspondence: (Z.H.); (H.W.); Tel.: +86-133-4524-7715 (Z.H.); +86-532-8203-1825 (H.W.)
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3
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Cui M, Wang Z, Yang Y, Liu R, Wu M, Li Y, Zhang Q, Xu D. Comparative Transcriptomic Analysis Reveals the Regulated Expression Profiles in Oreochromis niloticus in Response to Coinfection of Streptococcus agalactiae and Streptococcus iniae. Front Genet 2022; 13:782957. [PMID: 35309129 PMCID: PMC8927537 DOI: 10.3389/fgene.2022.782957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Tilapia (Oreochromis sp.) is one of the important economical fishes in the world. Streptococcosis is commonly found in tilapia, causing severe and devastating effects in tilapia cultures. Streptococcus agalactiae and Streptococcus iniae are the predominant pathogens causing tilapia streptococcosis. To understand the molecular mechanisms underlying differential streptococcal infection patterns, Nile tilapias (Oreochromis niloticus) were infected by 1 × 107 CFU/mL S. agalactiae, 1 × 107 CFU/mL S. iniae, and 1 × 107 CFU/mL S. agalactiae and S. iniae (1:1), respectively, and transcriptome analysis was conducted to the intestine samples of Nile tilapia (Oreochromis niloticus) at 6, 12, 24 h, and 7 days post-infection. A total of 6,185 genes that differentially expressed among groups were identified. Eight differentially expressed genes (DEGs) including E3 ubiquitin-protein ligase TRIM39-like, C-X-C motif chemokine 10-like(CXCL 10), C-C motif chemokine 19-like, interleukin-1 beta-like, IgM heavy chain VH region, partial, IgG Fc-binding protein, proteasome subunit beta type-8 (PSMB8), and ATP synthase F(0) complex subunit B1, mitochondrial that involved in the immune system were selected, and their expression levels in the coinfection group were significantly higher than those in either of the single infection groups. These genes were associated with four different KEGG pathways. Additionally, the differential expression of eight DEGs was validated by using the RT-qPCR approach, and their immunological importance was discussed. The results provided insights into the responses of tilapia against S. agalactiae and S. iniae at the transcriptome level, promoting our better understanding of immune responses for aquatic animal against Streptococcus.
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Affiliation(s)
- Miao Cui
- *Correspondence: Miao Cui, ; Delin Xu,
| | | | | | | | | | | | | | - Delin Xu
- *Correspondence: Miao Cui, ; Delin Xu,
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4
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Recurrent expansions of B30.2-associated immune receptor families in fish. Immunogenetics 2021; 74:129-147. [PMID: 34850255 DOI: 10.1007/s00251-021-01235-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022]
Abstract
B30.2 domains, also known as PRY/SPRY, are key components of specific subsets of two large families of proteins involved in innate immunity: the tripartite motif proteins (TRIMs) and the Nod-like receptors (NLRs). TRIM proteins are important, often inducible factors of antiviral innate immunity, targeting multiple steps of viral cycles through a variety of mechanisms. NLRs prime and regulate systemic innate defenses, especially against bacteria, and control inflammation. Large TRIM and NLR subsets characterized by the presence of a B30.2 domain have been reported from a few fish species including zebrafish and seem to be strongly prone to gene duplication/expansion. Here, we performed a large-scale survey of these receptors across about 150 fish genomes, focusing on ray-finned fishes. We assessed the number and genomic distribution of domains and domain combinations associated with TRIMs, NLRs, and other genes containing B30.2 domains and looked for gene expansion patterns across fish groups. We then used a model to test the impact of taxonomy, genome size, and environmental variables on the copy numbers of these genes. Our findings reveal novel domain structures, clade-specific gains and losses. They also assist with the timing of the gene expansions, reveal patterns associated with the MHC, and lay the groundwork for further studies delving deeper into the forces that drive the copy number variation of immune genes on a species level.
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Colgan TJ, Moran PA, Archer LC, Wynne R, Hutton SA, McGinnity P, Reed TE. Evolution and Expression of the Immune System of a Facultatively Anadromous Salmonid. Front Immunol 2021; 12:568729. [PMID: 33717060 PMCID: PMC7952528 DOI: 10.3389/fimmu.2021.568729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/07/2021] [Indexed: 12/24/2022] Open
Abstract
Vertebrates have evolved a complex immune system required for the identification of and coordinated response to harmful pathogens. Migratory species spend periods of their life-cycle in more than one environment, and their immune system consequently faces a greater diversity of pathogens residing in different environments. In facultatively anadromous salmonids, individuals may spend parts of their life-cycle in freshwater and marine environments. For species such as the brown trout Salmo trutta, sexes differ in their life-histories with females more likely to migrate to sea while males are more likely to stay and complete their life-cycle in their natal river. Salmonids have also undergone a lineage-specific whole genome duplication event, which may provide novel immune innovations but our current understanding of the differences in salmonid immune expression between the sexes is limited. We characterized the brown trout immune gene repertoire, identifying a number of canonical immune genes in non-salmonid teleosts to be duplicated in S. trutta, with genes involved in innate and adaptive immunity. Through genome-wide transcriptional profiling (“RNA-seq”) of male and female livers to investigate sex differences in gene expression amplitude and alternative splicing, we identified immune genes as being generally male-biased in expression. Our study provides important insights into the evolutionary consequences of whole genome duplication events on the salmonid immune gene repertoire and how the sexes differ in constitutive immune expression.
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Affiliation(s)
- Thomas J Colgan
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Peter A Moran
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Louise C Archer
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Robert Wynne
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Stephen A Hutton
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Philip McGinnity
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Marine Institute, Newport, Ireland
| | - Thomas E Reed
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
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6
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Christensen KA, Le Luyer J, Chan MTT, Rondeau EB, Koop BF, Bernatchez L, Devlin RH. Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon. G3 (BETHESDA, MD.) 2021; 11:jkab021. [PMID: 33712817 PMCID: PMC8022943 DOI: 10.1093/g3journal/jkab021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/13/2021] [Indexed: 12/24/2022]
Abstract
Genotype-by-environment (GxE) interactions are non-parallel reaction norms among individuals with different genotypes in response to different environmental conditions. GxE interactions are an extension of phenotypic plasticity and consequently studying such interactions improves our ability to predict effects of different environments on phenotype as well as the fitness of genetically distinct organisms and their capacity to interact with ecosystems. Growth hormone transgenic coho salmon grow much faster than non-transgenics when raised in tank environments, but show little difference in growth when reared in nature-like streams. We used this model system to evaluate potential mechanisms underlying this growth rate GxE interaction, performing RNA-seq to measure gene transcription and whole-genome bisulfite sequencing to measure gene methylation in liver tissue. Gene ontology (GO) term analysis revealed stress as an important biological process potentially influencing growth rate GxE interactions. While few genes with transcription differences also had methylation differences, in promoter or gene regions, many genes were differentially methylated between tank and stream environments. A GO term analysis of differentially methylated genes between tank and stream environments revealed increased methylation in the stream environment of more than 95% of the differentially methylated genes, many with biological processes unrelated to liver function. The lower nutritional condition of the stream environment may cause increased negative regulation of genes less vital for liver tissue function than when fish are reared in tanks with unlimited food availability. These data show a large effect of rearing environment both on gene expression and methylation, but it is less clear that the detected epigenetic marks are responsible for the observed altered growth and physiological responses.
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Affiliation(s)
- Kris A Christensen
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Jérémy Le Luyer
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V OA6, Canada
| | - Michelle T T Chan
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada
- Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Eric B Rondeau
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V OA6, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada
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7
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Hou ZS, Xin YR, Zeng C, Zhao HK, Tian Y, Li JF, Wen HS. GHRH-SST-GH-IGF axis regulates crosstalk between growth and immunity in rainbow trout (Oncorhynchus mykiss) infected with Vibrio anguillarum. FISH & SHELLFISH IMMUNOLOGY 2020; 106:887-897. [PMID: 32866610 DOI: 10.1016/j.fsi.2020.08.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/15/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
An energy trade-off is existed between immunological competence and growth. The axis of growth hormone releasing hormone, somatostatin, growth hormone, insulin-like growth factor (GHRH-SST-GH-IGF axis) regulates growth performances and immune competences in rainbow trout (Oncorhynchus mykiss). The salmonid-specific whole genome duplication event is known to result in duplicated copies of several key genes in GHRH-SST-GH-IGF axis. In this study, we evaluated the physiological functions of GHRH-SST-GH-IGF axis in regulating crosstalk between growth and immunity. Based on principal components analysis (PCA), we observed the overall expression profiles of GHRH-SST-GH-IGF axis were significantly altered by Vibrio anguillarum infection. Trout challenged with Vibrio anguillarum showed down-regulated igf1s subtypes and up-regulated igfbp1a1. The brain sst genes (sst1a, sst1b, sst3b and sst5) and igfpbs genes (igfbp4s and igfbp5b2) were significantly affected by V. anguillarum infection, while the igfbp4s, igfbp5s, igfbp6s and igf2bps genes showed significant changes in peripheral immune tissues in response to V. anguillarum infection. Gene enrichment analyses showed functional and signaling pathways associated with apoptosis (such as p53, HIF-1 or FoxO signaling) were activated. We further proposed a possible model that describes the IGF and IGFBPs-regulated interaction between cell growth and programmed death. Our study provided new insights into the physiological functions and potentially regulatory mechanisms of the GHRH-SST-GH-IGF axis, indicating the pleiotropic effects of GHRH-SST-GH-IGF axis in regulating crosstalk between growth and immunity in trout.
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Affiliation(s)
- Zhi-Shuai Hou
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China.
| | - Yuan-Ru Xin
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China
| | - Chu Zeng
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China
| | - Hong-Kui Zhao
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China
| | - Yuan Tian
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China
| | - Ji-Fang Li
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China
| | - Hai-Shen Wen
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China.
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