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Robinson NA, Robledo D, Sveen L, Daniels RR, Krasnov A, Coates A, Jin YH, Barrett LT, Lillehammer M, Kettunen AH, Phillips BL, Dempster T, Doeschl‐Wilson A, Samsing F, Difford G, Salisbury S, Gjerde B, Haugen J, Burgerhout E, Dagnachew BS, Kurian D, Fast MD, Rye M, Salazar M, Bron JE, Monaghan SJ, Jacq C, Birkett M, Browman HI, Skiftesvik AB, Fields DM, Selander E, Bui S, Sonesson A, Skugor S, Østbye TK, Houston RD. Applying genetic technologies to combat infectious diseases in aquaculture. REVIEWS IN AQUACULTURE 2023; 15:491-535. [PMID: 38504717 PMCID: PMC10946606 DOI: 10.1111/raq.12733] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/24/2022] [Accepted: 08/16/2022] [Indexed: 03/21/2024]
Abstract
Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.
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Affiliation(s)
- Nicholas A. Robinson
- Nofima ASTromsøNorway
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Andrew Coates
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Luke T. Barrett
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
- Institute of Marine Research, Matre Research StationMatredalNorway
| | | | | | - Ben L. Phillips
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Tim Dempster
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Francisca Samsing
- Sydney School of Veterinary ScienceThe University of SydneyCamdenAustralia
| | | | - Sarah Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | | | | | | | - Dominic Kurian
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Mark D. Fast
- Atlantic Veterinary CollegeThe University of Prince Edward IslandCharlottetownPrince Edward IslandCanada
| | | | | | - James E. Bron
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Sean J. Monaghan
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Celeste Jacq
- Blue Analytics, Kong Christian Frederiks Plass 3BergenNorway
| | | | - Howard I. Browman
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | - Anne Berit Skiftesvik
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | | | - Erik Selander
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
| | - Samantha Bui
- Institute of Marine Research, Matre Research StationMatredalNorway
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Zhao T, Zou Y, Yan H, Chang Y, Zhan Y. Non-coding RNAs targeting NF-κB pathways in aquatic animals: A review. Front Immunol 2023; 14:1091607. [PMID: 36825023 PMCID: PMC9941745 DOI: 10.3389/fimmu.2023.1091607] [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] [Received: 11/07/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
Nuclear factor-kappa B (NF-κB) pathways have a close relationship with many diseases, especially in terms of the regulation of inflammation and the immune response. Non-coding RNAs (ncRNAs) are a heterogeneous subset of endogenous RNAs that directly affect cellular function in the absence of proteins or peptide products; these include microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), etc. Studies on the roles of ncRNAs in targeting the NF-κB pathways in aquatic animals are scarce. A few research studies have confirmed detailed regulatory mechanisms among ncRNAs and the NF-κB pathways in aquatic animals. This comprehensive review is presented concerning ncRNAs targeting the NF-κB pathway in aquatic animals and provides new insights into NF-κB pathways regulatory mechanisms of aquatic animals. The review discusses new possibilities for developing non-coding-RNA-based antiviral applications in fisheries.
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Affiliation(s)
- Tanjun Zhao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.,College of Life Science, Liaoning Normal University, Dalian, China
| | - Yang Zou
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Hanyu Yan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.,College of Life Science, Liaoning Normal University, Dalian, China
| | - Yaoyao Zhan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
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Ramberg S, Krasnov A, Colquhoun D, Wallace C, Andreassen R. Expression Analysis of Moritella viscosa-Challenged Atlantic Salmon Identifies Disease-Responding Genes, MicroRNAs and Their Predicted Target Genes and Pathways. Int J Mol Sci 2022; 23:ijms231911200. [PMID: 36232504 PMCID: PMC9569996 DOI: 10.3390/ijms231911200] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Moritella viscosa is a bacterial pathogen causing winter-ulcer disease in Atlantic salmon. The lesions on affected fish lead to increased mortality, decreased fish welfare, and inferior meat quality in farmed salmon. MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional regulation by guiding the miRNA-induced silencing complex to specific mRNA transcripts (target genes). The goal of this study was to identify miRNAs responding to Moritella viscosa in salmon by investigating miRNA expression in the head-kidney and the muscle/skin from lesion sites caused by the pathogen. Protein coding gene expression was investigated by microarray analysis in the same materials. Seventeen differentially expressed guide-miRNAs (gDE-miRNAs) were identified in the head-kidney, and thirty-nine in lesion sites, while the microarray analysis reproduced the differential expression signature of several thousand genes known as infection-responsive. In silico target prediction and enrichment analysis suggested that the gDE-miRNAs were predicted to target genes involved in immune responses, hemostasis, angiogenesis, stress responses, metabolism, cell growth, and apoptosis. The majority of the conserved gDE-miRNAs (e.g., miR-125, miR-132, miR-146, miR-152, miR-155, miR-223 and miR-2188) are known as infection-responsive in other vertebrates. Collectively, the findings indicate that gDE-miRNAs are important post-transcriptional gene regulators of the host response to bacterial infection.
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Affiliation(s)
- Sigmund Ramberg
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, 0167 Oslo, Norway
| | - Aleksei Krasnov
- Division of Aquaculture, Norwegian Institute of Fisheries and Aquaculture (Nofima), 1430 Ås, Norway
| | | | | | - Rune Andreassen
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, 0167 Oslo, Norway
- Correspondence:
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Inducible MicroRNA-132 Inhibits the Production of Inflammatory Cytokines by Targeting TRAF6, TAK1, and TAB1 in Teleost Fish. Infect Immun 2022; 90:e0012022. [PMID: 35416706 DOI: 10.1128/iai.00120-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The innate immune response is the first line of defense against pathogen infection. Eradication of pathogen infection requires appropriate immune and inflammatory responses, but excessive inflammation may cause inflammatory and autoimmune diseases. MicroRNAs (miRNAs) are a group of small noncoding RNAs, and accumulating evidence has shown that in mammals, they can act as negative regulators that participate in the regulation of inflammation and immune responses. However, the miRNA-mediated immune regulation networks in the inflammatory responses of lower vertebrates are largely unknown. In this study, we report an miRNA, miR-132, identified from miiuy croaker, that acts as a negative regulator in the host's bacterium-induced inflammatory response. We found that miR-132 expression was dramatically increased upon infection by the Gram-negative bacterium Vibrio harveyi and lipopolysaccharide (LPS). Inducible miR-132 inhibits the production of inflammatory cytokines by targeting tumor necrosis factor receptor-associated factor 6 (TRAF6), transforming growth factor-activated protein kinase 1 (TAK1), and TAK1 binding protein 1 (TAB1), thus avoiding an excessive inflammatory response. Furthermore, we demonstrate that miR-132 modulates the inflammatory response through a TRAF6-, TAK1-, and TAB1-mediated NF-κB signaling pathway. These results collectively reveal that miR-132 plays a negative regulatory role in the host antibacterial immune response, which will help to gain insight into the intricate network of host resistance to pathogen infection in lower vertebrates.
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Valenzuela-Muñoz V, Gallardo-Escárate C, Benavente BP, Valenzuela-Miranda D, Núñez-Acuña G, Escobar-Sepulveda H, Váldes JA. Whole-Genome Transcript Expression Profiling Reveals Novel Insights into Transposon Genes and Non-Coding RNAs during Atlantic Salmon Seawater Adaptation. BIOLOGY 2021; 11:1. [PMID: 35052999 PMCID: PMC8772943 DOI: 10.3390/biology11010001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/11/2022]
Abstract
The growing amount of genome information and transcriptomes data available allows for a better understanding of biological processes. However, analysis of complex transcriptomic experimental designs involving different conditions, tissues, or times is relevant. This study proposes a novel approach to analyze complex data sets combining transcriptomes and miRNAs at the chromosome-level genome. Atlantic salmon smolts were transferred to seawater under two strategies: (i) fish group exposed to gradual salinity changes (GSC) and (ii) fish group exposed to a salinity shock (SS). Gills, intestine, and head kidney samples were used for total RNA extraction, followed by mRNA and small RNA illumina sequencing. Different expression patterns among the tissues and treatments were observed through a whole-genome transcriptomic approach. Chromosome regions highly expressed between experimental conditions included a great abundance of transposable elements. In addition, differential expression analysis showed a greater number of transcripts modulated in response to SS in gills and head kidney. miRNA expression analysis suggested a small number of miRNAs involved in the smoltification process. However, target analysis of these miRNAs showed a regulatory role in growth, stress response, and immunity. This study is the first to evidence the interplaying among mRNAs and miRNAs and the structural relationship at the genome level during Atlantic salmon smoltification.
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Affiliation(s)
- Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (C.G.-E.); (B.P.B.); (D.V.-M.); (G.N.-A.); (H.E.-S.); (J.A.V.)
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370035, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (C.G.-E.); (B.P.B.); (D.V.-M.); (G.N.-A.); (H.E.-S.); (J.A.V.)
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Bárbara P. Benavente
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (C.G.-E.); (B.P.B.); (D.V.-M.); (G.N.-A.); (H.E.-S.); (J.A.V.)
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (C.G.-E.); (B.P.B.); (D.V.-M.); (G.N.-A.); (H.E.-S.); (J.A.V.)
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Gustavo Núñez-Acuña
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (C.G.-E.); (B.P.B.); (D.V.-M.); (G.N.-A.); (H.E.-S.); (J.A.V.)
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Hugo Escobar-Sepulveda
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (C.G.-E.); (B.P.B.); (D.V.-M.); (G.N.-A.); (H.E.-S.); (J.A.V.)
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Juan Antonio Váldes
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (C.G.-E.); (B.P.B.); (D.V.-M.); (G.N.-A.); (H.E.-S.); (J.A.V.)
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370035, Chile
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Salazar C, Galaz M, Ojeda N, Marshall SH. Expression of ssa-miR-155 during ISAV infection in vitro: Putative role as a modulator of the immune response in Salmo salar. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 122:104109. [PMID: 33930457 DOI: 10.1016/j.dci.2021.104109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Multiple cellular components are involved in pathogen-host interaction during viral infection; in this context, the role of miRNAs have become highly relevant. We assessed the expression of selected miRNAs during an in vitro infection of a Salmo salar cell line with Infectious Salmon Anemia Virus (ISAV), the causative agent of a severe disease by the same name. Salmon orthologs for miRNAs that regulate antiviral responses were measured using RT-qPCR in an in vitro time-course assay. We observed a modulation of specific miRNAs expression, where ssa-miR-155-5p was differentially over-expressed. Using in silico analysis, we identified the putative mRNA targets for ssa-miR-155-5p, finding a high prevalence of hosts immune response-related genes; moreover, several mRNAs involved in the viral infective process were also identified as targets for this miRNA. Our results suggest a relevant role for miR-155-5p in Salmo salar during an ISAV infection as a regulator of the immune response to the virus.
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Affiliation(s)
- Carolina Salazar
- Instituto de Biologia, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile
| | - Martín Galaz
- Instituto de Biologia, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile
| | - Nicolás Ojeda
- Instituto de Biologia, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile
| | - Sergio H Marshall
- Instituto de Biologia, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile.
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Valenzuela-Muñoz V, Váldes JA, Gallardo-Escárate C. Transcriptome Profiling of Long Non-coding RNAs During the Atlantic Salmon Smoltification Process. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:308-320. [PMID: 33638736 DOI: 10.1007/s10126-021-10024-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
For salmon aquaculture, one of the most critical phase is the parr-smolt transformation. Studies around this process have mainly focused on physiological changes and the Na+/K+-ATPase activity during the osmoregulatory activity. However, understanding how the salmon genome regulates the parr-smolt transformation, specifically the molecular mechanisms involved, remains uncovered. This study aimed to explore the transcriptional modulation of long non-coding RNAs (lncRNAs), as key molecular regulators, during the freshwater (FW) to seawater (SW) transfer in Atlantic salmon. Transcriptome sequencing was performed from gill samples of Atlantic salmon adapted from FW to SW through gradual salinity changes from 0 to 30 PSU. The results showed that most transcripts differently modulated were downregulated in all salinity conditions. Relevant biological processes were associated with growth, collagen formation, immune response, metabolism, and heme transport. Notably, 2864 putative lncRNAs were identified in Atlantic salmon gills differently expressed during fish smoltification. The highest number of lncRNAs differently modulated was observed at 30 PSU. Correlation expression analysis suggests putative regulatory roles of lncRNAs with smoltification-related genes. Herein, co-localization of Na+/K+-ATPase, growth hormone receptor, and thyroid hormone receptor genes with lncRNAs differentially expressed suggest putative regulatory mechanisms in the Atlantic salmon genome. The lncRNAs can be used as novel biomarkers for the fish smoltification process. Here, the lncRNA_145326 and lncRNA_18762 are putatively related to the parr-smolt transfer in Atlantic salmon. This study is the first description of lncRNAs with putative regulatory roles in Atlantic salmon during the SW adaptation.
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Affiliation(s)
- Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile.
- Laboratorio de Biotecnología Molecular, Universidad Andrés Bello, Facultad de Ciencias de la Vida, Santiago, Chile.
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepción, Chile.
| | - Juan Antonio Váldes
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile
- Laboratorio de Biotecnología Molecular, Universidad Andrés Bello, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepción, Chile
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Gallardo-Escárate C, Valenzuela-Muñoz V, Nuñez-Acuña G, Valenzuela-Miranda D, Gonçalves AT, Escobar-Sepulveda H, Liachko I, Nelson B, Roberts S, Warren W. Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis. Sci Data 2021; 8:60. [PMID: 33574331 PMCID: PMC7878743 DOI: 10.1038/s41597-021-00842-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 01/25/2021] [Indexed: 12/19/2022] Open
Abstract
Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecule real-time sequencing (SMRT) and proximity ligation (Hi-C) analysis. Coding RNAs and non-coding RNAs, and specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were identified through whole transcriptome sequencing from different life stages. A total of 23,686 protein-coding genes and 12,558 non-coding RNAs were annotated. In addition, 6,308 lncRNAs and 5,774 miRNAs were found to be transcriptionally active from larvae to adult stages. Taken together, this genomic resource for C. rogercresseyi represents a valuable tool to develop sustainable control strategies in the salmon aquaculture industry.
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Affiliation(s)
- Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile.
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile.
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Gustavo Nuñez-Acuña
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Ana Teresa Gonçalves
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Hugo Escobar-Sepulveda
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | | | | | - Steven Roberts
- School of Aquatic and Fishery Sciences (SAFS), University of Washington, Seattle, USA
| | - Wesley Warren
- Bond Life Sciences Center, University of Missouri, Columbia, USA
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Shwe A, Østbye TKK, Krasnov A, Ramberg S, Andreassen R. Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon. Genes (Basel) 2020; 11:genes11091059. [PMID: 32911670 PMCID: PMC7565298 DOI: 10.3390/genes11091059] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022] Open
Abstract
Smoltification and early seawater phase are critical developmental periods with physiological and biochemical changes in Atlantic salmon that facilitates survival in saltwater. MicroRNAs (miRNAs) are known to have important roles in development, but whether any miRNAs are involved in regulation of gene expression during smoltification and the adaption to seawater is largely unknown. Here, small RNA sequencing of materials from head kidney before, during smoltification and post seawater transfer were used to study expression dynamics of miRNAs, while microarray analysis was applied to study mRNA expression dynamics. Comparing all timepoints, 71 miRNAs and 2709 mRNAs were identified as differentially expressed (DE). Hierarchical clustering analysis of the DE miRNAs showed three major clusters with characteristic expression changes. Eighty-one DE mRNAs revealed negatively correlated expression patterns to DE miRNAs in Cluster I and III. Furthermore, 42 of these mRNAs were predicted as DE miRNA targets. Gene enrichment analysis of negatively correlated target genes showed they were enriched in gene ontology groups hormone biosynthesis, stress management, immune response, and ion transport. The results strongly indicate that post-transcriptional regulation of gene expression by miRNAs is important in smoltification and sea water adaption, and this study identifies several putative miRNA-target pairs for further functional studies.
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Affiliation(s)
- Alice Shwe
- Department of Life Science and Health, Faculty of Health Sciences, OsloMet‒Oslo Metropolitan University, N-0130 Oslo, Norway; (A.S.); (S.R.)
| | - Tone-Kari Knutsdatter Østbye
- Nofima (Norwegian Institute of Food, Fisheries and Aquaculture Research), Postboks 210, NO-1431 Ås, Norway; (T.-K.K.Ø.); (A.K.)
| | - Aleksei Krasnov
- Nofima (Norwegian Institute of Food, Fisheries and Aquaculture Research), Postboks 210, NO-1431 Ås, Norway; (T.-K.K.Ø.); (A.K.)
| | - Sigmund Ramberg
- Department of Life Science and Health, Faculty of Health Sciences, OsloMet‒Oslo Metropolitan University, N-0130 Oslo, Norway; (A.S.); (S.R.)
| | - Rune Andreassen
- Department of Life Science and Health, Faculty of Health Sciences, OsloMet‒Oslo Metropolitan University, N-0130 Oslo, Norway; (A.S.); (S.R.)
- Correspondence: ; Tel.: +47-6723-627-4
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Bai J, Hu X, Wang R, Lü A, Sun J. MicroRNA expression profile analysis of skin immune response in crucian carp (Carassius auratus) infected by Aeromonas hydrophila. FISH & SHELLFISH IMMUNOLOGY 2020; 104:673-685. [PMID: 32505719 DOI: 10.1016/j.fsi.2020.05.077] [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: 02/20/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs) are non-coding RNA molecules that regulate gene expression in fish, but its regulatory mechanism of the skin mucosal immune response remains poorly understood. In order to investigate the immunological role of miRNAs, three sRNA libraries (mSC, mST1, mST2) from skin samples of crucian carp (Carassiusauratus) infected with Aeromonas hydrophila at three time points (0, 6 and 12 hpi) were constructed and examined using Illumina Hiseq 2000 platform. All of the identified miRNA, rRNA and tRNA were 69444 (13.39%), 29550 (5.70%) and 10704 (2.06%) in skin, respectively. At 6 and 12 hpi, 829 and 856 miRNAs were differentially expressed, respectively. Among these DEMs, 53 known and 10 novel miRNAs were all significantly differentially expressed during early infection (p < 0.01). GO and KEGG enrichment analyses revealed that 118111 target-genes were primarily involved in cellular process, metabolic process, biological regulation and stress response, such as antigen processing and presentation, complement and coagulation cascades, phagosome, MAPK, TLR, NF-κB and JAK-STAT signaling pathways. These results will help to elucidate the mechanism of miRNAs involved in the skin mucosal immune response of crucian carp against Aeromonas hydrophila infection.
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Affiliation(s)
- Jie Bai
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Ruixia Wang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Aijun Lü
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Jingfeng Sun
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
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11
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Micro-Transcriptome Analysis Reveals Immune-Related MicroRNA Regulatory Networks of Paralichthys olivaceus Induced by Vibrio anguillarum Infection. Int J Mol Sci 2020; 21:ijms21124252. [PMID: 32549342 PMCID: PMC7352997 DOI: 10.3390/ijms21124252] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding regulatory RNAs that play a vital part in the host immune response to pathogen infection. Japanese flounder (Paralichthys olivaceus) is an important aquaculture fish species that has suffered from bacterial diseases, including that caused by Vibrio anguillarum infection. In a previous study, we examined the messenger RNA (mRNA) expression profiles of flounder during V. anguillarum infection and identified 26 hub genes in the flounder immune response. In this study, we performed the micro-transcriptome analysis of flounder spleen in response to V. anguillarum infection at 3 different time points. Approximately 277 million reads were obtained, from which 1218 miRNAs were identified, including 740 known miRNAs and 478 novel miRNAs. Among the miRNAs, 206 were differentially expressed miRNAs (DEmiRs), and 104 of the 206 DEmiRs are novel miRNAs identified for the first time. Most of the DEmiRs were strongly time-dependent. A total of 1355 putative target genes of the DEmiRs (named DETGs) were identified based on integrated analysis of miRNA-mRNA expressions. The DETGs were enriched in multiple functional categories associated with immunity. Thirteen key DEmiRs and 66 immune DETGs formed an intricate regulatory network constituting 106 pairs of miRNAs and DETGs that span five immune pathways. Furthermore, seven of the previously identified hub genes were found to be targeted by 73 DEmiRs, and together they formed interlinking regulatory networks. These results indicate that V. anguillarum infection induces complicated miRNA response with extensive influences on immune gene expression in Japanese flounder.
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12
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Gallardo-Escárate C, Valenzuela-Muñoz V, Núñez-Acuña G, Carrera C, Gonçalves AT, Valenzuela-Miranda D, Benavente BP, Roberts S. Catching the complexity of salmon-louse interactions. FISH & SHELLFISH IMMUNOLOGY 2019; 90:199-209. [PMID: 31048036 DOI: 10.1016/j.fsi.2019.04.065] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The study of host-parasite relationships is an integral part of the immunology of aquatic species, where the complexity of both organisms has to be overlayed with the lifecycle stages of the parasite and immunological status of the host. A deep understanding of how the parasite survives in its host and how they display molecular mechanisms to face the immune system can be applied for novel parasite control strategies. This review highlights current knowledge about salmon and sea louse, two key aquatic animals for aquaculture research worldwide. With the aim to catch the complexity of the salmon-louse interactions, molecular information gleaned through genomic studies are presented. The host recognition system and the chemosensory receptors found in sea lice reveal complex molecular components, that in turn, can be disrupted through specific molecules such as non-coding RNAs.
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Affiliation(s)
- Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile.
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Gustavo Núñez-Acuña
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Crisleri Carrera
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Ana Teresa Gonçalves
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Bárbara P Benavente
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Steven Roberts
- School of Aquatic and Fishery Sciences (SAFS), University of Washington, Seattle, USA
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13
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Transcriptomic response of rainbow trout (Oncorhynchus mykiss) skeletal muscle to Flavobacterium psychrophilum. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 31:100596. [PMID: 31174158 DOI: 10.1016/j.cbd.2019.100596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 01/12/2023]
Abstract
Flavobacterium psychrophilum is the etiologic agent of rainbow trout fry syndrome (RTFS). This pathogen infects a wide variety of salmonid species during freshwater stages, causing significant losses in the aquaculture industry. Rainbow trout (Oncorhynchus mykiss) infected with F. psychrophilum, presents as the main external clinical sign ulcerative lesions and necrotic myositis in skeletal muscle. We previously reported the in vitro cytotoxic activity of F. psychrophilum on rainbow trout myoblast, however little is known about the molecular mechanisms underlying the in vivo pathogenesis in skeletal muscle. In this study, we examined the transcriptomic profiles of skeletal muscle tissue of rainbow trout intraperitoneally challenged with low infection dose of F. psychrophilum. Using high-throughput RNA-seq, we found that 233 transcripts were up-regulated, mostly associated to ubiquitin mediated proteolysis and apoptosis. Conversely, 189 transcripts were down-regulated, associated to skeletal muscle contraction. This molecular signature was consistent with creatine kinase activity in plasma and oxidative damage in skeletal muscle. Moreover, the increased caspase activity suggests as a whole skeletal muscle atrophy induced by F. psychrophilum. This study offers an integrative analysis of the skeletal muscle response to F. psychrophilum infection and reveals unknown aspects of its pathogenesis in rainbow trout.
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14
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Gonçalves AT, Núñez-Acuña G, Détrée C, Gallardo-Escárate C. Coding/non-coding cross-talk in intestinal epithelium transcriptome gives insights on how fish respond to stocking density. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 29:14-23. [DOI: 10.1016/j.cbd.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 02/04/2023]
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15
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Expanding the miRNA Repertoire in Atlantic Salmon; Discovery of IsomiRs and miRNAs Highly Expressed in Different Tissues and Developmental Stages. Cells 2019; 8:cells8010042. [PMID: 30641951 PMCID: PMC6356880 DOI: 10.3390/cells8010042] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) are important post-transcriptional gene expression regulators. Here, 448 different miRNA genes, including 17 novel miRNAs, encoding for 589 mature Atlantic salmon miRNAs were identified after sequencing 111 samples (fry, pathogen challenged fry, various developmental and adult tissues). This increased the reference miRNAome with almost one hundred genes. Prior to isomiR characterization (mature miRNA variants), the proportion of erroneous sequence variants (ESVs) arising in the analysis pipeline was assessed. The ESVs were biased towards 5’ and 3’ end of reads in unexpectedly high proportions indicating that measurements of ESVs rather than Phred score should be used to avoid misinterpreting ESVs as isomiRs. Forty-three isomiRs were subsequently discovered. The biological effect of the isomiRs measured as increases in target diversity was small (<3%). Five miRNA genes showed allelic variation that had a large impact on target gene diversity if present in the seed. Twenty-one miRNAs were ubiquitously expressed while 31 miRNAs showed predominant expression in one or few tissues, indicating housekeeping or tissue specific functions, respectively. The miR-10 family, known to target Hox genes, were highly expressed in the developmental stages. The proportion of miR-430 family members, participating in maternal RNA clearance, was high at the earliest developmental stage.
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16
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Wang M, Jiang S, Wu W, Yu F, Chang W, Li P, Wang K. Non-coding RNAs Function as Immune Regulators in Teleost Fish. Front Immunol 2018; 9:2801. [PMID: 30546368 PMCID: PMC6279911 DOI: 10.3389/fimmu.2018.02801] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/13/2018] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are functional RNA molecules that are transcribed from DNA but not translated into proteins. ncRNAs function as key regulators of gene expression and chromatin modification. Recently, the functional role of ncRNAs in teleost fish has been extensively studied. Teleost fish are a highly diverse group among the vertebrate lineage. Fish are also important in terms of aquatic ecosystem, food production and human life, being the source of animal proteins worldwide and models of biomedical research. However, teleost fish always suffer from the invasion of infectious pathogens including viruses and bacteria, which has resulted in a tremendous economic loss to the fishing industry worldwide. Emerging evidence suggests that ncRNAs, especially miRNAs and lncRNAs, may serve as important regulators in cytokine and chemokine signaling, antigen presentation, complement and coagulation cascades, and T cell response in teleost fish. In this review, we summarize current knowledge and understanding of the roles of both miRNAs and lncRNAs in immune regulation in teleost fish. Molecular mechanism insights into the function of ncRNAs in fish immune response may contribute to the development of potential biomarkers and therapeutic targets for the prevention and treatment of fish diseases.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Shuai Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Wu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Fei Yu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Wenguang Chang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Kun Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
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17
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Mohamed AR, King H, Evans B, Reverter A, Kijas JW. Multi-Tissue Transcriptome Profiling of North American Derived Atlantic Salmon. Front Genet 2018; 9:369. [PMID: 30271423 PMCID: PMC6146974 DOI: 10.3389/fgene.2018.00369] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/22/2018] [Indexed: 12/23/2022] Open
Abstract
The availability of a reference genome assembly for Atlantic salmon, Salmo salar, SNP genotyping platforms and low cost sequencing are enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analyzed transcriptomes from selected tissues of Atlantic salmon to inform future functional and comparative genomics studies. Messenger RNA (mRNA) was isolated from pituitary gland, brain, ovary, and liver before Illumina sequencing produced a total of 640 million 150-bp paired-end reads. Following read mapping, feature counting, and normalization, cluster analysis identified genes highly expressed in a tissue-specific manner. We identified a cluster of 508 tissue specific genes for pituitary gland, 3395 for brain, 2939 for ovary, and 539 for liver. Functional profiling identified gene clusters describing the unique functions of each tissue. Moreover, highly-expressed transcription factors (TFs) present in each tissue-specific gene cluster were identified. TFs belonging to homeobox and bhlh families were identified for pituitary gland, pou and zf-c2h2 families for brain, arid, and zf-c2h2 for ovary and rxr-like family for liver. The data and analysis presented are relevant to the emerging Functional Annotation of All Salmonid Genomes (FAASG) initiative that is seeking to develop a detailed understanding of both salmonid evolution and the genomic elements that drive gene expression and regulation.
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Affiliation(s)
- Amin R Mohamed
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia.,Zoology Department, Faculty of Science, Benha University, Benha, Egypt
| | - Harry King
- Commonwealth Scientific and Industrial Research Organisation Agriculture, Hobart, TAS, Australia
| | | | - Antonio Reverter
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - James W Kijas
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
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18
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Zhou Z, Lin Z, Pang X, Shan P, Wang J. MicroRNA regulation of Toll-like receptor signaling pathways in teleost fish. FISH & SHELLFISH IMMUNOLOGY 2018; 75:32-40. [PMID: 29408644 DOI: 10.1016/j.fsi.2018.01.036] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/12/2018] [Accepted: 01/25/2018] [Indexed: 06/07/2023]
Abstract
The innate immune system is the first line defense mechanism that recognizes, responds to, controls or eliminates invading pathogens. Toll-like receptors (TLRs) are a critical family of pattern recognition receptors (PRRs) tightly regulated by complex mechanisms involving many molecules to ensure a beneficial outcome in response to foreign invaders. MicroRNAs (miRNAs), a transcriptional and posttranscriptional regulator family in a wide range of biological processes, have been identified as new molecules related to the regulation of TLR-signaling pathways in immune responses. To date, at least 22 TLR types have been identified in more than a dozen different fish species. However, the functions and underlying mechanisms of miRNAs in the regulation of inflammatory responses related to the TLR-signaling pathway in fish is lacking. In this review, we summarize the regulation of miRNA expression profiles in the presence of TLR ligands or pathogen infections in teleost fish. We focus on the effects of miRNAs in regulating TLR-signaling pathways by targeting multiple molecules, including TLRs themselves, TLR-associated signaling proteins, and TLR-induced cytokines. An understanding of the relationship between the TLR-signaling pathways and miRNAs may provide new insights for drug intervention to manipulate immune responses in fish.
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Affiliation(s)
- Zhixia Zhou
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China.
| | - Zhijuan Lin
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China; Key Lab for Immunology in Universities of Shandong Province, School of Clinical Medicine, Weifang Medical University, Weifang 261053, China
| | - Xin Pang
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Peipei Shan
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Jianxun Wang
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China.
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19
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Herkenhoff ME, Oliveira AC, Nachtigall PG, Costa JM, Campos VF, Hilsdorf AWS, Pinhal D. Fishing Into the MicroRNA Transcriptome. Front Genet 2018; 9:88. [PMID: 29616080 PMCID: PMC5868305 DOI: 10.3389/fgene.2018.00088] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/02/2018] [Indexed: 01/18/2023] Open
Abstract
In the last decade, several studies have been focused on revealing the microRNA (miRNA) repertoire and determining their functions in farm animals such as poultry, pigs, cattle, and fish. These small non-protein coding RNA molecules (18-25 nucleotides) are capable of controlling gene expression by binding to messenger RNA (mRNA) targets, thus interfering in the final protein output. MiRNAs have been recognized as the main regulators of biological features of economic interest, including body growth, muscle development, fat deposition, and immunology, among other highly valuable traits, in aquatic livestock. Currently, the miRNA repertoire of some farmed fish species has been identified and characterized, bringing insights about miRNA functions, and novel perspectives for improving health and productivity. In this review, we summarize the current advances in miRNA research by examining available data on Neotropical and other key species exploited by fisheries and in aquaculture worldwide and discuss how future studies on Neotropical fish could benefit from this knowledge. We also make a horizontal comparison of major results and discuss forefront strategies for miRNA manipulation in aquaculture focusing on forward-looking ideas for forthcoming research.
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Affiliation(s)
- Marcos E. Herkenhoff
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| | - Arthur C. Oliveira
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| | - Pedro G. Nachtigall
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| | - Juliana M. Costa
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| | - Vinicius F. Campos
- Laboratory of Structural Genomics (GenEstrut), Graduate Program of Biotechnology, Technology Developmental Center, Federal University of Pelotas, Pelotas, Brazil
| | | | - Danillo Pinhal
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
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20
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Valenzuela-Miranda D, Valenzuela-Muñoz V, Farlora R, Gallardo-Escárate C. MicroRNA-based transcriptomic responses of Atlantic salmon during infection by the intracellular bacterium Piscirickettsia salmonis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 77:287-296. [PMID: 28870451 DOI: 10.1016/j.dci.2017.08.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/28/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that have emerged as key regulators in diverse biological processes across taxa. However, despite the importance of these transcripts, little is known about their role during the immune response in salmonids. Because of this, we use deep sequencing technologies to explore the microRNA-based transcriptomic response of the Atlantic salmon (Salmo salar) to the intracellular bacteria Piscirickettsia salmonis, one of the main threats to salmon aquaculture in Chile. Hence, 594 different miRNAs were identified from head kidney and spleen transcriptomic data. Among them, miRNA families mir-181, mir-143 and mir-21 were the most abundant in control groups, while after infection with P. salmonis, mir-21, mir-181 and mir-30 were the most predominant families. Furthermore, transcriptional analysis revealed 84 and 25 differentially expressed miRNAs in head kidney and spleen respectively, with an overlapping response of 10 miRNAs between the analyzed tissues. Target prediction, coupled with GO enrichment analysis, revealed that the possible targets of the most regulated miRNAs were genes involved in the immune response, such as cortisol metabolism, chemokine-mediated signaling pathway and neutrophil chemotaxis genes. Among these, predicted putative target genes such as C-C motif chemokine 19-like, stromal cell-derived factor 1-like, myxovirus resistance protein 2 and hepcidin-1 were identified. Overall, our results suggest that miRNA expression in co-modulation with transcription activity of target genes is related to putative roles of non-coding RNAs in the immune response of Atlantic salmon against intracellular bacterial pathogens.
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Affiliation(s)
- Diego Valenzuela-Miranda
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P. O. Box 160-C, Concepción, Chile
| | - Valentina Valenzuela-Muñoz
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P. O. Box 160-C, Concepción, Chile
| | - Rodolfo Farlora
- Laboratorio de Biotecnología Acuática y Genómica Reproductiva/Instituto de Biología, Facultad de Ciencias Universidad de Valparaíso, Chile
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P. O. Box 160-C, Concepción, Chile.
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