INTRO TO OMICS
The term “Omics” refers to the study of the role of genes in how an organism responds to its environment. The process of gene expression broadly includes four main components: the genome, transcriptome, proteome, and metabolome, and the study of these components collectively is omics. The potential for omics science to be applied in fisheries and wildlife management is enormous! However, despite this potential, the uptake of omics technologies to facilitate real-world management decisions is lagging. This is likely due to two main issues: 1) a lack of knowledge about omics, and 2) limited applied science that targets fishery management needs.
Members of the GEN-FISH Research Team and project partners are working on a Great Lakes Fishery Commission Science Transfer Program project to make omics more accessible for fisheries managers. It’s our goal to translate the techniques, applications, and benefits of omics technology for fisheries science; for instance, omics could be applied to solve or address many concerns for fisheries, such as quantifying fish population responses to management actions, or measuring fish stress and health. Specifically, we will combine the extensive omics, fisheries, and economics experience of our team with information from the broader scientific community to develop and provide non-technical visual educational materials, written resources, and decision-guiding tools for Great Lakes Fisheries Managers—and fisheries managers globally!
Our deliverables will include: 1) graphical or video omics education material based on our assessment of knowledge and data gaps; 2) a website hosting supporting materials and resources, such as decision-guiding trees, published literature/reports, and connections to omics professionals for questions or collaborations); and 3) a publishable synthesis of the state of omics in fisheries management tailored to the Laurentian Great Lakes.
Want to get involved?
Are you an omics specialist or a resource manager? Help support the application of molecular tools in fisheries science and management—sign up with: OMICS LINK!
Omics Literature Database
| Omics Type | Management Concern | Summary | Citation | Date Published | DOI | Keywords | Paper Type | Applied / Theoretical | Capacity / Scale | Cost | Salinity | Locality | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Genomics - Genome-Wide | Research surveys; Bottom trawl; Data Collection; genomic methods; Fish stock assessment | This opinion paper provides background on the use of trawl surveys for marine fish stock assessment and an overview of four potential genomic applications to complement the trawl surveys. Abundance can be estimated using close-kin mark and recapture, while eDNA can give relative abundance. The authors describe using DNA modification to age fish (not proven yet) and to use genome sequencing to assess stock structure more acurately than using a few markers. | Rodríguez-Mendoza R and Saborido-Rey F (2023) The potential use of genomic methods in bottom trawl surveys to improve stock assessments in Europe. Front. Mar. Sci. 10:1095171. | 29-May-2023 | https://doi.org/10.3389/fmars.2023.1095171 | DNA methylation; Reproduction; Marine fisheries; Fish; Otoliths; Marine fish; Stock assessment; Surveys; Fishery data; Marine ecosystems; Age; Epigenetics; Marine fishes; Bottom trawling; Working groups; Research; Fisheries; Ecosystems; Genomics; Data collection; Fishery resources; Hydroacoustics; Stocks; Fish stocks; Benthos collecting devices; Methods; Fishing; Commercial fishing; Polls & surveys; Fisheries management | Opinion / Review | Theoretical | Member States of the European Union | Some discussion | SW | Europe | |
| Genomics - Genome-Wide | CKMR; SNP markers; genotyping; Kinship analysis; fisheries assessments | This paper provides a review of the close-kin mark recapture method of stock assessment using genomic data to determine relatedness with high accuracy. The paper gives a good description of the power of using kin relatedness of randomly captured fish to assess stock size and other demographic parameters, as well as giving an overview of how this method can be used in stock assessment models. | Casas L and Saborido-Rey F (2023) A review of genomics methods and bioinformatics tools for the analysis of close-kin mark-recapture. Front. Mar. Sci. 10:1113870. | 7-Jul-2023 | https://doi.org/10.3389/fmars.2023.1113870 | Fishery sciences; Parameters; Genotyping; Fisheries; Fish; Bioinformatics; Stocks; Fish stocks; Uptake; Stock assessment; Tracking; Uncertainty; Genomes; Statistical methods; Genomics; Probability theory; Capture-recapture studies | Opinion / Review | Theoretical | Fishery | Some discussion | NA | NA | |
| Genomics - Genome-Wide | Genome; global change; candidate genes; Environmental challenges; Benguela hake | This paper is primarily a technical report of a genome sequence developed for one species of exploited hake. It would have limited value for a non-technical fishery managers, although it represents basic genomics studies that contribute to the background data necessary for future management applications | Mateo JL, Blanco-Fernandez C, Garcia-Vazquez E and Machado-Schiaffino G (2023) A new Merluccius polli reference genome to investigate the effects of global change in West African waters. Front. Mar. Sci. 10:1111107. | 24-Apr-2023 | https://doi.org/10.3389/fmars.2023.1111107 | Metals; Genes; Geographical distribution; Pollutants; Marine fisheries; Fish; Global warming; Fisheries; Marine fish; Genomes; Hypoxia; Species diversity; Climate change; Contaminants; Nucleotide sequence; Marine fishes; Pollution; Temperature gradients; Consortia; Taxonomy; Heavy metals; Single-nucleotide polymorphism; Fishing; Heterozygosity; Sequencing; Merluccius polli | Technical / Data | Theoretical | SW | Africa | |||
| Genomics - Genome-Wide | Conservation genomics; Fisheries management; Harvesting; Hybridization; Next-generation sequencing; Simulations | This paper describes the value of testing for hybridization effects in fish raised in captivity for release into the wild for stocking. The authors provide a strong rationale for the use of large scale genomic data to detect such hybridization with a strong test case. However, the actual impact of hybridization on the health and performance of the wild fish is not explored. Where hybridization between closely-related species or among stocks is a potential problem, genomic detection and quanitification of the hybrids is well decsribed here | Attard Catherine, R. M., Sandoval-Castillo, J., Gilligan, D. M., Unmack, P. J., Faulks, L. K., & Beheregaray, L. B. (2022). Genomics outperforms genetics to manage mistakes in fisheries stocking of threatened species. Biodiversity & Conservation, 31(3), 895-908. | 8-Apr-2022 | https://doi.org/10.1007/s10531-022-02369-x | Lake basins; Fish; Fisheries; Fish stocking; Fingerlings; Biodiversity; Genetic variation; Hatcheries; Fish hatcheries; Genomics; Genomes; Hybridization; Genetic diversity; Threatened species; Nucleotides; Impoundments; Wildlife conservation; Basins; Outbreeding; Inland waters; Microsatellites; Stocking; Lakes; Breeding stock; Fisheries management; Endangered & extinct species; Genetics; Restocking; Single-nucleotide polymorphism; Datasets; Macquaria ambigua | Technical / Data | Applied | FW | Australia | |||
| Genomics - Whole-Genome | Largemouth bass; Whole-genome | This paper describes a whole genome analysis of Largemouth Bass strains that have been domesticated (genetically selected) to improve their performance. The authors show strong evidence for selection acting to change the genome of the selected strains. While this is an interesting paper documenting the genomic signals of selection, it would have litte relevance for wild stock management unless genetically altered strains were being considered for release to address special environmental challenges (e.g., low oxtgen and heat stress) | Sun, C., Zhang, X., Dong, J., You, X., Tian, Y., Gao, F., . . . Ye, X. (2023). Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass (micropterus salmoides). Zoological Research, 44(1), 78-8. | 18-Jan-2023 | https://doi.org/10.24272/j.issn.2095-8137.2022.274 | Genes; Signal analysis; Genetic analysis; Fish; Phylogenetics; Bass; Domestication; Fisheries; Animals; Breeding; Genetic variation; Genomes; Nucleotide sequence; Genetic diversity; Population structure; Genomics; Population genetics; Bcl-6 protein; Nucleotides; Populations; Whitefish; Fishing; Freshwater fishes; Micropterus salmoides | Technical / Data | Theoretical | FW | North America; Asia | |||
| Genomics - Genome-Wide | ship sturgeon; genome re-sequencing; effective population size; Ili River; China | This paper describes a restricted whole genome analysis of a highly endangered sturgeon species with the goal of determining when the species experienced a population bottleneck and how severe that bottleneck was. This application of genomics is very relevant for extreme at risk species, where captive breeding is being considered as a conservation/management option. Not very relevant for most exploited species. | Hu, G., Chen, F., Zhang, Y., Luan, P., Luo, Z., Niu, J., . . . Ji, F. (2023). Estimates of the effective population size and genetic structure of the critically endangered ship sturgeon (acipenser nudiventris) in the chinese section of the ili river. Fishes, 8(7), 354. | 7-Jul-2023 | https://doi.org/10.3390/fishes8070354 | Nature conservation; Software; Fish conservation; Fish; Endangered species; Aquaculture techniques; Rare species; Rivers; Genomes; Genetic structure; Genomics; Wildlife conservation; Genetic testing; Reproductive techniques; Threatened species; Sturgeon; Conservation; Endangered animals; Coefficients; Population genetics; Endangered & extinct species; Induced breeding; Ships; Single-nucleotide polymorphism; Fishing; Commercial fishing; Population number; Population decline; Freshwater fishes; Fisheries management; Acipenser nudiventris | Technical / Data | Theoretical | FW | Asia | |||
| Genomics - Whole-Genome | Next-generation sequencing; Shortfin mako shark; Single nucleotide polymorphism; Marine omics | This paper is primarily a technical report of a genome and transcriptome sequence analysis for one exploited shark species with little metadata on their biology available. By itself, it would have limited value for a non-technical fishery managers, although it provides valuable genetic markers for population health and demographic assessments Such studies would be valuable for any exploited species with limited demographic and biological data, but requires very specialized skills to develop and interpret, especially for practical management applications. | Domingues, R. R., Mastrochirico-Filho, V., Mendes, N. J., Hashimoto, D. T., Coelho, R., Antunes, A., . . . Mendonça, F. F. (2022). Gene-associated markers as a genomic and transcriptomic resource for a highly migratory and apex predator shark (isurus oxyrinchus). Marine Biology, 169(9) | 5-Aug-2022 | https://doi.org/10.1007/s00227-022-04094-z | Genes; Analysis; Sharks; DNA sequencing; Oceans; Fisheries; Pelagic fisheries; Locomotion; Molecular evolution; Predators; Transcriptomics; Annotations; Genotyping; Genomics; Biology; Polymorphism; Nucleotides; Gene sequencing; DNA sequence; RNA sequencing; Deoxyribonucleic acid--DNA; Biomarkers; Single-nucleotide polymorphism; Nucleotide sequence; Longline fishing; Marine fishes; Isurus; Isurus oxyrinchus | Technical / Data | Theoretical | SW | Global | |||
| Transcriptomics | HPG/HPI axis; maturation; photoperiod; Scomber japonicus; stress response; wavelength | This paper describes an experimental manipulation of photoperiod using captive mackerel to assess possible sexual maturation control. The work includes gene transcription profiling; however it includes only a few very targted genes. This work is primarily aimed at aquaculture applications and is of limited relevance for fishery applications. | Choi, Y. J., Seul Gi Na Ra, P., A-Hyun, J., & Jun-Hwan, K. (2023). Physiological effect of extended photoperiod and green wavelength on the pituitary hormone, sex hormone and stress response in chub mackerel, scomber japonicus. Fishes, 8(2), 77. | 16-May-2023 | https://doi.org/10.3390/fishes8020077 | Aquaculture; Physiology; Pituitary; Behavior; Hormones; Fish; Environmental effects; Follicle-stimulating hormone; Sex hormones; Plasma levels; Wavelength; Gonadotropin-releasing hormone; Pituitary gland; Sexual maturity; Metabolism; Testosterone; Photoperiods; Enzyme-linked immunosorbent assay; Immunoassays; Stress response; Photoperiodicity; Fatty acids; Gene expression; Luteinizing hormone; ELISA; Pituitary (anterior); Light effects; Trout; Steroids; Gonadotropins; Pituitary hormones; PCR; 17β-Estradiol; Nucleotide sequence; Light; Wavelengths; Biological stress; Marine fishes; Scomber japonicus | Technical / Data | Theoretical | SW | Asia | |||
| Genomics - Whole-Genome | Salmonidae; Mexican golden trout; Nelson’s trout; mitochondrial genome; taxonomic status; fish | This paper reports on the results of whole mitochondrial genome sequencing for two species of trout. While these data will be useful for possible fishery-related genomic applications, it is not relevant to non-technical readers. It does, however, add to the growing database of mitochondrial and nuclear genomes in freshwater fishes. | Colín, A., Del Río-Portilla, M.,A., Lafarga-De la Cruz, F., Genoveva Ingle-De, l. M., & García-De León, F.,J. (2023). Assembly, characterization, and phylogenetic relationships of mitogenomes of two species of mexican trout (oncorhynchus chrysogaster and O. mykiss nelsoni). Fishes, 8(4), 178. | 27-Mar-2023 | https://doi.org/10.3390/fishes8040178 | rRNA; Genes; Phylogenetics; tRNA; Genomes; Cladistics; Genomics; Mitochondria; Mitochondrial DNA; Servers; Replication origins; Phylogeny; Radiation; Trout; Salmon; Genetic engineering; Native species; Taxonomy; Sibling species; Freshwater fishes; Synteny; Oncorhynchus chrysogaster; Oncorhynchus mykiss nelsoni | Technical / Data | Theoretical | FW | North America | |||
| Genomics - Whole-Genome | Chondrichthyes; chimaeras; elasmobranchs; omics; transcriptome; review | This paper used existing RNA sequence data for sharks to assess the depth of that database and possible applications for management and conservation. No new data is generated. The paper provides good background on how RNA sequence (transcriptome) data may be useful for fisheries management; however, no such applications are provided. Good background information. | Seixas, M. J., Domingues, R. R., & Antunes, A. (2023). Decoding the transcriptome of sharks, rays, and chimaeras: Insights into their physiology, morphology, evolution, and biomedical applications. Fishes, 8(5), 271. | 19-May-2023 | https://doi.org/10.3390/fishes8050271 | Opinion / Review | Theoretical | SW | Global | ||||
| Genomics - Genome-Wide | population genomics, Engraulis japonicus, single nucleotide polymorphism, RAD-seq, genetic structures | This paper describes an analysis of genome-wide genetic markers to detect subpopulation structure in E. japonicus (a fished species) in the North Pacific. The authors note that genome-wide markers can detect subtle population structure and provide evidence for local adaptation. Although this case study may have limited relevance for most fishery managers, it provides a framework for how such genomic data can be used in complex stock or subpopulation situations. | Zhang, B., Li, Y., Xue, D., & Liu, J. (2020). Population genomics reveals shallow genetic structure in a connected and ecologically important fish from the northwestern pacific ocean. Frontiers in Marine Science, | 28-May-2020 | https://doi.org/10.3389/fmars.2020.00374 | Population; DNA sequencing; Economic importance; Fish; Pelagic fisheries; Ocean currents; Cytochrome; Animal behavior; Commercial fishing; Adaptation; Pelagic fish; Gene flow; Genetic structure; Genomics; Mitochondrial DNA; Natural selection; Genomes; Fish populations; Genetic diversity; Fisheries management; Fishery management; Population genetics; Dispersal; Economics; Deoxyribonucleic acid--DNA; Single-nucleotide polymorphism; Fishing; DNA; Population studies; Nucleotides; Marine fish; Stock assessment | Technical / Data | Theoretical | SW | Asia | |||
| Genomics - Whole-Genome | Fish Immune response; omics; Genomics; Transcriptomics; Proteomics; Metabolomics | This is a review and synthesis of how 'omics can be used to assess disease/pathogen responses in fishes. The primary focus is on captive rearing, specifically aquaculture, but the background information on the nature of the different 'omics data is valuable. May be of specific interest formanagers charged with hatchey production for reintroduction or supplementation. | Natnan, M. E., Low, C., Chong, C., Bunawan, H., & Baharum, S. N. (2021). Integration of omics tools for understanding the fish immune response due to microbial challenge. Frontiers in Marine Science, | 21-Jun-2021 | https://doi.org/10.3389/fmars.2021.668771 | Aquaculture; Fish; Mortality; Fish culture; Infectious diseases; Cytokines; Skin; Genomics; Peptides; Fishery products; Granulocytes; Biomarkers; Adaptive immunity; Defence mechanisms; Aquatic animals; Proteomics; Proteins; Immune response; Biology; Thymus gland; Spleen; Gene expression; Viruses; Medical treatment; Pathogens; Economics; Infections; Lymphocytes; Parasites; Agricultural production; Lectins; Immunoglobulins; Immunity; Genes; Antibodies; Disease; Metabolomics; Sustainable aquaculture; Nutrition; Immune system; Antigens; Fish hatcheries | Opinion / Review | Theoretical | NA | Global | |||
| Genomics - Genome-Wide | Marine fish; Population genomics; RAD sequencing; SNP; Tropical tuna; Tuna fishery | This is a strong paper describing using whole-genome genetic markers to detect population structure across the global range of yellowfin tuna. While the specific results reported here may be of limited interest to fishery managers in general, the approach and conclusion are of value. This paper adds to growing body of published litertaure that indicates whole-genome genetic markers are needed to detect subtle population structure | Pecoraro, C., Babbucci, M., Villamor, A., Franch, R., Papetti, C., Leroy, B., . . . Cariani, A. (2016). Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna (thunnus albacares). Marine Genomics, 25, 43-48. | 1-Feb-2016 | https://doi.org/10.1016/j.margen.2015.12.002 | Biological surveys; Marine fish; Genetics; Population genetics; Migratory Fish; Stock assessment; Population structure; Pipelines; Stacks; Tuna fisheries; Differentiation; Single-nucleotide polymorphism; Scales; Running; Oceans; Genotyping; Fisheries; Recruitment; Dispersal; Thunnus albacares; Marine | Technical / Data | Theoretical | SW | Global | |||
| Genomics - Whole-Genome | conservation physiology; fisheries management; genomics; field physiology; climate change | This paper is a review of progress made in using physiological and genomic tools to help with the complex challenges of salmonid conservation and management. The paper provides a good theoretical background with examples from the authors past resercah. This paper is valuable for managers facing declining stock issues where the cause is not obvious. | Cooke, S. J., Hinch, S. G., Donaldson, M. R., Clark, T. D., Eliason, E. J., Crossin, G. T., . . . Farrell, A. P. (2012). Conservation physiology in practice: How physiological knowledge has improved our ability to sustainably manage pacific salmon during up-river migration. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences, 367(1596), 1757-1769. | 19-Jun-2012 | https://doi.org/10.1098/rstb.2012.0022 | Migrations; Rivers; Temperature effects; Fitness; Mortality; Reviews; Telemetry; Fisheries; Conservation; genomics; Migration; Models; Salmonidae | Opinion / Review | Applied | FW | North America | |||
| Genomics - Whole-Genome | Genomics; Genetics; Fisheries; Mariculture; Quantitative trait loci; Fish; Oyster | This paper provides a good overview of potential applications of genomics and transcriptomics in fisheries science and management; however, the specific technologies discussed are dated. Nevertheless, this review would be valuable for someone with little technical background as a primer, since it focusses on fishery and aquaculture applications. | Wenne, R., Boudry, P., Hemmer-Hansen, J., Lubieniecki, K. P., Was, A., & Kause, A. (2007). What role for genomics in fisheries management and aquaculture? Aquatic Living Resources, 20(3), 241-255. | 28-Aug-2007 | https://doi.org/10.1051/alr:2007037 | Scientific research; DNA sequencing; Fishery management; Chemical oxygen demand; genomics; Aquaculture; DNA microarrays; expressed sequence tags; oysters; Reviews; Physiology; DNA; Shellfish; Fish; fishery management; Technology; Dicentrarchus labrax; Tilapia; Salmonidae | Opinion / Review | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | A tlantic cod; divergent selection; genome scan; outlier loci; population genomics; single nucleotide polymorphism | This highly technical paper provides an excellent example of applied genomics in an exploted stock of conservation concern (Atlantic cod). While it is of most relevance for marine fish stocks, the approach and concepts explored are relevant for any exploited fish that is also of conservation concern. | Bradbury, I. R., Hubert, S., Higgins, B., Bowman, S., Borza, T., Paterson, I. G., . . . Bentzen, P. (2013). Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish. Evolutionary Applications, 6(3), 450-461. | 1-Apr-2013 | https://doi.org/10.1111/eva.12026 | Genomes; Genetics; Population genetics; Environmental impact; Conservation; Population structure; Divergence; Biopolymorphism; Nucleotides; Differentiation; Adaptations; Islands; Single-nucleotide polymorphism; Nucleotide sequence; Fisheries; genomics | Technical / Data | Theoretical | SW | Europe | |||
| Genomics - Whole-Genome | anthropogenic impacts; pacific salmonids; telemetry; genomics; enzymes; ions; impacts anthropiques; salmonides du Pacifique; telemetrie; genomique; enzymes; ions | This paper is a focussed review of the integrated use of multiple disciplines within "conservation physiology" to evaluate the impacts of hydrological manipulation (primarily hydopower dams) on fish stocks. With a focus on management options, this review provides a lot of information; however, the assessment of genomics is not a particular goal of the authors. This paper does give a good overview of sub-organismal biomarker use in fish management and conservation. | Hasler, C. T., Pon, L. B., Roscoe, D. W., Mossop, B., Patterson, D. A., Hinch, S. G., & Cooke, S. J. (2009). Expanding the 'toolbox' for studying the biological responses of individual fish to hydropower infrastructure and operating strategies. Environmental Reviews, 17, 179-197. | 15-Jul-2009 | https://doi.org/10.1139/A09-008 | Turbines; Community composition; Fishways; Fish physiology; Bioenergetics; Stock assessment; Irrigation; Migrations; Sustainable development; Freshwater fish; Rivers; Community structure; Forensic science; Conservation; genomics; Habitat; Drinking water; Migration; migration; anthropogenic factors; Physiology; hydroelectric power; irrigation water; case studies; Reviews; Fisheries; Fish; infrastructure; River Regulations; Drinking Water; Assessments; Hydroelectric Plants; Fish Populations; Benefits; Freshwater | Opinion / Review | Theoretical | FW | ||||
| Genomics - Genome-Wide | Seascape genetics · Genomics · Connectivity · Marine population genetics · Gene flow · Dispersal · Landscape genetics | This paper is a broad review of advances in population genetic applications to defining patterns of connectrivity among stocks or populations of (mostly) marine fishes. While most of the challenges identified are confined to marine fish management, the concepts explored here are valuable for any exploited fish stock of uncertain strock structure. | Selkoe, K. A., D'aloia, C.,C., Crandall, E. D., Iacchei, M., Liggins, L., Puritz, J. B., . . . Toonen, R. J. (2016). A decade of seascape genetics: Contributions to basic and applied marine connectivity. Marine Ecology Progress Series, 554, 1-19. | 28-Jul-2016 | https://doi.org/10.3354/meps11792 | Ecology; Temperature effects; Population genetics; Genetics; Resource management; Climate change; Marine parks; Geography; Ecosystem disturbance; Adaptations; Statistics; Data processing; Climatic changes; Statistical analysis; Oceanography; Demography; Reviews; Fisheries; Conservation; genomics; Sampling; Geographic information systems; Marine; Brackish | Opinion / Review | Theoretical | SW | Global | |||
| Genomics - Whole-Genome | Comparative genomics; Convergent mapping; Fish; Growth QTL; Linkage map; Marker assisted selection | This paper focusses on gene discovery for production-related traits in sea bass. While this aquaculture-related application of genomics is robust and interesting, it would be of little value to fisheries managers unless genomic modifications to improve performance in released fish were to be considered for extreme conservation action. | Louro, B., Kuhl, H., Tine, M., de Koning, D., Batargias, C., Volckaert, F. A. M., . . . Power, D. M. (2016). Characterization and refinement of growth related quantitative trait loci in european sea bass (dicentrarchus labrax) using a comparative approach. Aquaculture, 455, 8-21. | 20-Mar-2016 | https://doi.org/10.1016/j.aquaculture.2016.01.004 | Genomes; Marine fish; Bibliographic information; Population genetics; Growth; Taxonomy; Hormones; Fish culture; New species; Insulin-like growth factor I; Quantitative trait loci; Evolutionary conservation; Synteny; MAP kinase; Growth hormone; Data processing; Farms; Aquaculture; Insulin; Body weight; Breeding; Genetic markers; genomics; Gene mapping; Signal transduction; Feasibility studies; Proteins; Fish; Mapping; Dicentrarchus labrax; Teleostei; Marine | Technical / Data | Theoretical | SW | Europe | |||
| Genomics - Whole-Genome | Comparative genomics; Genome mapping; Teleost fish; Quantitative trait loci; Aquaculture | This paper describes a comparitive approach to use genomic data from "model" species (such as puffer fish or zerbrafish) to build genomic resources for exploited non-model species. However, given the huge reduction is genome sequencing costs and difficulty, the relevance of this work for fishery managers is low. | Sarropoulou, E., & Fernandes, J. M. O. (2011). Comparative genomics in teleost species: Knowledge transfer by linking the genomes of model and non-model fish species. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 6(1), 92-102. | 1-Mar-2011 | https://doi.org/10.1016/j.cbd.2010.09.003 | Phylogeny; Genomes; Population genetics; Fish physiology; Commercial species; Evolution; Modelling; Quantitative trait loci; Economics; proteomics; genomics; Gene mapping; Models; Teleostei; Pan troglodytes | Opinion / Review | Theoretical | NA | Global | |||
| Genomics - Whole-Genome | EST; gene expression; genetic linkage map; genomics; microarray; Pleuronectiformes | This paper provides a now somewhat dated review of 'omics data applied to flatfish biology. The concepts and approcahes decsribed are still relevant to groups of understudied fishes; however specific applications to practical management options are weak. This would be of limited value to most fishery managers today. | Cerda, J., Douglas, S., & Reith, M. (2010). Genomic resources for flatfish research and their applications. Journal of Fish Biology, 77(5), 1045-1070. | 30-Jun-2010 | https://doi.org/10.1111/j.1095-8649.2010.02695.x | Gene expression; Genomes; Marine fish; Fishery management; Fish physiology; Offshore structures; Fish culture; Databases; Data processing; Genetic control; genomics; Aquaculture; DNA microarrays; Gene mapping; Reviews; Physiology; Fish; Technology; Organizations; Construction; Fish Populations; Maps; Productivity; Teleostei; Marine | Opinion / Review | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | fisheries; genomics; next-generation sequencing; fisheries management; adaptive diversity; outlier loci | This review advocates for a role of genomic analyses in fisherie science primarily through identification of adaptive genomic regions and the potential for environmental stressors and fishing to drive maladaptive changes in the genome. The authors also note other potential genomic applications in fisheries (such as sample origin identification for fishery forensics). A good review of genomic technologies in fishery science. | Valenzuela-Quiñonez, F. (2016). How fisheries management can benefit from genomics? BRIEFINGS IN FUNCTIONAL GENOMICS, 15(5). | 19-Mar-2016 | http://dx.doi.org/10.1093/bfgp/elw006 | COD GADUS-MORHUA; POPULATION-STRUCTURE; INDUCED EVOLUTION; EUROPEAN HAKE; SNP DISCOVERY; ATLANTIC COD; GENETIC-STRUCTURE; FISH; CONSERVATION; SELECTION; Biotechnology & Applied Microbiology; Genetics & Heredity | Opinion / Review | Theoretical | NA | Global | |||
| Genomics - Genome-Wide | ddRAD; Fishery; Genomic; Dispersal; MPA | This paper proposes genomic applications in the assessment of the efficacy of marine protected areas (MPAs); however their ideas are relevant for any fishery management action involving protected areas to preserve stocks. The authors note that patterns of connectivity and recruitment are critical for MPAs to serve their intended function. While some of the technical details may not be helpful to fishery managers, the basic message is sound - population structure quantification is a powerful applictaion of genomics. | Willis, SC; Hollenbeck, CM; Puritz, JB; Portnoy, DS. (2022). Genetic recruitment patterns are patchy and spatiotemporally unpredictable in a deep-water snapper (Lutjanus vivanus) sampled in fished and protected areas of western Puerto Rico CONSERVATION GENETICS, 23(3). | 29-Jan-2022 | http://dx.doi.org/10.1007/s10592-021-01426-2 | EFFECTIVE POPULATION-SIZE; RED SNAPPER; SPATIAL AUTOCORRELATION; MARINE POPULATIONS; LARVAL DISPERSAL; CONNECTIVITY; CONSERVATION; RETENTION; DYNAMICS; SINKS; Biodiversity & Conservation; Genetics & Heredity | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | population genomics; fisheries; Scombridae; migratory; pelagic; fish | This paper provides a case study of Atlantic mackerel population genetic analysis using genome-wide genetic markers. Two groups of mackerel spawn in different jurisdicions, hence identifying the fish to source is important for management of the fishery in this declining species. The technical components of this paper may not be very useful for managers, but the application of genome-wide markers to detect subtle population structure in an exploited species is valuable. | Bourret, A; Smith, A; Van Beveren, E; Plourde, S; Curti, KL; Jansen, T; Richardson, DE; Castonguay, M; Rodriguez-Ezpeleta, N; Parent, GJ. (2023). Quantifying genetic differentiation and population assignment between two contingents of Atlantic mackerel (Scomber scombrus) in the Northwest Atlantic CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES, (). | 23-Mar-2023 | http://dx.doi.org/10.1139/cjfas-2022-0232 | VARIANT CALL FORMAT; NORDIC SEAS; R-PACKAGE; TOOL SET; NUMBER; PHYLOGEOGRAPHY; MANAGEMENT; INFERENCE; SOFTWARE; GENOMICS; Fisheries; Marine & Freshwater Biology | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | whole genome sequencing; Muskellunge; population genomics; Fisheries; inbreeding | This paper describes a population genetic analysis of genome-wide marker variation using data from a limited number of breeder muskellunge in Iowa and pre-existing data for >600 Canadian fish. The authors report population structure and and genetic markers showing evidence for local selection and inbreeding in some populations. While this paper demonstrates the power of whole-genome marker analyses, the outcomes are of limited practical value for fishery management. | Chinchilla-Vargas, J; Meerbeek, JR; Rothschild, MF; Bertolini, F. (2021). Signatures of Selection and Genomic Diversity of Muskellunge (Esox masquinongy) from Two Populations in North America GENES, 12(7). | 30-Jun-2021 | http://dx.doi.org/10.3390/genes12071021 | SITE FIDELITY; GENETIC-STRUCTURE; PIKE; DISCOVERY; SALMON; TROUT; MODEL; LAKE; SET; Genetics & Heredity | Technical / Data | Theoretical | FW | North America | |||
| Genomics - Genome-Wide | adaptive genetic variation; biophysical models; fisheries management; population genomics | This paper describes the potential for combining biophysical modelling and population genomics to better identify functional population connectivity and locally adaptive gene regions. The authors argue that the proposed approach provides a framework for evolutionary fisheries management. However, the practical outcomes of the evolutionary framework, in terms of management action, are not clear. | Baltazar-Soares, M; Hinrichsen, HH; Eizaguirre, C. (2018). Food for Thought Integrating population genomics and biophysical models towards evolutionary-based fisheries management ICES JOURNAL OF MARINE SCIENCE, 75(4). | 6-Jan-2018 | http://dx.doi.org/10.1093/icesjms/fsx244 | TOOTHFISH DISSOSTICHUS-MAWSONI; ANCHOVY ENGRAULIS-ENCRASICOLUS; HERRING CLUPEA-HARENGUS; EARLY-LIFE HISTORY; COD GADUS-MORHUA; NORTH-SEA COD; MARINE FISHES; ATLANTIC COD; ANTARCTIC TOOTHFISH; LOCAL ADAPTATION; Fisheries; Marine & Freshwater Biology; Oceanography | Opinion / Review | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | European fisheries; genomics; marine conservation; renewable resources; stock assessments | This paper is a critical review of the application of genetics (genomics) technology in fishery management, primarily marine fisheries. The authors note that developing new genomic tools for fishery management and conservation is not by itself helpful and the goal should be to define fishery-focussed needs, then determine if genomics can provide useful input. Very relevant for fishery managers, and not too technical. | Casey, J; Jardim, E; Martinsohn, JT. (2016). The role of genetics in fisheries management under the EU common fisheries policy JOURNAL OF FISH BIOLOGY, 89(6). | 19-Oct-2016 | http://dx.doi.org/10.1111/jfb.13151 | EUROPEAN HAKE; STOCK CONCEPT; POPULATION; CONSERVATION; MARKERS; Fisheries; Marine & Freshwater Biology | Opinion / Review | Theoretical | SW | Europe | |||
| Genomics - Genome-Wide | fisheries; genomics; stock assessment; high throughput sequencing; research surveys | This is an overview of a special issue of a journal. It just summarizes the papers in the issue, I'm not sure how relevant it is for this database. | Casas, L; Hanel, R; Piferrer, F; Saborido-Rey, F. (2023). Prospects and challenges for the implementation of HTS genetic methods in fisheries research surveys and stock assessments FRONTIERS IN MARINE SCIENCE, 10(). | 13-Jul-2013 | http://dx.doi.org/10.3389/fmars.2023.1238133 | ; Environmental Sciences & Ecology; Marine & Freshwater Biology | Opinion / Review | Applied | NA | Global | |||
| Genomics - Genome-Wide | conservation; deep-sea; fisheries management; orange roughy; population genomics | This is a data based study that uses ~4K genetic markers to examine the potential for genomic divergence in a species of marine fish. They found a lack of differentiation between the groups. The study is put in the context of how genomics approaches can be used to inform populations that can help restore overharvested populations. | da Silva, AG; Appleyard, SA; Upston, J. (2015). Establishing the evolutionary compatibility of potential sources of colonizers for overfished stocks: a population genomics approach MOLECULAR ECOLOGY, 24(3). | 17-Dec-2014 | http://dx.doi.org/10.1111/mec.13046 | ROUGHY HOPLOSTETHUS-ATLANTICUS; MULTILOCUS GENOTYPE DATA; TELEOST ORANGE ROUGHY; COD GADUS-MORHUA; GENE FLOW; MITOCHONDRIAL-DNA; FISHERIES MANAGEMENT; MIGRATION RATES; ADAPTIVE VARIATION; CONTINENTAL-SLOPE; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | SW | Australia | |||
| Genomics - Genome-Wide | comparative genomics; marine fisheries; microsatellite; stock structure; threatened species | This is a data based paper that uses laregly out of date methods to assess population differences between groups of species. This was likely fine at the time, however there are more cost-effective and high-throughput methods that can be used now to address these questions. | Buonaccorsi, VP; Kimbrell, CA; Lynn, EA; Hyde, JR. (2012). Comparative Population Genetic Analysis of Bocaccio Rockfish Sebastes paucispinis Using Anonymous and Gene-Associated Simple Sequence Repeat Loci JOURNAL OF HEREDITY, 103(3). | 4-Apr-2012 | http://dx.doi.org/10.1093/jhered/ess002 | MICROSATELLITES; SELECTION; ATLANTIC; SSRS; DIFFERENTIATION; ADAPTATION; MUTATIONS; PATTERNS; MARKERS; HEART; Evolutionary Biology; Genetics & Heredity | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | conservation genomics; fisheries management; native brook trout; SNP panels | This is a data based paper that uses reduced representation sequencing to identify 24K genetic markers that are useful for characterizing population structure of brook trout. They use these markers to discuss how this approach can be used to develop targetted panels for future population genetics work. This would be a valuable approach for setting up long term monitoring programs for species of interest. | Mamoozadeh, NR; Whiteley, AR; Letcher, BH; Kazyak, DC; Tarsa, C; Meek, MH. (2023). A new genomic resource to enable standardized surveys of SNPs across the native range of brook trout (Salvelinus fontinalis) MOLECULAR ECOLOGY RESOURCES, (). | 16-Aug-2023 | http://dx.doi.org/10.1111/1755-0998.13853 | GENETIC DIVERSITY; POPULATION ASSIGNMENT; PARENTAGE ASSIGNMENT; ASCERTAINMENT BIAS; R-PACKAGE; CONSERVATION; HATCHERY; CHARR; MANAGEMENT; PATTERNS; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | North America | ||||
| Genomics - Genome-Wide | adaptive divergence; fisheries; management; population genomics; SNP panel; temporal stability | This is a data based paper that uses a relatively small number of genetic markers to compare populations of a marine species that spawn at different times of year. They are able to establish genetic differences between the different spawning groups despite using a limited number of markers. | Kerr, Q; Fuentes-Pardo, AP; Kho, J; McDermid, JL; Ruzzante, DE. (2019). Temporal stability and assignment power of adaptively divergent genomic regions between herring (Clupea harengus) seasonal spawning aggregations ECOLOGY AND EVOLUTION, 9(1). | 11-Dec-2018 | http://dx.doi.org/10.1002/ece3.4768 | COD GADUS-MORHUA; GENE-FLOW; POPULATION DIVERSITY; SNP ANALYSIS; ATLANTIC; SELECTION; DIFFERENTIATION; HYBRIDIZATION; EVOLUTIONARY; STRATEGIES; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | fisheries genetics; Pool-Seq; genomic diversity; marine biodiversity; stock structure | This is a data based paper that uses 40K genetic markers to characterize population structure of a fish species. They used a pool-seq approach, which is a cost-effective sequencing strategy for only population-level assessments (i.e., the individual doesn't matter). | Schulze, MJ; von der Heyden, S; Japp, D; Singh, L; Durholtz, D; Kapula, VK; Ndjaula, HON; Henriques, R. (2020). Supporting Fisheries Management With Genomic Tools: A Case Study of Kingklip (Genypterus capensis) Off Southern Africa FRONTIERS IN MARINE SCIENCE, 7(). | 24-Sep-2020 | http://dx.doi.org/10.3389/fmars.2020.557146 | HIGH GENE FLOW; R-PACKAGE; ADAPTIVE DIFFERENTIATION; POPULATION-GENETICS; MOLECULAR MARKERS; LOCAL ADAPTATION; NEXT-GENERATION; READ ALIGNMENT; FRESH-WATER; MARINE; Environmental Sciences & Ecology; Marine & Freshwater Biology | Technical / Data | Theoretical | SW | Africa | |||
| Genomics - Genome-Wide | comparative genomics; fisheries; Pacific halibut; RAD; sex determination; sex identification | This is a data based paper that uses reduced representation sequencing to identity sex-linked genomic differences in male and females of a marine species. They take advantage of assembled reference genomes of closely related species to attempt to link some of the genetic markers with sex chromosomes. This demonstrates how to rapidly develop sex-link markers that can be used to quantify sex ratios in commercial catches. | Drinan, DP; Loher, T; Hauser, L. (2018). Identification of Genomic Regions Associated With Sex in Pacific Halibut JOURNAL OF HEREDITY, 109(3). | 9-Nov-2017 | http://dx.doi.org/10.1093/jhered/esx102 | FLATFISH; FISH; PLEURONECTIFORMES; LOCI; EVOLUTION; ALIGNMENT; GENETICS; STACKS; GROWTH; Evolutionary Biology; Genetics & Heredity | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Whole-Genome | population genomics; whole-genome sequencing; demography; conservation; tuna; fisheries management | This is a data based paper that uses whole genome sequencing from populations of a marine species to charaacterize population structure at a global scale. They also assembled a species-specific reference genome to facilitate population genetics studies for this species in the future. This is an example of the importance of developing genomic resources for species of importance. | Barth, JMI; Damerau, M; Matschiner, M; Jentoft, S; Hanel, R. (2017). Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations GENOME BIOLOGY AND EVOLUTION, 9(4). | 1-Apr-2017 | http://dx.doi.org/10.1093/gbe/evx067 | BIGEYE TUNA; KATSUWONUS-PELAMIS; MARINE FISHES; MISSING DATA; R-PACKAGE; FRAMEWORK; INFERENCE; ALIGNMENT; OBESUS; CONSEQUENCES; Evolutionary Biology; Genetics & Heredity | Technical / Data | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | conservation genomics; fisheries management; genomic diversity; Pool-Seq; population dynamics | This is a data based paper that uses a pool-seq strategy to characterize population structure in 2 species of fishes. Pool-seq is a cost-effective sequencing strategy for only population-level assessments (i.e., the individual doesn't matter). | Forde, S; von der Heyden, S; Le Moan, A; Nielsen, ES; Durholtz, D; Kainge, P; Kathena, JN; Lipinski, MR; Ndjaula, HON; Matthee, CA; Henriques, R. (2023). Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa MOLECULAR ECOLOGY RESOURCES, (). | 8-Jun-2023 | http://dx.doi.org/10.1111/1755-0998.13820 | GENETIC DIVERSITY; LOCAL SELECTION; M. PARADOXUS; DIFFERENTIATION; CAPENSIS; ATLANTIC; DNA; BENGUELA; HISTORY; COMPLEX; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | SW | Africa | |||
| Genomics - Genome-Wide | ddrad; fisheries management; marine biogeography; marine teleost; population genomics; stock delineation | This is a data based paper that uses reduced representation sequencing to characterize population structure in a marine species. This paper demonstrates how genomics can be used to identify population units for fishery management. | Bertram, A; Bell, J; Brauer, CJ; Fowler, A; Hamer, P; Sandoval-Castillo, J; Stewart, J; Wellenreuther, M; Beheregaray, LB. (2023). Biogeographic provinces and genomically delineated stocks are congruent in snapper (Chrysophrys auratus) from southeastern Australia ICES JOURNAL OF MARINE SCIENCE, 80(5). | 29-Apr-2023 | http://dx.doi.org/10.1093/icesjms/fsad068 | POPULATION-STRUCTURE; MARINE BIOGEOGRAPHY; SOUTHERN AUSTRALIA; PAGRUS-AURATUS; LIFE-HISTORY; CONNECTIVITY; TEMPERATURE; RECRUITMENT; SPARIDAE; GENETICS; Fisheries; Marine & Freshwater Biology; Oceanography | Technical / Data | Theoretical | SW | Australia | |||
| Genomics - Genome-Wide | demographic models; fishery management; population genomics; related species; Sebastes; spatial ecology | This is a data based paper that uses 24K markers to characterize population structure of 2 marine species. They are able to show that the large number of markers that are used in genomics can be successfully used to characterize differences between cryptic species. This work shows how population genomics approaches can inform management units for commercially harvested species. | Benestan, LM; Rougemont, Q; Senay, C; Normandeau, E; Parent, E; Rideout, R; Bernatchez, L; Lambert, Y; Audet, C; Parent, GJ. (2021). Population genomics and history of speciation reveal fishery management gaps in two related redfish species (Sebastes mentella and Sebastes fasciatus) EVOLUTIONARY APPLICATIONS, 14(2). | 30-Sep-2020 | http://dx.doi.org/10.1111/eva.13143 | GENETIC-STRUCTURE; GENUS SEBASTES; GEOMETRIC MORPHOMETRICS; CONSERVATION GENOMICS; ATLANTIC; INTROGRESSION; DIVERGENCE; ASSIGNMENT; MICROSATELLITES; DIVERSIFICATION; Evolutionary Biology | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | ddRADseq; fisheries management; marine connectivity; marine teleost; population genomics; stock structure | This is a data based study that uses reduced representation sequencing to characterize population structure of a marine fish across a large geographical area. They used ~11K markers to show that the genomic differences between regions do not match the fishery management regions. This is a useful example of how population genomics approaches can help inform and re-structure managment zones for fisheries species. | Bertram, A; Fairclough, D; Sandoval-Castillo, J; Brauer, C; Fowler, A; Wellenreuther, M; Beheregaray, LB. (2022). Fisheries genomics of snapper (Chrysophrys auratus) along the west Australian coast EVOLUTIONARY APPLICATIONS, 15(7). | 20-Jun-2022 | http://dx.doi.org/10.1111/eva.13439 | SPATIAL AUTOCORRELATION ANALYSIS; PAGRUS-AURATUS; LEEUWIN CURRENT; GENE FLOW; POPULATION-STRUCTURE; SPAWNING AGGREGATIONS; LARVAL DISPERSAL; CURRENT SYSTEM; LIFE-HISTORY; ATLANTIC COD; Evolutionary Biology | Technical / Data | Theoretical | SW | Australia | |||
| Genomics - Genome-Wide | fisheries-induced evolution; population genomics; genetic diversity; selective sweeps; historical DNA | This is a data based paper that uses whole genome sequencing to examine the effects of fishing pressure on a wild marine fish. They compare samples from 2 locations sampled years apart from each other and use >300k markers for the analyses, which would be needed to detect subtle changes in the genomes of these populations. This study shows that populations can maintain genetic diversity over time despite heavy fishing pressure and that phenotypic changes can occur in fished populations in the absence of large-scale genomic changes. | Pinsky, ML; Eikeset, AM; Helmerson, C; Bradbury, IR; Bentzen, P; Morris, C; Gondek-Wyrozemska, AT; Baalsrud, HT; Brieuc, MSO; Kjesbu, OS; Godiksen, JA; Barth, JMI; Matschiner, M; Stenseth, NC; Jakobsen, KS; Jentoft, S; Star, B. (2021). Genomic stability through time despite decades of in cod on both sides of the Atlantic PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118(15). | 7-Apr-2021 | http://dx.doi.org/10.1073/pnas.2025453118 | FISHERIES-INDUCED EVOLUTION; EFFECTIVE POPULATION-SIZE; GENE-EXPRESSION; LOCAL ADAPTATION; SIGNATURES; REVEALS; HISTORY; SEQUENCE; SHIFTS; YIELDS; Science & Technology - Other Topics | Technical / Data | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | Arctic; conservation; fish migration; fishery management; genotyping by sequencing; population genomics; RADseq | This is a data based paper that uses reduced representation DNA sequencing to characterize population structure in a migratory species. This study combines non-lethal tissue sampling and telemetry tagging to related genetic structure to migration patterns. This is a great example of how genomics analyses can improve our understanding of fish behavior and habitat use in the wild. | Moore, JS; Harris, LN; Le Luyer, J; Sutherland, BJG; Rougemont, Q; Tallman, RF; Fisk, AT; Bernatchez, L. (2017). Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char MOLECULAR ECOLOGY, 26(24). | 31-Oct-2017 | http://dx.doi.org/10.1111/mec.14393 | SALMON ONCORHYNCHUS-TSHAWYTSCHA; SALVELINUS-ALPINUS; ATLANTIC SALMON; PROVIDES INSIGHTS; SOCKEYE-SALMON; LINKAGE MAP; R-PACKAGE; ADAPTATION; LOCI; EVOLUTION; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | FW | North America | |||
| Genomics - Genome-Wide | fishery management; genomic differentiation; Lates angustifrons; Lates mariae; Lates microlepis; Lates stappersii | This is a data based paper that uses reduced representation DNA sequencing to characterize population structure in 4 species of fish in a single large lake system. This study highlights how using genomic data with a large number of markers can help detect subtle population divergence between populations. | Rick, JA; Junker, J; Kimirei, IA; Sweke, EA; Mosille, JB; Dinkel, C; Mwaiko, S; Seehausen, O; Wagner, CE. (2022). The Genetic Population Structure of Lake Tanganyika's Lates Species Flock, an Endemic Radiation of Pelagic Top Predators JOURNAL OF HEREDITY, 113(2). | 5-Dec-2021 | http://dx.doi.org/10.1093/jhered/esab072 | VARIANT CALL FORMAT; LARVAL DURATION; NILE PERCH; READ ALIGNMENT; NORTHERN PART; TOOL SET; MANAGEMENT; FISHERIES; FISH; ATLANTIC; Evolutionary Biology; Genetics & Heredity | Technical / Data | Theoretical | FW | Africa | |||
| Genomics - Genome-Wide | age and growth analysis; bioinformatic filtering; fisheries harvest; population genomics; RADseq; walleye | The paper is a response to another study that re-analyzed the genomic data to a different study and drew different conclusions about the potential for rapid fisheries induced evolution. The authors stress the importance of large sample sizes for drawing conclusions about rapid genomic changes in wild populations. This paper disagreeing with the orginal paper highlight how differences in analysis approaches can lead to different conclusions despite using the same data sets. | Larson, WA; Isermann, DA; Feiner, ZS. (2021). Incomplete bioinformatic filtering and inadequate age and growth analysis lead to an incorrect inference of harvested-induced changes EVOLUTIONARY APPLICATIONS, 14(2). | 12-Sep-2020 | http://dx.doi.org/10.1111/eva.13122 | WALLEYE SANDER-VITREUS; NORTHERN WISCONSIN; POPULATION; SIZE; MATURATION; MORTALITY; DENSITY; EXPLOITATION; RECRUITMENT; MANAGEMENT; Evolutionary Biology | Technical / Data | Theoretical | FW | North America | |||
| Genomics - Genome-Wide | Acanthocybium solandri; connectivity; demographic inference; fisheries management; population genomics; population structure; wahoo | This is a data based study that uses reduced representation DNA sequencing to examine population structure between different ocean basins. It uses a process known as pool seq, which effectively pools all individuals from a single collection location in preparing the samples for sequencing, therefore the inferences that can be made are only at the level of the population (i.e., the variation between individuals is ignored). This is a cost effective method for examining genomic divergence between populations. | Haro-Bilbao, I; Riginos, C; Baldwin, JD; Zischke, M; Tibbetts, IR; Thia, JA. (2021). Global connections with some genomic differentiation occur between Indo-Pacific and Atlantic Ocean wahoo, a large circumtropical pelagic fish JOURNAL OF BIOGEOGRAPHY, 48(8). | 24-May-2021 | http://dx.doi.org/10.1111/jbi.14135 | TUNA THUNNUS-ALBACARES; ACANTHOCYBIUM-SOLANDRI; REPRODUCTIVE-BIOLOGY; MITOCHONDRIAL-DNA; GENETIC-STRUCTURE; NEXT-GENERATION; BLUEFIN TUNA; POPULATION; CONSERVATION; EASTERN; Environmental Sciences & Ecology; Physical Geography | Technical / Data | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | fish; fisheries management; genomics; proteomics; invasive species; landscape genetics; population genetics - empirical | This is a data based paper that uses reduced representation sequencing to characterize genetic variation in multiple species of riverine fish separated by an upstream migration barrier. They are able to determine that in the presence of a migration barrier, there was evidence of unidirectional gene flow between populations and that genetic diversity increased below the barrier. This is a useful study for understanding the role of unidirectional gene flow in the genetic variation detected in wild populations. | Lujan, NK; Weir, JT; Noonan, BP; Lovejoy, NR; Mandrak, NE. (2020). Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome-wide SNP data from seven native species MOLECULAR ECOLOGY, 29(7). | 23-Mar-2020 | http://dx.doi.org/10.1111/mec.15406 | FRESH-WATER MUSSEL; POPULATION-GENETICS; SPATIAL-PATTERNS; DIVERSITY; DISPERSAL; RANGE; PHYLOGEOGRAPHY; RECESSION; MOVEMENT; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | FW | North America | |||
| Genomics - Genome-Wide | ancient DNA; archaeology; fish; fisheries; genomics; high-throughput sequencing; next-generation sequencing | This is a conceptual paper that describes the potential for the use of ancient DNA in contemporary fisheries studies. Ancient DNA involves extracting DNA from archived or museam samples. This is an interesting approach to be able to observe genetic change in wild populations during periods of intense human influence. | Oosting, T; Star, B; Barrett, JH; Wellenreuther, M; Ritchie, PA; Rawlence, NJ. (2019). Unlocking the potential of ancient fish DNA in the genomic era EVOLUTIONARY APPLICATIONS, 12(8). | 9-May-2019 | http://dx.doi.org/10.1111/eva.12811 | EFFECTIVE POPULATION-SIZE; SPECIES IDENTIFICATION; DIONISIO POINT; PACIFIC SALMON; CLIMATE-CHANGE; ATLANTIC COD; SNP ANALYSIS; FISHERIES; REVEALS; FUTURE; Evolutionary Biology | Opinion / Review | Theoretical | NA | Global | |||
| Genomics - Genome-Wide | forage fishes; Arctic; genotype-environment association analyses; population genomics; metadata; fisheries management | This is a meta-analysis that attempts to relate genomics data to environmental conditions in marine species. This work addresses the concept of seascape genomics, which is a term to describe genome and environment relationships between populations along a continuous gradient (i.e., the aquatic version of landscape genomics). This paper describes the metadata needs for papers submitted to journals that would help facilitate these types of studies in the future. | Timm, LE; Tucker, N; Rix, A; Labua, S; López, JA; Boswell, KM; Glass, JR. (2023). The untapped potential of seascape genomics in the North Pacific FRONTIERS IN CONSERVATION SCIENCE, 4(). | 14-Sep-2023 | http://dx.doi.org/10.3389/fcosc.2023.1249551 | GENETICS; Biodiversity & Conservation; Environmental Sciences & Ecology | Opinion / Review | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | high-throughput sequencing; genomics; species distribution model (SDMs); fisheries applications; evolutionary ecology | This is a conceptual paper that discusses how genomics data can be incorporated into species distribution models. The authors suggest that incorporating genomics data into these models will help predict range shifts in the future. | Baltazar-Soares, M; Lima, ARA; Silva, G; Gaget, E. (2023). Towards a unified eco-evolutionary framework for fisheries management: Coupling advances in next-generation sequencing with species distribution modelling FRONTIERS IN MARINE SCIENCE, 9(). | 6-Jan-2023 | http://dx.doi.org/10.3389/fmars.2022.1014361 | LOCAL ADAPTATION; CLIMATE-CHANGE; GENE-EXPRESSION; MARINE FISH; RANGE; GENOMICS; MICROSATELLITES; POPULATIONS; INFECTION; INFERENCE; Environmental Sciences & Ecology; Marine & Freshwater Biology | Opinion / Review | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | biodiversity; conservation genetics; fisheries; molecular population genetics; genomics; SNP; selection; aquatic organisms | This is a review paper that discusses the utility of genetic markers that can be identified using modern DNA sequencing approaches (i.e., SNPs). This paper discusses the applications for wild fishes and highlights the advantages of using a higher resolution SNP appraoch over traditional genetic markers. | Wenne, R. (2023). Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations ANIMALS, 13(6). | 18-Mar-2023 | http://dx.doi.org/10.3390/ani13061089 | COD GADUS-MORHUA; SALMON ONCORHYNCHUS-TSHAWYTSCHA; PARALLEL ADAPTIVE EVOLUTION; GENOME-WIDE DISCOVERY; ATLANTIC COD; SNP DISCOVERY; GENETIC DIFFERENTIATION; CHINOOK SALMON; INTROGRESSIVE HYBRIDIZATION; MARINE FISH; Agriculture; Veterinary Sciences; Zoology | Opinion / Review | Theoretical | NA | Global | |||
| Genomics - Genome-Wide | Atlantic cod (Gadus morhua); conservation; evolution; fisheries management; genetics; genomics; marine fishes | This is a data based paper that used 438 genetic markers to develop a 39 marker panel for genetic stock ID in a wild commercial species. This paper demonstrates how genetic ID can be incorporated into managine mixed-stock fisheries. | Hemmer-Hansen, J; Hüssy, K; Baktoft, H; Huwer, B; Bekkevold, D; Haslob, H; Herrmann, JP; Hinrichsen, HH; Krumme, U; Mosegaard, H; Nielsen, EE; Reusch, TBH; Storr-Paulsen, M; Velasco, A; von Dewitz, B; Dierking, J; Eero, M. (2019). Genetic analyses reveal complex dynamics within a marine fish management area EVOLUTIONARY APPLICATIONS, 12(4). | 30-Dec-2018 | http://dx.doi.org/10.1111/eva.12760 | COD GADUS-MORHUA; WESTERN BALTIC COD; MIXED-STOCK ANALYSIS; POPULATION-STRUCTURE; GEOGRAPHIC ORIGIN; EGG BUOYANCY; REAL-TIME; BELT SEA; ATLANTIC; CONSERVATION; Evolutionary Biology | Technical / Data | Theoretical | SW | Europe | |||
| Genomics - Genome-Wide | cryptic species; ecological speciation; genomics; mixed-stock fishery; otolith; Platichthys flesus; Platichthys solemdali | This is a synthesis paper that discusses how genomics have contributed to an increased understanding of the genetic differentiation between cryptic species that are harvested in a mixed-fishery. This is an example of how genomics can contribute to a better understanding of watch species are harvested and therefore can be used for managing the fishery. | Jokinen, H; Momigliano, P; Merilä, J. (2019). From ecology to genetics and back: the tale of two flounder species in the Baltic Sea ICES JOURNAL OF MARINE SCIENCE, 76(7). | 21-Aug-2019 | http://dx.doi.org/10.1093/icesjms/fsz151 | PLATICHTHYS-FLESUS; MARINE FISHES; POPULATION-STRUCTURE; SPECIATION; ATLANTIC; SALINITY; GENOMICS; ADAPTATION; DIVERGENCE; RECOMBINATION; Fisheries; Marine & Freshwater Biology; Oceanography | Opinion / Review | Theoretical | SW | Europe | |||
| Genomics - Genome-Wide | adaptation; conservation genetics; fisheries management; genomics; life history evolution; natural selection; pop`ulation genetics | This is a perspectives paper that discusses how genomics data can be used to understand the genetic basis of specific traits in species. This paper then discusses how this information can be used to inform conservation strategies by resource managers. | Waples, RS; Lindley, ST. (2018). Genomics and conservation units: The genetic basis of adult migration timing in Pacific salmonids EVOLUTIONARY APPLICATIONS, 11(9). | 1-Aug-2018 | http://dx.doi.org/10.1111/eva.12687 | CHINOOK SALMON; EVOLUTIONARY PROCESSES; POPULATION GENOMICS; PARALLEL EVOLUTION; DIVERSITY; ADAPTATION; STEELHEAD; HISTORY; DIVERGENCE; STRATEGIES; Evolutionary Biology | Opinion / Review | Theoretical | FW | North America | |||
| Genomics - Genome-Wide | fisheries management; heterogeneous genomic divergence; latitudinal cline; Northeast Pacific Ocean; population genomics; RAD sequencing | This is a data based paper that uses reduced representation DNA sequencing to identify distinct genetic clusters of a species of concern across a substantial latitudinal gradient. This paper describes genetics methods useful for characterizing population units for managing wild species. | Longo, GC; Lam, L; Basnett, B; Samhouri, J; Hamilton, S; Andrews, K; Williams, G; Goetz, G; McClure, M; Nichols, KM. (2020). Strong population differentiation in lingcod (Ophiodon elongatus) is driven by a small portion of the genome EVOLUTIONARY APPLICATIONS, 13(10). | 7-Jun-2020 | http://dx.doi.org/10.1111/eva.13037 | GENE FLOW; R-PACKAGE; RANGE SIZE; ROAD MAP; SPECIATION; ROCKFISH; CONSERVATION; MANAGEMENT; PROGRAM; FISHES; Evolutionary Biology | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | Indigenous knowledge; Western science; fisheries; population monitoring; genomics; life history; practices for weaving knowledge systems | This is a theoretical paper that compares traditional knowledge of Indigenous communites and genetics approaches for understanding fish populations. The authors state that the approaches are complimentary and they discuss when one approach may be more useful for a particular fisheries question. | Bowles, E; Jeon, HB; Marin, K; MacLeod, P; Fraser, DJ. (2022). Freshwater fisheries monitoring in northern ecosystems using Indigenous ecological knowledge, genomics, and life history: Insights for community decision-making FACETS, 7(). | 8-Sep-2022 | http://dx.doi.org/10.1139/facets-2021-0049 | EFFECTIVE POPULATION-SIZE; SCIENCE; MARINE; MODEL; Science & Technology - Other Topics | Technical / Data | Applied | FW | North America | |||
| Genomics - Genome-Wide | body size; fisheries-induced evolution; genomics; harvesting; Indigenous knowledge; Sander vitreus; size-at-age; walleye | This is a data based paper that uses 9K genetic markers to attempt to quantify the effects of harvest on wild fish populations. This paper demonstrates that genetic effects of harvest can happen quickly leading to potential fisheries induced evolution. | Bowles, E; Marin, K; Mogensen, S; MacLeod, P; Fraser, DJ. (2020). Size reductions and genomic changes within two generations in wild walleye populations: associated with harvest? EVOLUTIONARY APPLICATIONS, 13(6). | 28-Apr-2020 | http://dx.doi.org/10.1111/eva.12987 | FISHERIES-INDUCED EVOLUTION; TRADITIONAL ECOLOGICAL KNOWLEDGE; GROWING DEGREE-DAY; GENETIC-STRUCTURE; R-PACKAGE; LINKAGE DISEQUILIBRIUM; INDUCED SELECTION; N-E; MODEL; ADAPTATION; Evolutionary Biology | Technical / Data | Applied | FW | North America | |||
| Genomics - Whole-Genome | Biological invasion; conservation genomics; exotic species; fisheries; hybridization; Japan Sea stickleback; next-generation sequencer; rapid evolution | This is a data based paper that using whole genome sequencing to understand how some non-native species can become successful invaders despite the potential for genetic bottlenecks associated with colonizing new habitats. This paper demonstrates how hybridization with other species can maintain genetic diversity in an invasive population. This paper provides a potential mechanism for how invasive species can maintain genetic diversity after colonization. | Yoshida, K; Miyagi, R; Mori, S; Takahashi, A; Makino, T; Toyoda, A; Fujiyama, A; Kitano, J. (2016). Whole-genome sequencing reveals small genomic regions of introgression in an introduced crater lake population of threespine stickleback ECOLOGY AND EVOLUTION, 6(7). | 2-Mar-2016 | http://dx.doi.org/10.1002/ece3.2047 | ADAPTIVE EVOLUTION; GENETIC-VARIATION; BIOLOGICAL INVASION; PARALLEL EVOLUTION; CONSERVATION; HYBRIDIZATION; ADAPTATION; DIVERGENCE; GASTEROSTEUS; MORPHOLOGY; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | FW | Asia | |||
| Genomics - Whole-Genome | adaptive differentiation; allochronic reproduction; Atlantic cod; chromosomal inversions; fisheries management; heat shock proteins; population genomics; whole-genome resequencing | This is a data based paper that uses whole-genome sequencing to understand genetic differentiation between populations. This paper provides useful methodology for characterizing the genetic basis of local adaptation in wild fishes. | Clucas, GV; Lou, RN; Therkildsen, NO; Kovach, AI. (2019). Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole-genome sequencing EVOLUTIONARY APPLICATIONS, 12(10). | 29-Aug-2019 | http://dx.doi.org/10.1111/eva.12861 | GADUS-MORHUA; LOCAL ADAPTATION; STOCK IDENTIFICATION; STATIONARY ECOTYPES; SPATIAL STRUCTURE; RAINBOW-TROUT; SNP ANALYSIS; US WATERS; DIVERGENCE; MARINE; Evolutionary Biology | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | genome-wide association studies; fisheries genomics; aquaculture; teleost; ddRAD; reduced genome representation; ecological genomics; genomic prediction; GenPred; shared data resource | This is a data based paper that uses reduced representation DNA sequencing to identify genetic markers associated with growth in fish in a captivity. This paper describes genetics methods that would be useful for generating optimal traits for captive rearing conditions. | Sandoval-Castillo, J; Beheregaray, LB; Wellenreuther, M. (2022). Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus) G3-GENES GENOMES GENETICS, 12(3). | 20-Jan-2022 | http://dx.doi.org/10.1093/g3journal/jkac015 | QUANTITATIVE TRAIT LOCI; WIDE ASSOCIATION; GENE-EXPRESSION; LIFE-HISTORY; FISH; TEMPERATURE; VARIANT; GWAS; DOMESTICATION; SIGNATURES; Genetics & Heredity | Technical / Data | Theoretical | SW | Australia | |||
| Transcriptomics | aquaculture; climate change; fisheries management; phenotypic plasticity; transcriptomics | Valenza-Troubat, N., Davy, M., Storey, R., Wylie, M. J., Hilario, E., Ritchie, P., & Wellenreuther, M. (2022). Differential expression analyses reveal extensive transcriptional plasticity induced by temperature in New Zealand silver trevally (Pseudocaranx georgianus). Evolutionary Applications, 15, 237–248. | 7-Dec-2021 | https://doi-org.ledproxy2.uwindsor.ca/10.1111/eva.13332 | LIFE-HISTORY TRAITSCLIMATE-CHANGEGENE-EXPRESSIONYELLOWTAIL KINGFISHGROWTH-HORMONEDOMESTICATIONPERFORMANCEADAPTATIONEVOLUTIONIMPACTS | Technical / Data | Theoretical | SW | Australia | ||||
| Transcriptomics | This paper describes the de novo assembly and transcriptome analysis of liver, testes, and head kidney from two captive red drum males. The addtional transcriptomic data for this estuarine fish of high commercial value may help improve aquaculture practices and stock enhancement of wild populations. | Sherwood, TA; Main, KL; Wetzel, DL. (2019). De novo assembly and transcriptome dataset of liver, testis and head kidney from red drum (Sciaenops ocellatus). DATA BRIEF, 22(). | 11-Jan-2019 | http://dx.doi.org/10.1016/j.dib.2019.01.011 | Technical / Data | Theoretical | SW | North America | |||||
| Proteomics | Animal protein; Aqua food; Aquaculture; Omics; Safety and quality; Sustainable | This paper reviews basic to advanced proteomics technologies in the context of aquaculture. The authors cover sample preparation to bioinformatic ressources used for data analysis. The content and breadth of this review would be of interest to fisheries managers as this review includes studies that have applied proteomics to determine food quality and safety. | Nissa, MU; Pinto, N; Parkar, H; Goswami, M; Srivastava, S. (2021). Proteomics in fisheries and aquaculture: An approach for food security. FOOD CONTROL, 127(). | 1-Apr-2021 | http://dx.doi.org/10.1016/j.foodcont.2021.108125 | HEMOLYMPH VITELLOGENIN LEVELS; FRESH-WATER PRAWN; OVARIAN DEVELOPMENT; MARINE RESERVES; MACROBRACHIUM-ROSENBERGII; GENE-EXPRESSION; DECAPODA; CRUSTACEA; SEQUENCE; RESTRICTIONS | Opinion / Review | Theoretical | NA | Global | |||
| Transcriptomics | RNA-seq; transcriptional plasticity; non-model fish; non-lethal sampling; environmental stress | This paper applies a transcriptomics approach to determine which populations are experiencing stress in the wild. Using the transcriptional profiles from non-lethal gill samples, the authors identified sites where fish are experiencing environmental stressors, including low oxygen conditions. This example of a successful application of non-lethal sampling and transcriptomics may be of use to conservation managers wanting to assess the physiological status of wild fish. | Jeffrey, JD; Thorstensen, MJ; Enders, EC; Treberg, JR; Jeffries, KM. (2023). Using transcriptomics to examine the physiological status of wild-caught walleye (Sander vitreus). FACETS, 8(). | 21-Aug-2023 | http://dx.doi.org/10.1139/facets-2022-0177 | TROUT ONCORHYNCHUS-MYKISS; MASS-SPECTROMETRY; PROTEIN COMPLEXES; GENE-EXPRESSION; MUSCLE-TISSUE; FISH; QUALITY; IDENTIFICATION; AUTHENTICATION; SEAFOOD | Technical / Data | Applied | FW | North America (Canada) | |||
| DNA Barcoding | This paper reviews the use of molecular markers in the regulatory oversight of natural ressources in the forestry and fishery sectors. Although omics terms are mentioned, this review focusses largely on the use of DNA barcoding to enhance the reliability of certification programs to prevent fraud and mislabeling of consumer products. | Migone, A; Howlett, M. (2012). From Paper Trails to DNA Barcodes: Enhancing Traceability in Forest and Fishery Certification. NAT RESOUR J, 52(2). | https://digitalrepository.unm.edu/cgi/viewcontent.cgi?article=1096&context=nrj | RETINOID-X-RECEPTOR; MESSENGER-RNA EXPRESSION; CRUSTACEAN HYPERGLYCEMIC HORMONE; SHRIMP LITOPENAEUS-VANNAMEI; CDNA-ENCODING VITELLOGENIN; PACIFIC WHITE SHRIMP; CRAB CARCINUS-MAENAS; CHINESE MITTEN CRAB; MOLECULAR CHARACTERIZATION; KURUMA PRAWN | Opinion / Review | Theoretical | Some discussion | NA | Global | ||||
| Transcriptomics | This paper provides high-coverage liver RNA-seq datasets for four species of high commercial value in European fisheries. The authors describe a workflow for de novo transcriptome assembly and annotation which would require prior experience with bioinformatics to carry out. | Machado, AM; Muñoz-Merida, A; Fonseca, E; Veríssimo, A; Pinto, R; Felício, M; da Fonseca, RR; Froufe, E; Castro, LFC. (2020). Liver transcriptome resources of four commercially exploited teleost species. SCI DATA, 7(1). | 7-Jul-2020 | http://dx.doi.org/10.1038/s41597-020-0565-9 | HEMATOPOIETIC NECROSIS VIRUS; TROUT SALMO-TRUTTA; FLOUNDER PARALICHTHYS-OLIVACEUS; MUMMICHOG FUNDULUS-HETEROCLITUS; HEMORRHAGIC SEPTICEMIA VIRUS; PAIRS COREGONUS SP.; GENE-EXPRESSION; ATLANTIC SALMON; RAINBOW-TROUT; JAPANESE FLOUNDER | Technical / Data | Theoretical | SW | Europe | ||||
| Transcriptomics | antibiotics; fish microbiome; host–microbe interactions; probiotics; transcriptome | This paper uses transcriptional changes during early developmental processes to understand mechanisms leading to abnormal development in a non-model species. RNA-seq data identified changes in the expression of key genes that coincide with developmental milestones. This paper provides an example of how developmental transcriptomics could be used to determine which processes are disrupted in abnormal embryos. | Sorhus, E; Incardona, JP; Furmanek, T; Jentoft, S; Meier, S; Edvardsen, RB. (2016). Developmental transcriptomics in Atlantic haddock: Illuminating pattern formation and organogenesis in non-model vertebrates. DEV BIOL, 411(2). | 15-Mar-2016 | http://dx.doi.org/10.1016/j.ydbio.2016.02.012 | ORIENTAL RIVER PRAWN; CALLINECTES-SAPIDUS; BLUE-CRAB; MOLECULAR CHARACTERIZATION; GENE; EYESTALK; SEQUENCE; STIMPSON; PEPTIDE; BIOLOGY | Technical / Data | Theoretical | SW | Europe | |||
| Transcriptomics | Colouration; Next-generation sequencing; Ornamental fish; Transcriptomics; Unigene | This paper describes the use of next-generation sequencing to determine the molecular basis of pigmentation in a cyprinid. They identified key genes involved in colouration differences between wild and cultured individuals. This paper is of limited use for fisheries management, but may be of interest for ornamental fish production. | Mandal, SC; Tripathy, PS; Khatei, A; Behera, DU; Ghosh, A; Pandey, PK; Parhi, J. (2020). Genetics of colour variation in wild versus cultured queen loath, Botia dario (Hamilton, 1822). GENOMICS, 112(5). | 10-Jun-2020 | http://dx.doi.org/10.1016/j.ygeno.2020.06.012 | GLOBAL ENVIRONMENTAL GOVERNANCE; MITOCHONDRIAL-DNA; GENETIC IDENTIFICATION; NORTH-AMERICAN; PUBLIC-HEALTH; FOOD SAFETY; PRODUCTS; STEWARDSHIP; GENOMICS; SCIENCE | Technical / Data | Theoretical | FW | Asia | |||
| Transcriptomics | This paper is a review of proteomic and transcriptomic approaches to elucidate the effects of various effluent sources on Atlantic cod. The authors focus their review on early life stages (egg, larvae) and tissue-level responses to effluents and single contaminants. Their objective is to identify transcriptional and translational biomarkers that can be used in environmental monitoring and risk assessment. | Karlsen, OA; Bjorneklett, S; Berg, K; Brattås, M; Bohne-Kjersem, A; Grosvik, BE; Goksoyr, A. (2011). Integrative Environmental Genomics of Cod (Gadus morhua): The Proteomics Approach. J TOXICOL ENV HEAL A, 74(7-9). | 9-Mar-2011 | http://dx.doi.org/10.1080/15287394.2011.550559 | BROWN ADIPOSE-TISSUE; PACIFIC BLUEFIN TUNA; PHYLOGENETIC ANALYSIS; GENE TREES; NUCLEAR INTROGRESSION; MUSCLE TEMPERATURES; CONCATENATED DATA; METABOLIC-RATE; BIGEYE TUNA; MITOCHONDRIAL | Opinion / Review | Theoretical | SW | Europe | ||||
| Transcriptomics | Larimichthys polyactis; Transcriptome; Illumina HiSeq 2500; Functional annotation | This paper describes de novo transcriptome assemblies for eight tissues from wild-caught small yellow croaker. Tissue-specific transcriptomic data from this commercially important fish in eastern Asia can be used for gene expression and functional studies. | Liu, LW; Sui, YZ; Zhu, WB; Guo, A; Xu, KD; Zhou, YD. (2017). In-depth transcriptome analysis of Larimichthys polyactis, de novo assembly, functional annotation. MAR GENOM, 33(). | 1-Jun-2017 | http://dx.doi.org/10.1016/j.margen.2017.02.002 | DISCOVERY; ABUNDANCE; RIVER | Technical / Data | Theoretical | SW | Asia | |||
| Transcriptomics | 17 beta-oestradiol; largemouth bass; microarrays; pyrosequencing technology | This paper describes the development of a microarray for a non-model species. The microarray was validated by measuring the transcriptional response in the liver and gonads of male largemouth bass injected with 17β-oestradiol, an estrogenic compound. Before the advent of high-throughput sequencing, microarrays were commonly used for transcriptional profiling. | Garcia-Reyero, N; Griffitt, RJ; Liu, L; Kroll, KJ; Farmerie, WG; Barber, DS; Denslow, ND. (2008). Construction of a robust microarray from a non-model species largemouth bass, Micropterus salmoides (Lacepede), using pyrosequencing technology. J FISH BIOL, 72(9). | 28-Jun-2008 | http://dx.doi.org/10.1111/j.1095-8649.2008.01904.x | GENERATION; PROTEIN; FISH | Technical / Data | Theoretical | FW | North America | |||
| Food security; Genomics; Metabolomics; Metagenomics; Proteomics; Transcriptomics | This paper is a review of high-throughput techniques to assess microbial communities in aquaculture. This review includes genomic, transcriptomic, proteomic, and metabolomic approaches in the context of pathogen detection and identification, and biomarker discovery. | Cancellas, ALB; Costa, WF; Freitas-Silva, J; Lopes, IR; de Oliveira, BFR; Laport, MS. (2022). In sickness and in health: Insights into the application of omics in aquaculture settings under a microbiological perspective. AQUACULTURE, 554(). | 28-Jun-2008 | http://dx.doi.org/10.1016/j.aquaculture.2022.738132 | CRUDE-OIL; GENE-EXPRESSION; CATHEPSIN-K; ZEBRAFISH; GROWTH; IDENTIFICATION; LOCALIZATION; MECHANISMS; CHANNELS; PROTEIN | Opinion / Review | Theoretical | NA | Global | ||||
| Transcriptomics | Flatfish; Larvae; Transcriptome assembly; Illumina; Roche/454 | This paper decribes the de novo assembly of the senegalese sole transcriptome using published data from larvae at different developmental stages. The authors used TransFlow, an automated assembly workflow, to select the "best" transcriptome. | Córdoba-Caballero, J; Seoane-Zonjic, P; Manchado, M; Claros, MG. (2019). De novo Transcriptome Assembly of Solea senegalensis v5.0 Using TransFlow. LECT N BIOINFORMAT, 11465(). | 13-Apr-2019 | http://dx.doi.org/10.1007/978-3-030-17938-0_5 | TRANSCRIPTION FACTOR MITF; CAROTENOID COLORATION; CYPRINUS-CARPIO; READ ALIGNMENT; PIGMENTATION; FISH; EXPRESSION; PROTEIN; GROWTH; ALPHA | Technical / Data | Theoretical | Aquaculture | SW | Europe | ||
| aquaculture; genomics; marine biodiversity; next-generation sequencing, proteomics | This paper reviews omics approaches in marine aquaculture and fisheries. This review also briefly describes a research and training initiative in Central America that is building a genome archive, and the policy-level challenges that they have encountered. | Huete-Pérez, JA; Quezada, F. (2013). Genomic Approaches in Marine Biodiversity and Aquaculture. BIOL RES, 46(4). | http://dx.doi.org/10.4067/S0716-97602013000400007 | EARLY-LIFE STAGES; NORTH-SEA-OIL; DIETARY METHYLMERCURY; RAINBOW-TROUT; 2-DIMENSIONAL ELECTROPHORESIS; POLYCHLORINATED-BIPHENYLS; FISH; TOXICOLOGY; BIOMARKER; EXPOSURE | Opinion / Review | Theoretical | Some discussion | SW | Global | ||||
| Genomics - Genome-Wide | Coilia nasus; De novo transcriptome; SSR markers; Illumina sequencing | This paper describes the assembly and annotation of the brain transcriptome for coilia nasus, an anadromous fish found in the Yangtze River, China. The authors also identified simple sequence repeats that may be used to assess genetic variation within and among samples. | Fang, DA; Zhou, YF; Duan, JR; Zhang, MY; Xu, DP; Liu, K; Xu, P; Wei, Q. (2015). Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing. GENET MOL RES, 14(4). | 13-Nov-2015 | http://dx.doi.org/10.4238/2015.November.13.1 | VIRAL ENCEPHALOPATHY; COAT PROTEIN; QUANTIFICATION; BETANODAVIRUS; SEQUENCE; GENOME; FAMILY; CELLS; RNA | Technical / Data | Theoretical | FW | Asia | |||
| Transcriptomics | CRISPR/Cas9; Petromyzon marinus; Genetic biocontrol; Lamprey; Genome editing | This paper is a review of genetic tools used to study lamprey biology and the application of genomic technologies to control invasive sea lamprey in the North American Great Lakes. Much of this review discusses the use of CRISPR/Cas9 genome editing technologies to target invasive sea lamprey without negative impacts to non-target organisms. This paper would be of interest to fisheries managers wanting to develop alternate management strategies for sea lamprey control. | York, JR; Thresher, RE; McCauley, DW. (2021). Applying functional genomics to the study of lamprey development and sea lamprey population control. J GREAT LAKES RES, 47(). | 1-Dec-2021 | http://dx.doi.org/10.1016/j.jglr.2020.03.010 | BIVALVES CRASSOSTREA-VIRGINICA; OCEAN ACIDIFICATION; ELEVATED-TEMPERATURE; OXIDATIVE STRESS; CO2 LEVELS; RNA-SEQ; HEMOCYTES; IMPACTS; MUSSEL; FERTILIZATION | Opinion / Review | Theoretical | FW | North America | |||
| Transcriptomics | Transcriptome; Alkalinity; Oxidative stress; Inflammation; Immune | This paper analysed the spleen transcriptome of bulatmai barbel to determine the effects of exposure to high-alkalinity water. The authors found that fish exposed to high alkalinity differentially regulated genes involved in inflammation and immune function compared to control fish. | Shang, XC; Geng, LW; Yang, J; Zhang, YT; Xu, W. (2021). Transcriptome analysis reveals the mechanism of alkalinity exposure on spleen oxidative stress, inflammation and immune function of Luciobarbus capito. ECOTOX ENVIRON SAFE, 225(). | 3-Sep-2021 | http://dx.doi.org/10.1016/j.ecoenv.2021.112748 | OYSTER CRASSOSTREA-GIGAS; MUSSEL MYTILUS-GALLOPROVINCIALIS; DOUBLY UNIPARENTAL INHERITANCE; IN-SITU HYBRIDIZATION; SINGLE NUCLEOTIDE POLYMORPHISMS; 2-DOMAIN ARGININE KINASES; BYSSUS RETRACTOR MUSCLE; MOLLUSK DONAX-TRUNCULUS; AMINO-ACID-SEQUENCE; DEPENDENT SEX-RATIO | Technical / Data | Theoretical | SW | Asia | |||
| Transcriptomics | Thermal stress; Metabonomics; NMR; Multivariate analysis; Brachymystax lenok | This is a laboratory study that uses metabonomic and transcriptomic appoaches to assess effects of sublethal high temperatures on juvenile lenok, a coldwater fish. This approach identified metabolic pathways that are activated due to thermal stress and can be used to identify novel biomarkers. | Liu, Y; Liu, JS; Ye, SW; Bureau, DP; Liu, HB; Yin, JS; Mou, ZB; Lin, H; Hao, FH. (2019). Global metabolic responses of the lenok (Brachymystax lenok) to thermal stress. COMP BIOCHEM PHYS D, 29(). | 15-Jan-2019 | http://dx.doi.org/10.1016/j.cbd.2019.01.006 | EXPRESSION ANALYSIS; OVARIAN DEVELOPMENT; GLUTATHIONE-PEROXIDASE; MOLECULAR-CLONING; DYNAMIC ACTION; RNA-SEQ; PROTEIN; IDENTIFICATION; TESTIS; PCNA | Technical / Data | Theoretical | Aquaculture | FW | Asia | ||
| Proteomics | Authentication; Cod; Greenland halibut; Fishery products; Seafood substitution; SWATH-MS; Proteomics; Chemometrics | The study focused on the development and validation of protein biomarkers for accurate identification of Alaska pollock, Atlantic cod, and Greenland halibut. These markers can also used to identify the mislabelling of these three species. | Chien, HJ; Huang, YH; Zheng, YF; Wang, WC; Kuo, CY; Wei, GJ; Lai, CC. (2022). Proteomics for species authentication of cod and corresponding fishery products. FOOD CHEM, 374(). | http://dx.doi.org/10.1016/j.foodchem.2021.131631 | COMMERCIAL HAKE; IDENTIFICATION; MUSCLE; PARVALBUMIN; PROTEINS; MYOSIN; CHAIN | ||||||||
| Proteomics | Biomarker; fishery; food quality; mass spectrometry; proteomics; safety; seafood; traceability | This review summarizes the high-throughput advanced instruments available for the identification of proteomics-based biomarkers. Using these advanced instruments could aid in reducing the biomarker identification time. | Tedesco, S; Mullen, W; Cristobal, S. (2014). High-Throughput Proteomics: A New Tool for Quality and Safety in Fishery Products. CURR PROTEIN PEPT SC, 15(2). | http://dx.doi.org/10.2174/1389203715666140221120219 | ELECTROPHORESIS-MASS-SPECTROMETRY; MUSSELS MYTILUS-EDULIS; CAPILLARY-ELECTROPHORESIS; ZONE-ELECTROPHORESIS; BIOACTIVE PEPTIDES; CHAMAELEA-GALLINA; BIVALVE MOLLUSKS; CROSS-REACTIVITY; COMMERCIAL HAKE; MAJOR ALLERGEN | ||||||||
| Proteomics | Proteomics; Mass spectrometry; Fish authentication; Allergen detection; Bacteria; Quality and safety | This review highlights the studies where proteomics was successfully applied to identifying species and microbial contamination. How proteomics could help to identify the quality of fish during storage and processing. | Carrera, M; Cañas, B; Gallardo, JM. (2013). Proteomics for the assessment of quality and safety of fishery products. FOOD RES INT, 54(1). | http://dx.doi.org/10.1016/j.foodres.2012.10.027 | MUSCLE PROTEIN-DEGRADATION; MASS-SPECTROMETRY; 2-DIMENSIONAL ELECTROPHORESIS; MAJOR ALLERGEN; SPECIES IDENTIFICATION; CROSS-REACTIVITY; COMMERCIAL HAKE; PARVALBUMIN; PEPTIDES; BACTERIA | ||||||||
| Proteomics | Animal protein; Aqua food; Aquaculture; Omics; Safety and quality; Sustainable | This review highlights the applications of proteomics in accurate identification of fish. Further, it also highlights the development of protein-based markers that could be used to track the healthy growth of the fish. Such monitoring could help managers and aquaculture farmers take necessary actions and improve sustainability of fisheries. | Nissa, MU; Pinto, N; Parkar, H; Goswami, M; Srivastava, S. (2021). Proteomics in fisheries and aquaculture: An approach for food security. FOOD CONTROL, 127(). | http://dx.doi.org/10.1016/j.foodcont.2021.108125 | TROUT ONCORHYNCHUS-MYKISS; MASS-SPECTROMETRY; PROTEIN COMPLEXES; GENE-EXPRESSION; MUSCLE-TISSUE; FISH; QUALITY; IDENTIFICATION; AUTHENTICATION; SEAFOOD | ||||||||
| Proteomics | Fishes capita; Species identification; Feed conversion efficiency; Reproductive fitness; Matrix-assisted laser desorption; ionization; Abiotic stress | This review highlights how proteomics could be used in various applications (e.g., food safety, pathology, disease diagnosis, reproductive fitness, stress management). This review also highlights possiblity of development of proteomic-based user-friendly assays for performing field tests | Jaiswal, S; Rasal, KD; Chandra, T; Prabha, R; Iquebal, MA; Rai, A; Kumar, D. (2023). Proteomics in fish health and aquaculture productivity management: Status and future perspectives. AQUACULTURE, 566(). | http://dx.doi.org/10.1016/j.aquaculture.2022.739159 | ZEBRAFISH DANIO-RERIO; BREAM SPARUS-AURATA; GILTHEAD SEA BREAM; SALMON SALMO-SALAR; COD GADUS-MORHUA; IONIZATION MASS-SPECTROMETRY; DIFFERENTIALLY EXPRESSED PROTEINS; LASER-DESORPTION/IONIZATION-TIME; GOLDFISH CARASSIUS-AURATUS; MINNOW GOBIOCYPRIS-RARUS | ||||||||
| Proteomics | attenuated vaccines; bony fish; DNA vaccines; inactivated vaccines; recombinant vaccines; viral vaccines | This review focuses on the status of current vaccines (DNA-based or subunit-based) for bony fish. Their advantages and limitations | Salgado-Miranda, C; Loza-Rubio, E; Rojas-Anaya, E; García-Espinosa, G. (2013). Viral vaccines for bony fish: past, present and future. EXPERT REV VACCINES, 12(5). | http://dx.doi.org/10.1586/ERV.13.38 | PANCREATIC NECROSIS VIRUS; SALMO-SALAR L.; TROUT ONCORHYNCHUS-MYKISS; RED-SEA BREAM; RAINBOW-TROUT; DNA VACCINES; IMMUNE-RESPONSES; ATLANTIC SALMON; BACTERIAL-DNA; CPG MOTIFS | ||||||||
| Proteomics | Temperature; Larvae; Sparus aurata; Proteome; Climate change | This study focused on how increasing temperature could impact the larval fish (Sparus aurata) survival. Authors concluded that S. aurata could not fully acclimate to increased temperature and climate change could adversely affect S. aurata growth and survival. | Madeira, D; Araújo, JE; Vitorino, R; Capelo, JL; Vinagre, C; Diniz, MS. (2016). Ocean warming alters cellular metabolism and induces mortality in fish early life stages: A proteomic approach. ENVIRON RES, 148(). | http://dx.doi.org/10.1016/j.envres.2016.03.030 | HEAT-SHOCK PROTEINS; BREAM SPARUS-AURATA; CLIMATE-CHANGE; GENE-EXPRESSION; MARINE ORGANISMS; THERMAL TOLERANCE; MYTILUS-GALLOPROVINCIALIS; GILLICHTHYS-MIRABILIS; MOLECULAR CHAPERONES; TEMPERATURE STRESS | ||||||||
| Proteomics | Proteomics; Blood biomarker; Great Lakes; Parasite-host relationship; Ecosystem management; Fisheries | This lab study focused on the identification of proteomics-based biomarkers for fish wound assessment caused by Sea lamprey. Male siscowet lake charr was parasitized in a lab setting for four days and after that sea lamprey was removed. Blood samples were collected from the Male siscowet lake charr immediately and 7 months later. The study concluded that modified blood clot assays could provide an accurate estimate of wound damage caused by Sea lampreys. | Bullingham, OMN; Firkus, TJ; Goetz, FW; Murphy, CA; Alderman, SL. (2022). Lake charr (Salvelinus namaycush) clotting response may act as a plasma biomarker of sea lamprey (Petromyzon marinus) parasitism: Implications for management and wound assessment. J GREAT LAKES RES, 48(1). | http://dx.doi.org/10.1016/j.jglr.2021.11.005 | BUCCAL GLAND SECRETION; GREAT-LAKES; PROTEOMIC ANALYSIS; BLOOD-COAGULATION; TROUT; FIBRINOGEN; PURIFICATION; SISCOWET; BIOLOGY; MORPHOTYPES | ||||||||
| Proteomics | peptides; fermentation; ocnsortium; waste streams | This study focuses on the conversion of fish and dairy waste into useful products by fermentation. They characterized the peptides produced with and without the addition of lactic acid bacteria and concluded that rapid acidification of food waste is better. Results are preliminary and later could be used for the ferementation industry. | Mayta-Apaza, AC; Rocha-Mendoza, D; García-Cano, I; Jiménez-Flores, R. (2022). Characterization and Evaluation of Proteolysis Products during the Fermentation of Acid Whey and Fish Waste and Potential Applications. ACS FOOD SCI TECHNOL, 2(9). | http://dx.doi.org/10.1021/acsfoodscitech.2c00157 | ENZYMATIC-HYDROLYSIS; PROTEIN HYDROLYSATE; BY-PRODUCTS; BACTERIA; SILAGE; STRAINS; TRENDS; GUT | ||||||||
| Proteomics | This study attempted to identify the environmental stress markers in Atlantic cod by combining genomics and proteomics data. | Karlsen, OA; Bjorneklett, S; Berg, K; Brattås, M; Bohne-Kjersem, A; Grosvik, BE; Goksoyr, A. (2011). Integrative Environmental Genomics of Cod (Gadus morhua): The Proteomics Approach. J TOXICOL ENV HEAL A, 74(7-9). | http://dx.doi.org/10.1080/15287394.2011.550559 | EARLY-LIFE STAGES; NORTH-SEA-OIL; DIETARY METHYLMERCURY; RAINBOW-TROUT; 2-DIMENSIONAL ELECTROPHORESIS; POLYCHLORINATED-BIPHENYLS; FISH; TOXICOLOGY; BIOMARKER; EXPOSURE | |||||||||
| Proteomics | anthropogenic; Atlantic sturgeon; mucus; proteins; proteomics; stress | This study identified biomarkers for monitoring stress in Atlantic sturgeon using epidermal mucus (skin mucus) protease activity. This is a non-invasive method and could potentially improve conservation regulations. | Murphy, AE; Stokesbury, MJW; Easy, RH. (2020). Exploring epidermal mucus protease activity as an indicator of stress in Atlantic sturgeon (Acipenser oxyrinchusoxyrhinchus). J FISH BIOL, 97(5). | http://dx.doi.org/10.1111/jfb.14489 | OXYRINCHUS MITCHILL; RAINBOW-TROUT; UNITED-STATES; SKIN MUCUS; FISH; RESPONSES; POPULATIONS; MORTALITY; PATHWAY; ROLES | ||||||||
| Proteomics | EAA; Growth performance; Immunity; Nutrition; Proteome; Sparus aurata | This study focused on the addition of Tryptophan in plant-based fish meals and concluded that the addition of Tryptophan does not impact growth, however, it enhances immune response. This study was conducted on Gilthead seabream juveniles. | Cerqueira, M; Schrama, D; Silva, TS; Colen, R; Engrola, SAD; Conceiçao, LEC; Rodrigues, PML; Farinha, AP. (2020). How tryptophan levels in plant-based aquafeeds affect fish physiology, metabolism and proteome. J PROTEOMICS, 221(). | http://dx.doi.org/10.1016/j.jprot.2020.103782 | WINTER THERMAL-STRESS; BREAM SPARUS-AURATA; DICENTRARCHUS-LABRAX; AMINO-ACIDS; DIETS; MEAL; REPLACEMENT; REQUIREMENT; METHIONINE; CYTOSCAPE | ||||||||
| Proteomics | calcium carbonate; endolymph; extracellular serine/threonine protein kinase FAM20C; LC-MS/MS; reverse-phase HPLC; teleost | This study focused on identifying the Black beam (Acanthopagrus butcheri) proteins and molecular mechanisms involved in the otolith formation. | Thomas, ORB; Swearer, SE; Kapp, EA; Peng, P; Tonkin-Hill, GQ; Papenfuss, A; Roberts, A; Bernard, P; Roberts, BR. (2019). The inner ear proteome of fish. FEBS J, 286(1). | http://dx.doi.org/10.1111/febs.14715 | OTOLITH MATRIX PROTEINS; ACANTHOPAGRUS-BUTCHERI SPARIDAE; TROUT ONCORHYNCHUS-MYKISS; RAINBOW-TROUT; BLACK BREAM; IMMUNOHISTOCHEMICAL LOCALIZATION; CARBONIC-ANHYDRASE; MOLECULAR-CLONING; ESTUARINE FISH; CICHLID FISH | ||||||||
| Proteomics | Aquaculture animals; Proteomics; Immunology; Microbiology; Innate immunity | This review highlights the proteomics-based methodologies available for studying the fish response to bacterial and viral infections. | Peng, XX. (2013). Proteomics and its applications to aquaculture in China: Infection, immunity, and interaction of aquaculture hosts with pathogens. DEV COMP IMMUNOL, 39(1-2). | http://dx.doi.org/10.1016/j.dci.2012.03.017 | SPOT SYNDROME VIRUS; OUTER-MEMBRANE PROTEINS; FENNEROPENAEUS-CHINENSIS RESPONSE; AYU PLECOGLOSSUS-ALTIVELIS; EXCESSIVE FLUORIDE; MOLECULAR RESPONSE; PUFFER FISH; EXPRESSION PROFILE; EDWARDSIELLA-TARDA; ENVELOPE PROTEINS | ||||||||
| Proteomics | A high-throughput proteomics-based method was developed to identify the fish at the species level. Validation was done using 51 species. | Bi, HY; Zhong, CY; Shao, MK; Wang, CY; Yi, J; Qiao, L; Zhang, JB. (2019). Differentiation and authentication of fishes at the species level through analysis of fish skin by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RAPID COMMUN MASS SP, 33(16). | http://dx.doi.org/10.1002/rcm.8474 | PROTEIN PROFILES; IDENTIFICATION; BACTERIA; PROTEOMICS; PRODUCTS | |||||||||
| Proteomics | Animal proteomics; Energy metabolism; Flatfish; Larval development; Metamorphosis; Structural proteins | This is a lab-based study on flat fish larvae growth. Authors suggested understanding molecular changes occurring during its developmental stages could help in improving fish larval quality and increase juvenile disease resistance. This study focused on identifying proteins that change at developmental stages in many biological functions including stress response, and energy metabolism. | Chicano-Gálvez, E; Asensio, E; Cañavate, JP; Alhama, J; López-Barea, J. (2015). Proteomic analysis through larval development of Solea senegalensis flatfish. PROTEOMICS, 15(23-24). | http://dx.doi.org/10.1002/pmic.201500176 | HALIBUT HIPPOGLOSSUS-HIPPOGLOSSUS; DIFFERENTIAL GENE-EXPRESSION; ACID-BINDING PROTEIN; GROWTH-FACTOR-I; MOLECULAR CHARACTERIZATION; THYROID-HORMONES; MARINE FISH; POSTTRANSLATIONAL SYNTHESIS; PARALICHTHYS-OLIVACEUS; JAPANESE FLOUNDER | ||||||||
| Proteomics | aquaculture; genomics; marine biodiversity; next-generation sequencing, proteomics | This review focused on the application of genomic methods for understanding biodiversity and aquaculture. Highlights the need for Science policies to confront the challenges faced by small nations in this domain. | Huete-Pérez, JA; Quezada, F. (2013). Genomic Approaches in Marine Biodiversity and Aquaculture. BIOL RES, 46(4). | http://dx.doi.org/10.4067/S0716-97602013000400007 | PROTEOMIC ANALYSIS; ATLANTIC; FISH; METABOLOMICS; SELECTION; DIFFERENTIATION; IDENTIFICATION; DATABASE; RANGE; SNPS | ||||||||
| Proteomics | aquaculture; protein expression; mass spectrometry; Rohu; PTM | This is a proteomics-based study, the study of all proteins for Labeo rohita (important fish in aquaculture). This study has detailed the protein makeup of various tissues in L.rohita, identifying around 26% of its proteins and mapping out where these proteins are expressed and how they are modified. This information was made accessible via a new online resource, which could further help in aquaculture research. | Nissa, MU; Pinto, N; Mukherjee, A; Reddy, PJ; Ghosh, B; Sun, Z; Ghantasala, S; Chetanya, C; Shenoy, SV; Moritz, RL; Goswami, M; Srivastava, S. (2022). Organ-Based Proteome and Post-Translational Modification Profiling of a Widely Cultivated Tropical Water Fish, Labeo rohita. J PROTEOME RES, 21(2). | http://dx.doi.org/10.1021/acs.jproteome.1c00759 | MASS-SPECTROMETRY; IMMUNOLOGICAL CHARACTERIZATION; EXPRESSION ANALYSIS; LYSINE ACETYLATION; ANTEMORTEM STRESS; COLOR STABILITY; PROTEINS; PHOSPHORYLATION; POSTMORTEM; ROHU | ||||||||
| Proteomics | differential expression proteomics; 2D-gel electrophoresis; isotope coded affinity tagging; ICAT; 2D-LC MS/MS; infectious hematopoietic necrosis virus (IHNV); natural killer cell enhancing factor (NKEF); bacterial kidney disease (BKD) | This study was focused on using advanced protein analysis techniques to understand fish diseases that cause significant financial losses in aquaculture and fisheries. By comparing proteins in healthy and diseased Atlantic salmon, they have identified several that are involved in the fish's response to infectious diseases, providing insights that could lead to more effective treatments or vaccines for conditions like infectious hematopoietic necrosis and bacterial kidney disease. | Booy, AT; Haddow, JD; Ohlund, LB; Hardie, DB; Olafson, RW. (2005). Application of isotope coded affinity tag (ICAT) analysis for the identification of differentially expressed proteins following infection of Atlantic salmon (Salmo salar) with infectious hematopoietic necrosis virus (IHNV) or Renibacterium salmoninarum (BKD). J PROTEOME RES, 4(2). | http://dx.doi.org/10.1021/pr049840t | BACTERIAL KIDNEY-DISEASE | ||||||||
| Proteomics | Ion trap; High intensity focused ultrasound; Tandem mass spectrometry; Shrimps; SMIM; Species identification | Selecetd tandem mass spectrometry(SMIM) is a precise method for indentiifying known peptides in complex mixtures usin an ion-trap mass spectrometry. This study used SMIM to quickly authenticate seven dfferent closely related speceis of Decapoda shrimps, ensuring accurate labelling and safety in seafood products. | Ortea, I; Cañas, B; Gallardo, JM. (2011). Selected tandem mass spectrometry ion monitoring for the fast identification of seafood species. J CHROMATOGR A, 1218(28). | http://dx.doi.org/10.1016/j.chroma.2011.05.032 | LENGTH POLYMORPHISM METHOD; DNA-BASED METHODS; PROTEIN IDENTIFICATION; ARGININE KINASE; COMMERCIAL FISH; FOOD INTEREST; AUTHENTICATION; PEPTIDES; PRODUCTS | ||||||||
| Proteomics | Fish authentication; Proteomics; Mass spectrometry; Molecular profiling; Fish frauds | This is a review article focused on the application of proteomics for seafood authentication. This article summarizes the most relevant proteomic methods developed to efficiently identify authentic seas food products and detect mislabelling, offering a reliable solution for food quality and safety controls. | Mazzeo, MF; Siciliano, RA. (2016). Proteomics for the authentication of fish species. J PROTEOMICS, 147(). | http://dx.doi.org/10.1016/j.jprot.2016.03.007 | IONIZATION MASS-SPECTROMETRY; PCR-RFLP ANALYSIS; MALDI-TOF-MS; FOOD AUTHENTICATION; FAST IDENTIFICATION; COMMERCIAL HAKE; TECHNOLOGY; PEPTIDES; PRODUCTS; PARVALBUMIN | ||||||||
| Proteomics | Salem, M; Rexroad, CE; Wang, JN; Thorgaard, GH; Yao, JB. (2010). Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC GENOMICS, 11(). | http://dx.doi.org/10.1186/1471-2164-11-564 | MODEL; DUPLICATION; MICROARRAY; GENERATION; DATABASE; LIBRARY; GENOME; LINES; FISH | ||||||||||
| Proteomics | acclimation; global change; fish; phenotypic plasticity; proteome; temperature | This is a one-month laboratory study, that found that juvenile gilt-head sea breams can acclimate to a moderate temperature increase from 18 to 24 C, adjusting their muscle proteome to maintain metabolic processes, but struggle to survive at higher heat wave temperatures (30 C), Showing significant changes in protein expression related to stress response, inflammation and energy metabolism. The findings in the manuscript suggest that the recruitment of key fisheries species like the sea bream could be at risk due to ocean warming, emphasizing the necessity for better fish stock management strategies. | Madeira, D; Araújo, JE; Vitorino, R; Costa, PM; Capelo, JL; Vinagre, C; Diniz, MS. (2017). Molecular Plasticity under Ocean Warming: Proteomics and Fitness Data Provides Clues for a Better Understanding of the Thermal Tolerance in Fish. FRONT PHYSIOL, 8(). | http://dx.doi.org/10.3389/fphys.2017.00825 | GOBY GILLICHTHYS-MIRABILIS; HEAT-SHOCK PROTEINS; CREATINE-KINASE; STRESS-RESPONSE; CLIMATE-CHANGE; TEMPERATURE-ACCLIMATION; MARINE ORGANISMS; GENE-EXPRESSION; SPARUS-AURATA; MUSCLE-TISSUE | ||||||||
| Proteomics | Larimichthys polyactis; Heat stress; Liver response; Transcriptomic analysis; Proteomic analysis | This is a laboratory study conducted on Small yellow croaker fish. This study investigated how the Small yellow croaker fish responds to heat stress by analyzing changes in genes and proteins in its liver after exposure to high temperatures. They found some key metabolic pathways are key to the fish's response to heat. Improving understanding of those key processes could help address the problems of stress and diseases in fish farming. | Liu, F; Zhang, TL; He, Y; Zhan, W; Xie, QP; Lou, B. (2023). Integration of transcriptome and proteome analyses reveals the regulation mechanisms of Larimichthys polyactis liver exposed to heat stress. FISH SHELLFISH IMMUN, 135(). | http://dx.doi.org/10.1016/j.fsi.2023.108704 | OXIDATIVE STRESS; TEMPERATURE; FISH; RESPONSES; BLOOD; COLD; HISTOPATHOLOGY; METABOLISM; EXPRESSION; INTESTINE | ||||||||
| Proteomics | Aeromonas salmonicida; Furunculosis; Type-three secretion system; T3SS; Vaccine; AcrV; Inhibition of immune protection | This is a laboratory study conducted on Rainbow trout to understand how vaccines function to control a disease caused by Aeromonas salmonids. A. salmonids cause a serious disease in fish called furunculosis, which is typically controlled by vaccines, but how these vaccines work is not well understood. This study found that removing a specific part of the bacteria known as the type three secretion system (T3SS) before making the vaccine increased the survival rates of vaccinated fish, suggesting that this system may interfere with the vaccine effectiveness, and further studies are required to understand the best way to protect fish against the disease. | Vanden Bergh, P; Burr, SE; Benedicenti, O; von Siebenthal, B; Frey, J; Wahli, T. (2013). Antigens of the type-three secretion system of Aeromonas salmonicida subsp salmonicida prevent protective immunity in rainbow trout. VACCINE, 31(45). | http://dx.doi.org/10.1016/j.vaccine.2013.08.057 | YERSINIA-PESTIS; V-ANTIGEN; EXPERIMENTAL FURUNCULOSIS; SALVELINUS-FONTINALIS; ATTENUATED VIRULENCE; ANTIBODY-RESPONSES; EFFECTOR PROTEIN; BROOK TROUT; IMMUNIZATION; MACROPHAGES | ||||||||
| Proteomics | This paper is focused on the identification of potential targets for new vaccines against fish disease furunculosis. In this study, comparisons were performed between the proteins released by highly virulent strains of the bacterium Aeromonas salmonicida and a less virulent strain that lacks a key system for causing disease. | Vanden Bergh, P; Heller, M; Braga-Lagache, S; Frey, J. (2013). The Aeromonas salmonicida subsp salmonicida exoproteome: global analysis, moonlighting proteins and putative antigens for vaccination against furunculosis. PROTEOME SCI, 11(). | http://dx.doi.org/10.1186/1477-5956-11-44 | OUTER-MEMBRANE VESICLES; PEPTIDYLPROLYL ISOMERASE ACTIVITY; III SECRETION SYSTEM; PROTECTIVE IMMUNITY; VIRULENCE FACTORS; IDENTIFICATION; LOCALIZATION; PROTEOME; TRANSLOCATION; PLASMINOGEN | |||||||||
| Metabolomics | Biomarkers; Formaldehyde; Harpodon nehereus; metabolomic | This study focused on identifying the differences between naturally occurring and illegally added formaldehyde in Bombay duck fish. They used a technique called proton NMR to identify changes in specific chemicals. They found that three substances, trimethylamine oxide, trimethylamine, and lysine can act as markers to differentiate between natural and artificial formaldehyde in the fish. | Barokah, GR; Nurhayati, T; Januar, HI; Jacoeb, A. (2023). Identification of Endogenous and Artificial Formaldehyde Biomarkers in Bombay Duck (Harpodon nehereus) Using 1H NMR-Based Metabolomics Approach. J AQUAT FOOD PROD T, (). | http://dx.doi.org/10.1080/10498850.2023.2259364 | TRIMETHYLAMINE OXIDE; FROZEN STORAGE; FOOD SAFETY; FISH; DIMETHYLAMINE; PRODUCTS; FRESHNESS; PROTEINS; FILLETS; SQUID | ||||||||
| Metabolomics | European sea bass; By-products; Growth; Metabolomics; Gut microbiota | This is a laboratory diet study conducted on European sea bass. This study showed that by using by-products from fisheries and aquaculture instead of wild-caught fishmeal and fish oil, the health and growth of the fish were not greatly affected and this replacement might even boost the fish's immune system and disease resistance, suggesting a viable alternative for sustainable fish farming practices. | Marchi, A; Bonaldo, A; Di Biase, A; Cerri, R; Scicchitano, D; Nanetti, E; Candela, M; Picone, G; Capozzi, F; Dondi, F; Gatta, PP; Parma, L. (2023). Towards a free wild-caught fishmeal, fish oil and soy protein in European sea bass diet using by-products from fishery and aquaculture. AQUACULTURE, 573(). | http://dx.doi.org/10.1016/j.aquaculture.2023.739571 | NUCLEAR-MAGNETIC-RESONANCE; PLANT PROTEIN; PRODUCTION PERFORMANCE; INDUCED ENTERITIS; ATLANTIC SALMON; WHEAT GLUTEN; FATTY-ACIDS; GROWTH; METABOLOMICS; SUPPLEMENTATION | ||||||||
| Metabolomics | Metabolomics; High-resolution H-1 NMR; Highly migratory large pelagic fish; Purse seine tuna fisheries; Western Indian Ocean; Raw white and red muscles | This study focused on the development of methods for effectively differentiating Tunas from other species, tuna sizes, tuna storage conditions, and also the geographical origin of wild tropical tuna by analyzing the molecular components of their muscle tissues. This method proved to be a powerful tool in ensuring the traceability of tuna products in the market, protecting consumers and aiding in the conservation of tuna stocks | Bodin, N; Amiel, A; Fouché, E; Sardenne, F; Chassot, E; Debrauwer, L; Guillou, H; Tremblay-Franco, M; Canlet, C. (2022). NMR-based metabolic profiling and discrimination of wild tropical tunas by species, size category, geographic origin, and on-board storage condition. FOOD CHEM, 371(). | http://dx.doi.org/10.1016/j.foodchem.2021.131094 | AMINO-ACIDS; L-HISTIDINE; C-13 NMR; FISH; MUSCLE; SALMON; BIOCHEMISTRY; CARNOSINE; FISHERIES; SPOILAGE | ||||||||
| Metabolomics | Fish; food preservative; formaldehyde; metabolomics; Saurida tumbil | This study focused on differentiating between the naturally occurring formaldehyde and that were artificially added to preserve fish in Indonesia using metabolomics. The research found specific chemical markers, Trimethylamine oxide, trimethylamine that can indicate whether formaldehyde has been added to fish, paving the way for a new method to screen for artificial preservation in seafood. | Anissah, U; Ariyani, F; Barokah, G; Januar, HI. (2021). NMR Metabolomics of Saurida tumbil Fish Treated with Formaldehyde Solution as Misconduct Food Preservation Method. J AQUAT FOOD PROD T, 30(3). | http://dx.doi.org/10.1080/10498850.2021.1880510 | |||||||||
| Metabolomics | PFBS; Probiotic; Metabolome; DNA methylation; Bile acid; Zebrafish larvae | Probiotics (Lactobacillus rhamnosus) have been found to treat and counteract the harmful development effects caused by the pollutant PFBS in zebrafish larvae. This is a laboratory study conducted on Zebra fish and used a metabolomics approach to understand the role of probiotics in controlling the developmental toxicity of perfluorobutane sulfonate (PFBS) pollutants. They found that probiotics altered metabolic processes decreased stress responses and abnormal behavior induced by PFBS, and promoted gut health, suggesting probiotics could be a beneficial, eco-friendly addition to aquaculture and fisheries. | Hu, CY; Huang, ZL; Sun, BL; Liu, MY; Tang, LZ; Chen, LG. (2022). Metabolomic profiles in zebrafish larvae following probiotic and perfluorobutanesulfonate coexposure. ENVIRON RES, 204(). | http://dx.doi.org/10.1016/j.envres.2021.112380 | DNA METHYLATION; BILE-ACIDS; PERFLUOROALKYL; TOXICITY | ||||||||
| Metabolomics | Blue carbon; Seagrass; Mangroves; Saltmarsh; Stable isotopes; Metabolomics | In a study of castal ecosystem in northern Austrialia, reseerchers used various biomarker techniques, including stable isotope ratios and fatty acid analysis, to examine the connections between vegetation in river catchments and the cabon-based food sources for local crabs and fish. They found that the diets of these marine animals are influneced by the type of plants growing along the river banks, with different plant leaving distinct biochemical sigantures in the animals that conusme them. | Gorman, D; Beale, DJ; Crosswell, J; Stephenson, SA; Shah, RM; Hillyer, KE; Steven, ADL. (2023). Multiple-biomarkers show the importance of blue carbon to commercially important fishery species. SCI TOTAL ENVIRON, 881(). | http://dx.doi.org/10.1016/j.scitotenv.2023.163162 | ORGANIC-MATTER SOURCES; STABLE-ISOTOPE RATIO; FATTY-ACID; FLAT ECOSYSTEM; FOOD-WEB; MANGROVE; SEAGRASS; TRACERS; SEDIMENTS; ESTUARY | ||||||||
| Metabolomics | Water flow; Fishery resources supplementation; LC-MS; MS metabolomics; Glutathione; Sebastes schlegelii | The study examined in labouratory on how black rockfish, a speceis that prefers specific habitat conditions responded to different water flow rates over 45 days. It was found that the fish grew better in moving water than in still water, with the best growth at a flow rate of .5 body lengths per second. The study also revealed that water flow affects teh fish's metabolism amd immune response and indentified potential indicators of stress duw o high water flow. These inshights could help in mamanging black rockfish in both aquaculture and conservation efforts to ensure healthier fish and improved survival rates. | Ma, Z; Wang, J; Zhang, J; Ren, XZ; Zhang, X; Liu, Y; Shi, XT. (2023). Effect of water flow on growth and metabolism in Sebastes schlegelii. AQUACULTURE, 571(). | http://dx.doi.org/10.1016/j.aquaculture.2023.739485 | SALMON SALMO-SALAR; JUVENILE BLACK ROCKFISH; SWIMMING EXERCISE; PERFORMANCE; RESISTANCE; FITNESS; STRESS; IMPACT; OXYGEN; SERUM | ||||||||
| Metabolomics | Zebrafish; Tetracycline; Metabolism; Lipid accumulation; Gut microbiome | This is a study conducted on juvenile zebrafish in the laboratory by exposing them to common antibiotic levels found in the environment. Results found that significant weight gain without a change in body length, affected liver health, and altered important bodily functions and gut bacteria when exposed to antibiotics. It highlights how antibiotics like tetracycline in water systems can impact aquatic life even at levels considered environmentally relevant. | Keerthisinghe, TP; Wang, F; Wang, MJ; Yang, Q; Li, JW; Yang, JF; Xi, L; Dong, W; Fang, ML. (2020). Long-term exposure to TET increases body weight of juvenile zebrafish as indicated in host metabolism and gut microbiome. ENVIRON INT, 139(). | http://dx.doi.org/10.1016/j.envint.2020.105705 | ANTIBIOTICS; TETRACYCLINE; OBESITY; IMPACT; MASS; CONSUMPTION; EXTRACTION; RESPONSES | ||||||||
| Metabolomics | Habitat; Metabolites; Hilsa; Liver; Metabolomics; Transcriptomics | The study reveals that Tenualosa ilisha fish, a valuable food source from eh Padma and Hooghly rivers in India, shows differences in nutritional content based on their habitat, with a focus on fatty acids and amino acids, This is determined by analyzing the fish's metabolic processes and genetic responses to their environments. | Ganguly, S; Mitra, T; Mahanty, A; Mohanty, S; Mohanty, BP. (2020). A comparative metabolomics study on anadromous clupeid Tenualosa ilisha for better understanding the influence of habitat on nutritional composition. METABOLOMICS, 16(3). | http://dx.doi.org/10.1007/s11306-020-01655-5 | FATTY-ACID-METABOLISM; GENE-EXPRESSION; RNA-SEQ; TRANSCRIPTOME; PROTEIN; HILSA; 2ND-MESSENGER; QUALITY; LIVER; PCR | ||||||||
| Metabolomics | cross-species; epidermal mucus; metabolomics; monitoring; non-invasive | This study focused on using non-invasive metabolomics-based methods, by analyzing fish mucus, to study various eight freshwater fish species and asses their health and relationships. This approach can help identify specific biological markers for monitoring fish well-being without harming them, and this particular study found unique patterns of metabolites across different fish that could lead to new ways of protecting and tracking the health of fish populations. | Ekman, DR; Evich, MG; Mosley, JD; Doering, JA; Fay, KA; Ankley, GT; Collette, TW. (2023). Expanding non-invasive approaches for fish-health monitoring: A survey of the epidermal mucous metabolomes of phylogenetically diverse freshwater fish species. J FISH BIOL, (). | http://dx.doi.org/10.1111/jfb.15512 | NONNEURONAL CHOLINERGIC SYSTEM; MASS-SPECTROMETRY; SKIN MUCUS; ACETYLCHOLINE; EXPOSURE; IMPACTS | ||||||||
| Metabolomics | Saline-alkaline stress; Fish; Liver; Biochemical analysis; Metabolomics; Transcriptomics | This is laboratory study conducted on how crucian carp, a type of freshwater fish, respond to stress caused by exposure to sodium bicarbonate in water, which mimics saline-alkaline environments. The research involves a 30-day experiment measuring changes in the fish's liver enzymes, metabolites, and gene expression, finding that sodium bicarbonate exposure affects liver function, lipid metabolism, and energy balance, but the fish may adapt by adjusting their metabolism and boosting their antioxidant and immune responses. These findings offer a new understanding f how freshwater fish like crucian crap cope with saline-alkaline conditions, which could inform strategies for managing fisheries in these environments. | Wei, XF; Liu, YJ; Li, SW; Ding, L; Han, SC; Chen, ZX; Lu, H; Wang, P; Sun, YC. (2023). Stress response and tolerance mechanisms of NaHCO3 exposure based on biochemical assays and multi-omics approach in the liver of crucian carp (Carassius auratus). ECOTOX ENVIRON SAFE, 253(). | http://dx.doi.org/10.1016/j.ecoenv.2023.114633 | KETONE-BODIES; METABOLOMICS; BIOMARKERS; METABOLITE; DISCOVERY | ||||||||
| Metabolomics | Tilapia; Polyethylene microplastics; Dietary exposure; Growth; Gut microbiota; Metabolism; Gene expressions | This is a 9-week laboratory experimental study conducted on juvenile genetically improved farmed tilapia to understand how different-sized microplastics impact. Results showed that microplastics cause negative effects on fish growth, digestive enzymes, gut bacteria, liver metabolism, and brain gene expression with large particles more likely to be excreted and smaller ones accumulating in the intestines. The microplastics disrupt normal biological functions and pathways, demonstrating that the size and amount of microplastics are important factors in their harmful effects on fish health. | Lu, X; Zhang, JX; Zhang, L; Wu, D; Tian, J; Yu, LJ; He, L; Zhong, S; Du, H; Deng, DF; Ding, YZ; Wen, H; Jiang, M. (2022). Comprehensive understanding the impacts of dietary exposure to polyethylene microplastics on genetically improved farmed tilapia (Oreochromis niloticus): tracking from growth, microbiota, metabolism to gene expressions. SCI TOTAL ENVIRON, 841(). | http://dx.doi.org/10.1016/j.scitotenv.2022.156571 | FRESH-WATER ECOSYSTEMS; MASS-SPECTROMETRY; JUVENILE FISH; GUT; INFLAMMATION; ENVIRONMENT; CYTOSCAPE |