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Rondon R, Valdés C, Cosseau C, Bergami E, Cárdenas CA, Balbi T, Pérez-Toledo C, Garrido I, Perrois G, Chaparro C, Corre E, Corsi I, González-Aravena M. Transcriptomic responses of Antarctic clam Laternula elliptica to nanoparticles, at single and combined exposures reveal ecologically relevant biomarkers. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116523. [PMID: 38850707 DOI: 10.1016/j.ecoenv.2024.116523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
In recent years micro- and nanoplastics and metal-oxide nanomaterials have been found in several environmental compartments. The Antarctic soft clam Laternula elliptica is an endemic Antarctic species having a wide distribution in the Southern Ocean. Being a filter-feeder, it could act as suitable bioindicator of pollution from nanoparticles also considering its sensitivity to various sources of stress. The present study aims to assess the impact of polystyrene nanoparticles (PS-NP) and the nanometal titanium-dioxide (n-TiO2) on genome-wide transcript expression of L. elliptica either alone and in combination and at two toxicological relevant concentrations (5 and 50 µg/L) during 96 h exposure. Transcript-target qRT-PCR was performed with the aim to identify suitable biomarkers of exposure and effects. As expected, at the highest concentration tested, the clustering was clearer between control and exposed clams. A total of 221 genes resulted differentially expressed in exposed clams and control ones, and 21 of them had functional annotation such as ribosomal proteins, antioxidant, ion transport (osmoregulation), acid-base balance, immunity, lipid metabolism, cell adhesion, cytoskeleton, apoptosis, chromatin condensation and cell signaling. At functional level, relevant transcripts were shared among some treatments and could be considered as general stress due to nanoparticle exposure. After applying transcript-target approach duplicating the number of clam samples, four ecologically relevant transcripts were revealed as biomarkers for PS-NP, n-TiO2 and their combination at 50 µg/L, that could be used for monitoring clams' health status in different Antarctic localities.
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Affiliation(s)
- Rodolfo Rondon
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile.
| | - Catalina Valdés
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile; The University of Texas Health Science Center at Houston, Houston, USA
| | - Céline Cosseau
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Elisa Bergami
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - César Antonio Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile; Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, Modena, Chile
| | - Teresa Balbi
- Department of Earth Environment & Life Sciences, University of Genoa, Genoa, Italy
| | | | - Ignacio Garrido
- Centro de Investigaciones Dinámica de Ecosistemas Marinos de Altas Latitudes, Valdivia, Chile; Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Garance Perrois
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile; Tropical & Subtropical Research Center, Korea Institute of Ocean Science and Technology, Jeju 63349, the Republic of Korea
| | - Cristian Chaparro
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Erwan Corre
- Faculté de Sciences, CNRS, FR 2424 CNRS, ABIMS, Station Biologique de Roscoff, Université Sorbonne, Roscoff, France
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, Siena, Italy
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2
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Ren X, Zhao J, Hu J. Non-concordant epigenetic and transcriptional responses to acute thermal stress in western mosquitofish (Gambusia affinis). Mol Ecol 2024:e17332. [PMID: 38529738 DOI: 10.1111/mec.17332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 03/27/2024]
Abstract
Climate change is intensifying the frequency and severity of extreme temperatures. Understanding the molecular mechanisms underlying the ability to cope with acute thermal stress is key for predicting species' responses to extreme temperature events. While many studies have focused on the individual roles of gene expression, post-transcriptional processes and epigenetic modifications in response to acute thermal stress, the relative contribution of these molecular mechanisms remains unclear. The wide range of thermal limits of western mosquitofish (Gambusia affinis) provides an opportunity to explore this interplay. Here, we quantified changes in gene expression, alternative splicing, DNA methylation and microRNA (miRNA) expression in muscle tissue dissected from mosquitofish immediately after reaching high (CTmax) or low thermal limit (CTmin). Although the numbers of genes showing expression and splicing changes in response to acute temperature stress were small, we found a possibly larger and non-redundant role of splicing compared to gene expression, with more genes being differentially spliced (DSGs) than differentially expressed (DEGs), and little overlap between DSGs and DEGs. We also identified a small proportion of CpGs showing significant methylation change (i.e. differentially methylated cytosines, DMCs) in fish at thermal limits; however, there was no overlap between DEGs and genes annotated with DMCs in both CTmax and CTmin experiments. The weak interplay between epigenetic modifications and gene expression was further supported by our discoveries of no differentially expressed miRNAs. These findings provide novel insights into the relative role of different molecular mechanisms underlying immediate responses to extreme temperatures and demonstrate non-concordant responses of epigenetic and transcriptional mechanisms to acute temperature stress.
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Affiliation(s)
- Xingyue Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Junjie Zhao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
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3
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Bernatchez L, Ferchaud AL, Berger CS, Venney CJ, Xuereb A. Genomics for monitoring and understanding species responses to global climate change. Nat Rev Genet 2024; 25:165-183. [PMID: 37863940 DOI: 10.1038/s41576-023-00657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 10/22/2023]
Abstract
All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.
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Affiliation(s)
- Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.
- Parks Canada, Office of the Chief Ecosystem Scientist, Protected Areas Establishment, Quebec City, Quebec, Canada.
| | - Chloé Suzanne Berger
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Amanda Xuereb
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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4
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Joly LJ, Boersma M, Giraldo C, Mazurais D, Madec L, Collet S, Zambonino-Infante JL, Meunier CL. Smaller herring larval size-at-stage in response to environmental changes is associated with ontogenic processes and stress response. CONSERVATION PHYSIOLOGY 2023; 11:coad072. [PMID: 37711582 PMCID: PMC10498416 DOI: 10.1093/conphys/coad072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/03/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023]
Abstract
Global change puts coastal systems under pressure, affecting the ecology and physiology of marine organisms. In particular, fish larvae are sensitive to environmental conditions, and their fitness is an important determinant of fish stock recruitment and fluctuations. To assess the combined effects of warming, acidification and change in food quality, herring larvae were reared in a control scenario (11°C*pH 8.0) and a scenario predicted for 2100 (14°C*pH 7.6) crossed with two feeding treatments (enriched in phosphorus and docosahexaenoic acid or not). The experiment lasted from hatching to the beginning of the post-flexion stage (i.e. all fins present) corresponding to 47 days post-hatch (dph) at 14°C and 60 dph at 11°C. Length and stage development were monitored throughout the experiment and the expression of genes involved in growth, metabolic pathways and stress responses were analysed for stage 3 larvae (flexion of the notochord). Although the growth rate was unaffected by acidification and temperature changes, the development was accelerated in the 2100 scenario, where larvae reached the last developmental stage at a smaller size (-8%). We observed no mortality related to treatments and no effect of food quality on the development of herring larvae. However, gene expression analyses revealed that heat shock transcripts expression was higher in the warmer and more acidic treatment. Our findings suggest that the predicted warming and acidification environment are stressful for herring larvae, inducing a decrease in size-at-stage at a precise period of ontogeny. This could either negatively affect survival and recruitment via the extension of the predation window or positively increase the survival by reducing the larval stage duration.
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Affiliation(s)
- Léa J Joly
- English Channel and North Sea Research Unit, Ifremer, 150 Quai Gambetta, 62200 Boulogne-sur-Mer, France
- Shelf Sea System Ecology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Am Binnenhafen 1117, 27483 Helgoland, Germany
- Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Düsternbrooker Weg 20, D-24105 Kiel, Germany
| | - Maarten Boersma
- Shelf Sea System Ecology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Am Binnenhafen 1117, 27483 Helgoland, Germany
- FB2, University of Bremen, Leobener Str, 28359 Bremen, Germany
| | - Carolina Giraldo
- English Channel and North Sea Research Unit, Ifremer, 150 Quai Gambetta, 62200 Boulogne-sur-Mer, France
| | - David Mazurais
- Physiology of Marine Organisms, Ifremer, Univ Brest, CNRS, IRD, LEMAR, ZI de la Pointe au Diable, 29280 Plouzané, France
| | - Lauriane Madec
- Physiology of Marine Organisms, Ifremer, Univ Brest, CNRS, IRD, LEMAR, ZI de la Pointe au Diable, 29280 Plouzané, France
| | - Sophie Collet
- Physiology of Marine Organisms, Ifremer, Univ Brest, CNRS, IRD, LEMAR, ZI de la Pointe au Diable, 29280 Plouzané, France
| | - José-Luis Zambonino-Infante
- Physiology of Marine Organisms, Ifremer, Univ Brest, CNRS, IRD, LEMAR, ZI de la Pointe au Diable, 29280 Plouzané, France
| | - Cédric L Meunier
- Shelf Sea System Ecology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Am Binnenhafen 1117, 27483 Helgoland, Germany
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5
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Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3. [PMID: 36801111 DOI: 10.1016/j.tig.2023.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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Affiliation(s)
- Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Iliana Bista
- Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul R Berg
- NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
| | | | - Angelica Crottini
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | - José A Godoy
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Joanna Malukiewicz
- Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
| | - Rebekah A Oomen
- Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Hannes Svardal
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Constantina Theofanopoulou
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
| | - Robert M Waterhouse
- University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden.
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Malec M, Kurban H, Dalkilic M. ccImpute: an accurate and scalable consensus clustering based algorithm to impute dropout events in the single-cell RNA-seq data. BMC Bioinformatics 2022; 23:291. [PMID: 35869420 PMCID: PMC9306045 DOI: 10.1186/s12859-022-04814-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/27/2022] [Indexed: 12/13/2022] Open
Abstract
Background In recent years, the introduction of single-cell RNA sequencing (scRNA-seq) has enabled the analysis of a cell’s transcriptome at an unprecedented granularity and processing speed. The experimental outcome of applying this technology is a \documentclass[12pt]{minimal}
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\begin{document}$$M \times N$$\end{document}M×N matrix containing aggregated mRNA expression counts of M genes and N cell samples. From this matrix, scientists can study how cell protein synthesis changes in response to various factors, for example, disease versus non-disease states in response to a treatment protocol. This technology’s critical challenge is detecting and accurately recording lowly expressed genes. As a result, low expression levels tend to be missed and recorded as zero - an event known as dropout. This makes the lowly expressed genes indistinguishable from true zero expression and different than the low expression present in cells of the same type. This issue makes any subsequent downstream analysis difficult. Results To address this problem, we propose an approach to measure cell similarity using consensus clustering and demonstrate an effective and efficient algorithm that takes advantage of this new similarity measure to impute the most probable dropout events in the scRNA-seq datasets. We demonstrate that our approach exceeds the performance of existing imputation approaches while introducing the least amount of new noise as measured by clustering performance characteristics on datasets with known cell identities. Conclusions ccImpute is an effective algorithm to correct for dropout events and thus improve downstream analysis of scRNA-seq data. ccImpute is implemented in R and is available at https://github.com/khazum/ccImpute.
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Oomen RA, Knutsen H, Olsen EM, Jentoft S, Stenseth NC, Hutchings JA. Warming Accelerates the Onset of the Molecular Stress Response and Increases Mortality of Larval Atlantic Cod. Integr Comp Biol 2022; 62:1784-1801. [PMID: 36130874 PMCID: PMC9801969 DOI: 10.1093/icb/icac145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 01/05/2023] Open
Abstract
Temperature profoundly affects ectotherm physiology. Although differential thermal responses influence fitness, thus driving population dynamics and species distributions, our understanding of the molecular architecture underlying these responses is limited, especially during the critical larval stage. Here, using RNA-sequencing of laboratory-reared Atlantic cod (Gadus morhua) larvae of wild origin, we find changes in gene expression in thousands of transcripts consistent with a severe cellular stress response at both ambient and projected (+2°C and +4°C) temperatures. In addition, specific responses to stress, heat, and hypoxia were commonly identified in gene ontology enrichment analyses and 33 of the 44 genes comprising the minimum stress proteome of all organisms were upregulated. Earlier onset of the stress response was evident at higher temperatures; concomitant increased growth and mortality suggests a reduction in fitness. Temporal differences in gene expression levels do not correspond to differences in growing degree days, suggesting negative physiological consequences of warming beyond accelerated development. Because gene expression is costly, we infer that the upregulation of thousands of transcripts in response to warming in larval cod might act as an energetic drain. We hypothesize that the energetically costly stress response, coupled with increased growth rate at warmer temperatures, leads to faster depletion of energy reserves and increased risk of mortality in larval cod. As sea surface temperatures continue to rise over the next century, reduced fitness of Atlantic cod larvae might lead to population declines in this ecologically and socioeconomically important species. Further, our findings expand our understanding of transcriptomic responses to temperature by ectothermic vertebrate larvae beyond the critical first-feeding stage, a time when organisms begin balancing the energetic demands of growth, foraging, development, and maintenance. Linking the molecular basis of a thermal response to key fitness-related traits is fundamentally important to predicting how global warming will affect ectotherms.
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Affiliation(s)
| | - Halvor Knutsen
- Center for Coastal Research (CCR), Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway,Institute of Marine Research, Nye Flødevigveien 20, 4817 His, Norway
| | - Esben M Olsen
- Center for Coastal Research (CCR), Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway,Institute of Marine Research, Nye Flødevigveien 20, 4817 His, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway,Center for Coastal Research (CCR), Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway
| | - Jeffrey A Hutchings
- Center for Coastal Research (CCR), Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway,Institute of Marine Research, Nye Flødevigveien 20, 4817 His, Norway,Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
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8
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L E E CE, Downey K, Colby RS, Freire CA, Nichols S, Burgess MN, Judy KJ. Recognizing salinity threats in the climate crisis. Integr Comp Biol 2022; 62:441-460. [PMID: 35640911 DOI: 10.1093/icb/icac069] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 11/14/2022] Open
Abstract
Climate change is causing habitat salinity to transform at unprecedented rates across the globe. While much of the research on climate change has focused on rapid shifts in temperature, far less attention has focused on the effects of changes in environmental salinity. Consequently, predictive studies on the physiological, evolutionary, and migratory responses of organisms and populations to the threats of salinity change are relatively lacking. This omission represents a major oversight, given that salinity is among the most important factors that define biogeographic boundaries in aquatic habitats. In this perspective, we briefly touch on responses of organisms and populations to rapid changes in salinity occurring on contemporary time scales. We then discuss factors that might confer resilience to certain taxa, enabling them to survive rapid salinity shifts. Next, we consider approaches for predicting how geographic distributions will shift in response to salinity change. Finally, we identify additional data that are needed to make better predictions in the future. Future studies on climate change should account for the multiple environmental factors that are rapidly changing, especially habitat salinity.
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Affiliation(s)
- Carol Eunmi L E E
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA
| | - Kala Downey
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Rebecca Smith Colby
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Carolina A Freire
- Department of Physiology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Sarah Nichols
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK.,Department of Life Sciences, Natural History Museum, London, UK
| | - Michael N Burgess
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Kathryn J Judy
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
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9
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Oomen RA, Hutchings JA. Genomic reaction norms inform predictions of plastic and adaptive responses to climate change. J Anim Ecol 2022; 91:1073-1087. [PMID: 35445402 PMCID: PMC9325537 DOI: 10.1111/1365-2656.13707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
Abstract
Genomic reaction norms represent the range of gene expression phenotypes (usually mRNA transcript levels) expressed by a genotype along an environmental gradient. Reaction norms derived from common‐garden experiments are powerful approaches for disentangling plastic and adaptive responses to environmental change in natural populations. By treating gene expression as a phenotype in itself, genomic reaction norms represent invaluable tools for exploring causal mechanisms underlying organismal responses to climate change across multiple levels of biodiversity. Our goal is to provide the context, framework and motivation for applying genomic reaction norms to study the responses of natural populations to climate change. Here, we describe the utility of integrating genomics with common‐garden‐gradient experiments under a reaction norm analytical framework to answer fundamental questions about phenotypic plasticity, local adaptation, their interaction (i.e. genetic variation in plasticity) and future adaptive potential. An experimental and analytical framework for constructing and analysing genomic reaction norms is presented within the context of polygenic climate change responses of structured populations with gene flow. Intended for a broad eco‐evo readership, we first briefly review adaptation with gene flow and the importance of understanding the genomic basis and spatial scale of adaptation for conservation and management of structured populations under anthropogenic change. Then, within a high‐dimensional reaction norm framework, we illustrate how to distinguish plastic, differentially expressed (difference in reaction norm intercepts) and differentially plastic (difference in reaction norm slopes) genes, highlighting the areas of opportunity for applying these concepts. We conclude by discussing how genomic reaction norms can be incorporated into a holistic framework to understand the eco‐evolutionary dynamics of climate change responses from molecules to ecosystems. We aim to inspire researchers to integrate gene expression measurements into common‐garden experimental designs to investigate the genomics of climate change responses as sequencing costs become increasingly accessible.
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Affiliation(s)
- Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Centre for Coastal Research (CCR), University of Agder, Kristiansand, Norway
| | - Jeffrey A Hutchings
- Centre for Coastal Research (CCR), University of Agder, Kristiansand, Norway.,Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute of Marine Research, Flødevigen Marine Research Station, His, Norway
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10
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Manzon LA, Zak MA, Agee M, Boreham DR, Wilson JY, Somers CM, Manzon RG. Thermal acclimation alters both basal heat shock protein gene expression and the heat shock response in juvenile lake whitefish (Coregonus clupeaformis). J Therm Biol 2022; 104:103185. [DOI: 10.1016/j.jtherbio.2021.103185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 12/26/2022]
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11
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Roncalli V, Niestroy J, Cieslak MC, Castelfranco AM, Hopcroft RR, Lenz PH. Physiological Acclimatization in High-Latitude Zooplankton. Mol Ecol 2022; 31:1753-1765. [PMID: 35048451 DOI: 10.1111/mec.16354] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 11/30/2022]
Abstract
How individual organisms adapt to non-optimal conditions through physiological acclimatization is central to predicting the consequences of unusual abiotic and biotic conditions such as those produced by marine heat waves. The Northeast Pacific, including the Gulf of Alaska experienced an extreme warming event (2014-2016, "The Blob") that affected all trophic levels leading to large-scale changes in the community. The marine copepod Neocalanus flemingeri is one key member of the subarctic Pacific pelagic ecosystem. During the spring phytoplankton bloom this copepod builds substantial lipid stores as it prepares for its non-feeding adult phase. A three-year comparison of gene expression profiles of copepods collected in Prince William Sound in the Gulf of Alaska between 2015 and 2017 included two high-temperature years (2015 and 2016) and one year with very low phytoplankton abundances (2016). The largest differences in gene expression were between high and low chlorophyll years, and not between warm and cool years. The observed gene expression patterns were indicative of physiological acclimatization. The predominant signal in 2016 was the down-regulation of genes involved in glycolysis and its incoming pathways, consistent with the modulation of metabolic rates in response to prolonged low food conditions. Despite the down-regulation of genes involved in metabolism, there was no evidence of suppression of protein synthesis based on gene expression or behavioral activity. Genes involved in muscle function were up-regulated, and the copepods were actively swimming and responsive to stimuli at collection. However, genes involved in fatty acid metabolism were down-regulated in 2016, suggesting reduced lipid accumulation.
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Affiliation(s)
- Vittoria Roncalli
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd, Honolulu, HI, 96822, USA.,Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Jeanette Niestroy
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd, Honolulu, HI, 96822, USA.,Institute of Pathology, Klinikum Chemnitz gGmbH, 09111, Chemnitz, Germany
| | - Matthew C Cieslak
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd, Honolulu, HI, 96822, USA
| | - Ann M Castelfranco
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd, Honolulu, HI, 96822, USA
| | - Russell R Hopcroft
- Institute of Marine Science, University of Alaska, Fairbanks, 120 O'Neill, Fairbanks, AK, 99775-7220, USA
| | - Petra H Lenz
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd, Honolulu, HI, 96822, USA
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12
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Verta JP, Jacobs A. The role of alternative splicing in adaptation and evolution. Trends Ecol Evol 2021; 37:299-308. [PMID: 34920907 DOI: 10.1016/j.tree.2021.11.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/26/2021] [Accepted: 11/19/2021] [Indexed: 01/02/2023]
Abstract
Regulation of gene expression plays a central role in adaptive divergence and evolution. Although the role of gene regulation in microevolutionary processes is gaining wide acceptance, most studies have only investigated the evolution of transcript levels, ignoring the potentially significant role of transcript structures. We argue that variation in alternative splicing plays an important and widely unexplored role in adaptation (e.g., by increasing transcriptome and/or proteome diversity, or buffering potentially deleterious genetic variation). New studies increasingly highlight the potential for independent evolution in alternative splicing and transcript level, providing alternative paths for selection to act upon. We propose that alternative splicing and transcript levels can provide contrasting, nonredundant mechanisms of equal importance for adaptive diversification of gene function and regulation.
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Affiliation(s)
- Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00790, Helsinki, Finland.
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, G12 8QQ, Glasgow, UK.
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13
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Cascarano MC, Stavrakidis-Zachou O, Mladineo I, Thompson KD, Papandroulakis N, Katharios P. Mediterranean Aquaculture in a Changing Climate: Temperature Effects on Pathogens and Diseases of Three Farmed Fish Species. Pathogens 2021; 10:1205. [PMID: 34578236 PMCID: PMC8466566 DOI: 10.3390/pathogens10091205] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 02/07/2023] Open
Abstract
Climate change is expected to have a drastic effect on aquaculture worldwide. As we move forward with the agenda to increase and diversify aquaculture production, rising temperatures will have a progressively relevant impact on fish farming, linked to a multitude of issues associated with fish welfare. Temperature affects the physiology of both fish and pathogens, and has the potential to lead to significant increases in disease outbreaks within aquaculture systems, resulting in severe financial impacts. Significant shifts in future temperature regimes are projected for the Mediterranean Sea. We therefore aim to review and discuss the existing knowledge relating to disease outbreaks in the context of climate change in Mediterranean finfish aquaculture. The objective is to describe the effects of temperature on the physiology of both fish and pathogens, and moreover to list and discuss the principal diseases of the three main fish species farmed in the Mediterranean, namely gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax), and meagre (Argyrosomus regius). We will attempt to link the pathology of each disease to a specific temperature range, while discussing potential future disease threats associated with the available climate change trends for the Mediterranean Sea.
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Affiliation(s)
- Maria Chiara Cascarano
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
- Department of Biology, University of Crete, 71003 Heraklion, Greece
| | - Orestis Stavrakidis-Zachou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
- Department of Biology, University of Crete, 71003 Heraklion, Greece
| | - Ivona Mladineo
- Biology Center of Czech Academy of Sciences, Laboratory of Functional Helminthology, Institute of Parasitology, 370 05 Ceske Budejovice, Czech Republic;
| | - Kim D. Thompson
- Vaccines and Diagnostics, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian EH26 0PZ, UK;
| | - Nikos Papandroulakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
| | - Pantelis Katharios
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
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14
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Jeffries KM, Teffer A, Michaleski S, Bernier NJ, Heath DD, Miller KM. The use of non-lethal sampling for transcriptomics to assess the physiological status of wild fishes. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110629. [PMID: 34058376 DOI: 10.1016/j.cbpb.2021.110629] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
Fishes respond to different abiotic and biotic stressors through changes in gene expression as a part of an integrated physiological response. Transcriptomics approaches have been used to quantify gene expression patterns as a reductionist approach to understand responses to environmental stressors in animal physiology and have become more commonly used to study wild fishes. We argue that non-lethal sampling for transcriptomics should become the norm for assessing the physiological status of wild fishes, especially when there are conservation implications. Processes at the level of the transcriptome provide a "snapshot" of the cellular conditions at a given time; however, by using a non-lethal sampling protocol, researchers can connect the transcriptome profile with fitness-relevant ecological endpoints such as reproduction, movement patterns and survival. Furthermore, telemetry is a widely used approach in fisheries to understand movement patterns in the wild, and when combined with transcriptional profiling, provides arguably the most powerful use of non-lethal sampling for transcriptomics in wild fishes. In this review, we discuss the different tissues that can be successfully incorporated into non-lethal sampling strategies, which is particularly useful in the context of the emerging field of conservation transcriptomics. We briefly describe different methods for transcriptional profiling in fishes from high-throughput qPCR to whole transcriptome approaches. Further, we discuss strategies and the limitations of using transcriptomics for non-lethally studying fishes. Lastly, as 'omics' technology continues to advance, transcriptomics paired with different omics approaches to study wild fishes will provide insight into the factors that regulate phenotypic variation and the physiological responses to changing environmental conditions in the future.
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Affiliation(s)
- Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada.
| | - Amy Teffer
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, United States of America
| | - Sonya Michaleski
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Nicholas J Bernier
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Daniel D Heath
- Department of Integrative Biology, Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
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15
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RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish. BMC Genomics 2021; 22:273. [PMID: 33858341 PMCID: PMC8048188 DOI: 10.1186/s12864-021-07592-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/05/2021] [Indexed: 01/03/2023] Open
Abstract
Background Messenger RNA sequencing is becoming more common in studies of non-model species and is most often used for gene expression-based investigations. However, the method holds potential for numerous other applications as well—including analyses of alternative splicing, population structure, and signatures of selection. To maximize the utility of mRNA data sets, distinct analyses may be combined such as by exploring dynamics between gene expression with signatures of selection in the context of population structure. Here, we compare two published data sets describing two populations of a minnow species endemic to the San Francisco Estuary (Sacramento splittail, Pogonichthys macrolepidotus): a microsatellite data set showing population structure, and an mRNA whole transcriptome data set obtained after the two populations were exposed to a salinity challenge. We compared measures of population structure and genetic variation using single nucleotide polymorphisms (SNPs) called from mRNA from the whole transcriptome sequencing study with those patterns determined from microsatellites. For investigating plasticity and evolution, intra- and inter-population transcriptome plasticity was investigated with differential gene expression, differential exon usage, and gene expression variation. Outlier SNP analysis was also performed on the mRNA data set and signatures of selection and phenotypic plasticity were investigated on an individual-gene basis. Results We found that mRNA sequencing revealed patterns of population structure consistent with those found with microsatellites, but with lower magnitudes of genetic variation and population differentiation consistent with widespread purifying selection expected when using mRNA. In addition, within individual genes, phenotypic plasticity or signatures of selection were found in almost mutual exclusion (except heatr6, nfu1, slc22a6, sya, and mmp13). Conclusions These results show that an mRNA sequencing data set may have multiple uses, including describing population structure and for investigating the mechanistic interplay of evolution and plasticity in adaptation. MRNA sequencing thus complements traditional sequencing methods used for population genetics, in addition to its utility for describing phenotypic plasticity. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07592-4.
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16
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Yates MC, Derry AM, Cristescu ME. Environmental RNA: A Revolution in Ecological Resolution? Trends Ecol Evol 2021; 36:601-609. [PMID: 33757695 DOI: 10.1016/j.tree.2021.03.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022]
Abstract
Current advancements in environmental RNA (eRNA) exploit its relatively fast turnover rate relative to environmental DNA (eDNA) to assess 'metabolically active' or temporally/spatially recent community diversity. However, this focus significantly underutilizes the trove of potential ecological information encrypted in eRNA. Here, we argue for pushing beyond current species-level eDNA detection capabilities by using eRNA to detect any organisms with unique eRNA profiles, potentially including different life-history stages, sexes, or even specific phenotypes within a species. We also discuss the future of eRNA as a means of assessing the physiological status of organisms and the ecological health of populations and communities, reflecting ecosystem-level conditions. We posit that eRNA has the potential to significantly improve the resolution of organism detection, biological monitoring, and biomonitoring applications in ecology.
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Affiliation(s)
- Matthew C Yates
- Département des Sciences Biologiques, Université du Québec à Montréal, 141 Avenue Président-Kennedy, Montréal, QC, H2X 1Y4, Canada.
| | - Alison M Derry
- Département des Sciences Biologiques, Université du Québec à Montréal, 141 Avenue Président-Kennedy, Montréal, QC, H2X 1Y4, Canada
| | - Melania E Cristescu
- Department of Biology, McGill University, 1205 Dr Penfield Avenue, Montreal, QC, H3A 1B1, Canada
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17
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Song J, McDowell JR. Comparative transcriptomics of spotted seatrout ( Cynoscion nebulosus) populations to cold and heat stress. Ecol Evol 2021; 11:1352-1367. [PMID: 33598136 PMCID: PMC7863673 DOI: 10.1002/ece3.7138] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/25/2022] Open
Abstract
Resilience to climate change depends on a species' adaptive potential and phenotypic plasticity. The latter can enhance survival of individual organisms during short periods of extreme environmental perturbations, allowing genetic adaptation to take place over generations. Along the U.S. East Coast, estuarine-dependent spotted seatrout (Cynoscion nebulosus) populations span a steep temperature gradient that provides an ideal opportunity to explore the molecular basis of phenotypic plasticity. Genetically distinct spotted seatrout sampled from a northern and a southern population were exposed to acute cold and heat stress (5 biological replicates in each treatment and control group), and their transcriptomic responses were compared using RNA-sequencing (RNA-seq). The southern population showed a larger transcriptomic response to acute cold stress, whereas the northern population showed a larger transcriptomic response to acute heat stress compared with their respective population controls. Shared transcripts showing significant differences in expression levels were predominantly enriched in pathways that included metabolism, transcriptional regulation, and immune response. In response to heat stress, only the northern population significantly upregulated genes in the apoptosis pathway, which could suggest greater vulnerability to future heat waves in this population as compared to the southern population. Genes showing population-specific patterns of expression, including hpt, acot, hspa5, and hsc71, are candidates for future studies aiming to monitor intraspecific differences in temperature stress responses in spotted seatrout. Our findings contribute to the current understanding of phenotypic plasticity and provide a basis for predicting the response of a eurythermal fish species to future extreme temperatures.
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Affiliation(s)
- Jingwei Song
- Virginia Institute of Marine Science (VIMS)College of William and MaryGloucester PointVAUSA
| | - Jan R. McDowell
- Virginia Institute of Marine Science (VIMS)College of William and MaryGloucester PointVAUSA
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18
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Li P, Liu Q, Li J, Wang F, Wen S, Li N. Transcriptomic responses to heat stress in gill and liver of endangered Brachymystax lenok tsinlingensis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100791. [PMID: 33465733 DOI: 10.1016/j.cbd.2021.100791] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/21/2022]
Abstract
Global warming significantly affects fish, particularly cold-water fish, because increased temperature adversely impacts their abilities to grow or reproduce, and eventually influences their fitness or even causes death. To survive, fish may alter their distribution or behavior to avoid the stress, and perhaps acclimate or evolve resistance to the elevated temperature. Brachymystax lenok tsinlingensis is an endangered cold-water species in China, and it has been found to alter the altitudinal distribution, decrease swimming efficiency and develop resistance under heat exposure, which badly impact the continuing conservation work. To better protect them, it is essential to understand how they respond to thermal stress behaviorally and physiologically. Therefore, the fish were exposed to 24.5 °C and based on the time taken for them to lose equilibrium, they were separately sampled as sensitive and tolerant groups. Both gill and liver tissues were collected from both groups for transcriptome sequencing. Sequencing results demonstrated that control and tolerant groups were similar in transcriptomic patterns and sensitive groups differentially expressed more genes than tolerant ones, suggesting the gene expression of tolerant groups may return to base levels as exposure time increased. Tissue differences were the major factor affecting gene expression, and they also displayed different physiological responses to heat stress. Consistent with other studies, heat shock response, immune response, metabolic adjustment and ion transport were found to be triggered after exposed to elevated temperature. The findings would contribute to a better understanding of responding mechanisms of fish to thermal stress and provide guidance for future conservation programs.
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Affiliation(s)
- Ping Li
- Center for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Qigen Liu
- Center for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Feng Wang
- Yellow River Fisheries Research Institute, Chinese Academy of Fishery Science, Xi'an 710086, China
| | - Sien Wen
- Yellow River Fisheries Research Institute, Chinese Academy of Fishery Science, Xi'an 710086, China
| | - Ning Li
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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19
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Anastasiadi D, Shao C, Chen S, Piferrer F. Footprints of global change in marine life: Inferring past environment based on DNA methylation and gene expression marks. Mol Ecol 2020; 30:747-760. [PMID: 33372368 DOI: 10.1111/mec.15764] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/17/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022]
Abstract
Ocean global warming affects the distribution, life history and physiology of marine life. Extreme events, like marine heatwaves, are increasing in frequency and intensity. During sensitive stages of early fish development, the consequences may be long-lasting and mediated by epigenetic mechanisms. Here, we used European sea bass as a model to study the possible long-lasting effects of a marine heatwave during early development. We measured DNA methylation and gene expression in four tissues (brain, muscle, liver and testis) and detected differentially methylated regions (DMRs). Six genes were differentially expressed and contained DMRs three years after exposure to increased temperature, indicating direct phenotypic consequences and representing persistent changes. Interestingly, nine genes contained DMRs around the same genomic regions across tissues, therefore consisting of common footprints of developmental temperature in environmentally responsive loci. These loci are, to our knowledge, the first metastable epialleles (MEs) described in fish. MEs may serve as biomarkers to infer past life history events linked with persistent consequences. These results highlight the importance of subtle phenotypic changes mediated by epigenetics to extreme weather events during sensitive life stages. Also, to our knowledge, it is the first time the molecular effects of a marine heatwave during the lifetime of individuals are assessed. MEs could be used in surveillance programs aimed at determining the footprints of climate change on marine life. Our study paves the way for the identification of conserved MEs that respond equally to environmental perturbations across species. Conserved MEs would constitute a tool of assessment of global change effects in marine life at a large scale.
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Affiliation(s)
- Dafni Anastasiadi
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Songlin Chen
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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20
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Komoroske LM, Jeffries KM, Whitehead A, Roach JL, Britton M, Connon RE, Verhille C, Brander SM, Fangue NA. Transcriptional flexibility during thermal challenge corresponds with expanded thermal tolerance in an invasive compared to native fish. Evol Appl 2020. [DOI: 10.1111/eva.13172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Lisa M. Komoroske
- Department of Environmental Conservation University of Massachusetts Amherst Amherst MA USA
- Department of Wildlife, Fish & Conservation Biology University of California, Davis Davis CA USA
| | - Ken M. Jeffries
- Department of Biological Sciences University of Manitoba Winnipeg MB Canada
| | - Andrew Whitehead
- Department of Environmental Toxicology University of California, Davis Davis CA USA
| | - Jennifer L. Roach
- Department of Environmental Toxicology University of California, Davis Davis CA USA
| | - Monica Britton
- Bioinformatics Core Facility, Genome Center University of California, Davis Davis CA USA
| | - Richard E. Connon
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine University of California, Davis Davis CA USA
| | | | - Susanne M. Brander
- Department of Fisheries and Wildlife, Coastal Oregon Marine Experiment Station Oregon State University Corvallis OR USA
| | - Nann A. Fangue
- Department of Wildlife, Fish & Conservation Biology University of California, Davis Davis CA USA
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21
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Jeffrey JD, Carlson H, Wrubleski D, Enders EC, Treberg JR, Jeffries KM. Applying a gene-suite approach to examine the physiological status of wild-caught walleye ( Sander vitreus). CONSERVATION PHYSIOLOGY 2020; 8:coaa099. [PMID: 33365129 PMCID: PMC7745715 DOI: 10.1093/conphys/coaa099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/25/2020] [Accepted: 10/04/2020] [Indexed: 06/12/2023]
Abstract
Molecular techniques have been increasingly used in a conservation physiology framework to provide valuable information regarding the mechanisms underlying responses of wild organisms to environmental and anthropogenic stressors. In the present study, we developed a reference gill transcriptome for walleye (Sander vitreus), allowing us to pair a gene-suite approach (i.e. multiple genes across multiple cellular processes) with multivariate statistics to examine the physiological status of wild-caught walleye. For molecular analyses of wild fish, the gill is a useful target for conservation studies, not only because of its importance as an indicator of the physiological status of fish but also because it can be biopsied non-lethally. Walleye were non-lethally sampled following short- (~1.5 months) and long-term (~3.5 months) confinement in the Delta Marsh, which is located south of Lake Manitoba in Manitoba, Canada. Large-bodied walleye are confined in the Delta Marsh from late April to early August by exclusion screens used to protect the marsh from invasive common carp (Cyprinus carpio), exposing fish to potentially stressful water quality conditions. Principal components analysis revealed patterns of transcript abundance consistent with exposure of fish to increasingly high temperature and low oxygen conditions with longer holding in the marsh. For example, longer-term confinement in the marsh was associated with increases in the mRNA levels of heat shock proteins and a shift in the mRNA abundance of aerobic to anaerobic metabolic genes. Overall, the results of the present study suggest that walleye confined in the Delta Marsh may be exhibiting sub-lethal responses to high temperature and low oxygen conditions. These results provide valuable information for managers invested in mediating impacts to a local species of conservation concern. More broadly, we highlight the usefulness of pairing transcriptomic techniques with multivariate statistics to address potential confounding factors that can affect measured physiological responses of wild-caught fish.
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Affiliation(s)
- Jennifer D Jeffrey
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Hunter Carlson
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Dale Wrubleski
- Institute for Wetland and Waterfowl Research, Ducks Unlimited Canada, Stonewall, Manitoba, R0C 2Z0 Canada
| | - Eva C Enders
- Fisheries and Oceans Canada, Winnipeg, Manitoba, R3T 2N6 Canada
| | - Jason R Treberg
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
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22
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Kim HM, Long NP, Min JE, Anh NH, Kim SJ, Yoon SJ, Kwon SW. Comprehensive phenotyping and multi-omic profiling in the toxicity assessment of nanopolystyrene with different surface properties. JOURNAL OF HAZARDOUS MATERIALS 2020; 399:123005. [PMID: 32937704 DOI: 10.1016/j.jhazmat.2020.123005] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
There is a growing concern regarding the toxic effects of terrestrial nanoplastic contaminants. However, an all-encompassing phenotyping- and omics-based strategy for the toxicity assessment of nanoplastics with different surface properties on soil living organisms remains to be established. Herein, we devised a comprehensive phenotyping and multi-omic profiling method to examine the molecular disturbance of nanopolystyrene (PS)-exposed Caenorhabditis elegans. The exposure time was 24 h with either 1 μg/mL or 10 μg/mL of PS. We found that PS considerably affected the reproduction and locomotion, as well as increased the oxidative stress of worms regardless of their surface properties. Nevertheless, each type of PS affected the metabolome and lipidome of the nematodes differently. Uncharged PS (PS-N) triggered significant metabolic disturbances, whereas the metabolic influences from PS-NH2 and PS-COOH were subtle. The dysregulated transcriptome profiles of PS-N were strongly associated with the metabolic pathways. Besides, the altered expression of several genes associated with autophagy and longevity was observed. Collectively, we demonstrated that comprehensive phenotyping and omics-based profiling establish a practical framework that allows us to gain deeper insights into the maladaptive consequences of PS in nematodes. It can be utilized for the evaluation of other environmental contaminants in the terrestrial ecosystem.
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Affiliation(s)
- Hyung Min Kim
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Nguyen Phuoc Long
- Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jung Eun Min
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Nguyen Hoang Anh
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sun Jo Kim
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang Jun Yoon
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung Won Kwon
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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23
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Fé-Gonçalves LM, Araújo JDA, dos Santos CHDA, de Almeida-Val VMF. Transcriptomic evidences of local thermal adaptation for the native fish Colossoma macropomum (Cuvier, 1818). Genet Mol Biol 2020; 43:e20190377. [PMID: 32915948 PMCID: PMC7485747 DOI: 10.1590/1678-4685-gmb-2019-0377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/13/2020] [Indexed: 11/22/2022] Open
Abstract
Brazil has five climatically distinct regions, with an annual average temperature difference up to 14 ºC between the northern and southern extremes. Environmental variation of this magnitude can lead to new genetic patterns among farmed fish populations. Genetically differentiated populations of tambaqui (Colossoma macropomum Cuvier, 1818), an important freshwater fish for Brazilian continental aquaculture, may be associated with regional adaptation. In this study, we selected tambaquis raised in two thermally distinct regions, belonging to different latitudes, to test this hypothesis. De novo transcriptome analysis was performed to compare the significant differences of genes expressed in the liver of juvenile tambaqui from a northern population (Balbina) and a southeastern population (Brumado). In total, 2,410 genes were differentially expressed (1,196 in Balbina and 1,214 in Brumado). Many of the genes are involved in a multitude of biological functions such as biosynthetic processes, homeostasis, biorhythm, immunity, cell signaling, ribosome biogenesis, modification of proteins, intracellular transport, structure/cytoskeleton, and catalytic activity. Enrichment analysis based on biological networks showed a different protein interaction profile for each population, whose encoding genes may play potential functions in local thermal adaptation of fish to their respective farming environments.
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Affiliation(s)
- Luciana Mara Fé-Gonçalves
- Instituto Nacional de Pesquisas da Amazônia, Laboratório de
Ecofisiologia e Evolução Molecular, Manaus, AM, Brazil
| | - José Deney Alves Araújo
- Universidade de São Paulo, Laboratório de Biologia de Sistema
Computacional, São Paulo, SP, Brazil
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24
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Sävilammi T, Papakostas S, Leder EH, Vøllestad LA, Debes PV, Primmer CR. Cytosine methylation patterns suggest a role of methylation in plastic and adaptive responses to temperature in European grayling ( Thymallus thymallus) populations. Epigenetics 2020; 16:271-288. [PMID: 32660325 DOI: 10.1080/15592294.2020.1795597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Temperature is a key environmental parameter affecting both the phenotypes and distributions of organisms, particularly ectotherms. Rapid organismal responses to thermal environmental changes have been described for several ectotherms; however, the underlying molecular mechanisms often remain unclear. Here, we studied whole genome cytosine methylation patterns of European grayling (Thymallus thymallus) embryos from five populations with contemporary adaptations of early life history traits at either 'colder' or 'warmer' spawning grounds. We reared fish embryos in a common garden experiment using two temperatures that resembled the 'colder' and 'warmer' conditions of the natal natural environments. Genome-wide methylation patterns were similar in populations originating from colder thermal origin subpopulations, whereas single nucleotide polymorphisms uncovered from the same data identified strong population structure among isolated populations, but limited structure among interconnected populations. This was surprising because the previously studied gene expression response among populations was mostly plastic, and mainly influenced by the developmental temperature. These findings support the hypothesis of the magnified role of epigenetic mechanisms in modulating plasticity. The abundance of consistently changing methylation loci between two warmer-to-colder thermal origin population pairs suggests that local adaptation has shaped the observed methylation patterns. The dynamic nature of the methylomes was further highlighted by genome-wide and site-specific plastic responses. Our findings support both the presence of a plastic response in a subset of CpG loci, and the evolutionary role of methylation divergence between populations adapting to contrasting thermal environments.
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Affiliation(s)
- Tiina Sävilammi
- Department of Biology, University of Turku , Turku, Finland.,Department of Biological and Environmental Science, University of Jyväskylä , Jyväskylä, Finland
| | | | - Erica H Leder
- Department of Biology, University of Turku , Turku, Finland.,Natural History Museum, University of Oslo , Oslo, Norway
| | - L Asbjørn Vøllestad
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo , Oslo, Norway
| | - Paul V Debes
- Organismal & Evolutionary Biology Research Program, Faculty of Biological & Environmental Sciences, University of Helsinki , Helsinki, Finland.,Institute of Biotechnology, University of Helsinki , Helsinki, Finland.,Department of Aquaculture and Fish Biology, Hólar University College , Sauðárkrókur, Iceland
| | - Craig R Primmer
- Organismal & Evolutionary Biology Research Program, Faculty of Biological & Environmental Sciences, University of Helsinki , Helsinki, Finland.,Institute of Biotechnology, University of Helsinki , Helsinki, Finland
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25
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Studivan MS, Voss JD. Transcriptomic plasticity of mesophotic corals among natural populations and transplants of
Montastraea cavernosa
in the Gulf of Mexico and Belize. Mol Ecol 2020; 29:2399-2415. [DOI: 10.1111/mec.15495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/14/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Michael S. Studivan
- Harbor Branch Oceanographic Institute Florida Atlantic University Fort Pierce FL USA
- Cooperative Institute for Marine and Atmospheric Studies University of Miami Rosenstiel School of Marine and Atmospheric Sciences Miami FL USA
| | - Joshua D. Voss
- Harbor Branch Oceanographic Institute Florida Atlantic University Fort Pierce FL USA
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26
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Fé-Gonçalves LM, Araújo JDA, Santos CHDAD, Val AL, Almeida-Val VMFD. How will farmed populations of freshwater fish deal with the extreme climate scenario in 2100? Transcriptional responses of Colossoma macropomum from two Brazilian climate regions. J Therm Biol 2020; 89:102487. [PMID: 32364997 DOI: 10.1016/j.jtherbio.2019.102487] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/29/2019] [Accepted: 12/22/2019] [Indexed: 12/27/2022]
Abstract
Tambaqui (Colossoma macropomum Cuvier, 1818) is an endemic fish of the Amazon and Orinoco basins, and it is the most economically important native species in Brazil being raised in five climatically distinct regions. In the face of current global warming, environmental variations in farm ponds represent additional challenges that may drive new adaptive regional genetic variations among broodstocks of tambaqui. In an experimental context based on the high-emission scenario of the 5th Intergovernmental Panel on Climate Change (IPCC) report, we used two farmed tambaqui populations to test this hypothesis. RNA-seq transcriptome analysis was performed in the liver of juvenile tambaqui from northern (Balbina Experimental Station, Balbina, AM) and southeastern (Brumado Fish Farming, Mogi Mirim, SP) Brazilian regions kept for 30 days in artificial environmental rooms mimicking the current and extreme climate scenarios. Three Illumina MiSeq runs produced close to 120 million 500 bp paired-end reads; 191,139 contigs were assembled with N50 = 1595. 355 genes were differentially expressed for both populations in response to the extreme scenario. After enrichment analysis, each population presented a core set of genes to cope with climate change. Northern fish induced genes related to the cellular response to stress, activation of MAPK activity, response to unfolded protein, protein metabolism and cellular response to DNA damage stimuli. Genes biologically involved in regulating cell proliferation, protein stabilisation and protein ubiquitination for degradation through the ubiquitin-proteasome system were downregulated. Genes associated with biological processes, including the cellular response to stress, MAPK cascade activation, homeostatic processes and positive regulation of immune responses were upregulated in southeastern fish. The downregulated genes were related to cytoskeleton organisation, energy metabolism, and the regulation of transcription and biological rhythms. Our findings reveal the signatures of promising candidate genes involved in the regional plasticity of each population of tambaqui in dealing with upcoming climate changes.
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Affiliation(s)
- Luciana Mara Fé-Gonçalves
- Laboratory of Ecophysiology and Molecular Evolution, Brazilian National Institute for Research of the Amazon, André Araújo Avenue, 2936, 69067-375, Petrópolis, Manaus, AM, Brazil.
| | - José Deney Alves Araújo
- Computational Systems Biology Laboratory, University of São Paulo, Professor Lúcio Martins Rodrigues Avenue, 370, 05508020, Butantã, São Paulo, SP, Brazil
| | - Carlos Henrique Dos Anjos Dos Santos
- Laboratory of Ecophysiology and Molecular Evolution, Brazilian National Institute for Research of the Amazon, André Araújo Avenue, 2936, 69067-375, Petrópolis, Manaus, AM, Brazil
| | - Adalberto Luis Val
- Laboratory of Ecophysiology and Molecular Evolution, Brazilian National Institute for Research of the Amazon, André Araújo Avenue, 2936, 69067-375, Petrópolis, Manaus, AM, Brazil
| | - Vera Maria Fonseca de Almeida-Val
- Laboratory of Ecophysiology and Molecular Evolution, Brazilian National Institute for Research of the Amazon, André Araújo Avenue, 2936, 69067-375, Petrópolis, Manaus, AM, Brazil
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27
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Transcriptome profiling reveals exposure to predicted end-of-century ocean acidification as a stealth stressor for Atlantic cod larvae. Sci Rep 2019; 9:16908. [PMID: 31729401 PMCID: PMC6858462 DOI: 10.1038/s41598-019-52628-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 10/17/2019] [Indexed: 01/12/2023] Open
Abstract
Ocean acidification (OA), a direct consequence of increasing atmospheric CO2 concentration dissolving in ocean waters, is impacting many fish species. Little is known about the molecular mechanisms underlying the observed physiological impacts in fish. We used RNAseq to characterize the transcriptome of 3 different larval stages of Atlantic cod (Gadus morhua) exposed to simulated OA at levels (1179 µatm CO2) representing end-of-century predictions compared to controls (503 µatm CO2), which were shown to induce tissue damage and elevated mortality in G. morhua. Only few genes were differentially expressed in 6 and 13 days-post-hatching (dph) (3 and 16 genes, respectively), during a period when maximal mortality as a response to elevated pCO2 occurred. At 36 dph, 1413 genes were differentially expressed, most likely caused by developmental asynchrony between the treatment groups, with individuals under OA growing faster. A target gene analysis revealed only few genes of the universal and well-defined cellular stress response to be differentially expressed. We thus suggest that predicted ocean acidification levels constitute a "stealth stress" for early Atlantic cod larvae, with a rapid breakdown of cellular homeostasis leading to organismal death that was missed even with an 8-fold replication implemented in this study.
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28
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Jeffrey JD, Jeffries KM, Suski CD. Physiological status of silver carp (Hypophthalmichthys molitrix) in the Illinois River: An assessment of fish at the leading edge of the invasion front. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 32:100614. [PMID: 31419603 DOI: 10.1016/j.cbd.2019.100614] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/08/2019] [Accepted: 07/24/2019] [Indexed: 01/29/2023]
Abstract
Silver carp (Hypophthalmichthys molitrix) are invasive to North America, and their range has expanded within the Mississippi River Basin, seemingly unchecked, since their introduction in the late 1970s, with the exception of the upper reaches of the Illinois River. With the imminent threat of their movement into the Great Lakes, the goal of the present study was to assess whether differences in the physiological status between silver carp at the leading edge of their invasion front and core population sites could explain their lack of expansion upstream toward Lake Michigan over the past decade. A transcriptomic approach using RNA sequencing and analysis of plasma variables were used to quantify differences among fish at the leading edge and two downstream core population sites. Leading-edge fish exhibited upregulation of genes associated with xenobiotic defense (e.g., ATP-binding cassette C1 [abcc1], abcc2, abcc6), decreased cell integrity (i.e., macroautophagy and apoptosis; autophagy-related protein 9A [atg9a], caspase 3b [casp3b]), and cholesterol metabolism (e.g., abca1, apolipoprotein A1 [apoa1], sterol O-acyltransferase [soat1]) and downregulation of genes associated with DNA repair (e.g., tumor suppressor p53-binding protein 1 [tp53bp1]) compared to core population sites. Transcriptomic profiles of leading-edge fish were consistent with fish inhabiting a polluted environment and suggest that poorer water quality conditions upstream of the leading edge may represent a non-permanent barrier to silver carp range expansion. The present study provides potential molecular targets for monitoring the physiological status of silver carp over time and in response to future improvements in water quality upstream of their leading edge.
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Affiliation(s)
- Jennifer D Jeffrey
- Department of Natural Resources and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Ken M Jeffries
- Department of Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Cory D Suski
- Department of Natural Resources and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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29
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Lafuente E, Beldade P. Genomics of Developmental Plasticity in Animals. Front Genet 2019; 10:720. [PMID: 31481970 PMCID: PMC6709652 DOI: 10.3389/fgene.2019.00720] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
Developmental plasticity refers to the property by which the same genotype produces distinct phenotypes depending on the environmental conditions under which development takes place. By allowing organisms to produce phenotypes adjusted to the conditions that adults will experience, developmental plasticity can provide the means to cope with environmental heterogeneity. Developmental plasticity can be adaptive and its evolution can be shaped by natural selection. It has also been suggested that developmental plasticity can facilitate adaptation and promote diversification. Here, we summarize current knowledge on the evolution of plasticity and on the impact of plasticity on adaptive evolution, and we identify recent advances and important open questions about the genomics of developmental plasticity in animals. We give special attention to studies using transcriptomics to identify genes whose expression changes across developmental environments and studies using genetic mapping to identify loci that contribute to variation in plasticity and can fuel its evolution.
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Affiliation(s)
| | - Patrícia Beldade
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- CNRS-UMR5174, Université Paul Sabatier, Toulouse, France
- Centre for Ecology, Evolution, and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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30
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Houde ALS, Akbarzadeh A, Günther OP, Li S, Patterson DA, Farrell AP, Hinch SG, Miller KM. Salmonid gene expression biomarkers indicative of physiological responses to changes in salinity and temperature, but not dissolved oxygen. J Exp Biol 2019; 222:jeb198036. [PMID: 31209112 PMCID: PMC6633282 DOI: 10.1242/jeb.198036] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 06/06/2019] [Indexed: 12/27/2022]
Abstract
An organism's ability to respond effectively to environmental change is critical to its survival. Yet, life stage and overall condition can dictate tolerance thresholds to heightened environmental stressors, such that stress may not be equally felt across individuals and at all times. Also, the transcriptional responses induced by environmental changes can reflect both generalized responses as well as others that are highly specific to the type of change being experienced. Thus, if transcriptional biomarkers specific to a stressor, even under multi-stressor conditions, can be identified, the biomarkers could then be applied in natural environments to determine when and where an individual experiences such a stressor. Here, we experimentally challenged juvenile Chinook salmon (Oncorhynchus tshawytscha) to validate candidate gill gene expression biomarkers. A sophisticated experimental design manipulated salinity (freshwater, brackish water and seawater), temperature (10, 14 and 18°C) and dissolved oxygen (normoxia and hypoxia) in all 18 possible combinations for 6 days using separate trials for three smolt statuses (pre-smolt, smolt and de-smolt). In addition, changes in juvenile behaviour, plasma variables, gill Na+/K+-ATPase activity, body size, body morphology and skin pigmentation supplemented the gene expression responses. We identified biomarkers specific to salinity and temperature that transcended the multiple stressors, smolt status and mortality (live, dead and moribund). Similar biomarkers for dissolved oxygen were not identified. This work demonstrates the unique power of gene expression biomarkers to identify a specific stressor even under multi-stressor conditions, and we discuss our next steps for hypoxia biomarkers using an RNA-seq study.
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Affiliation(s)
- Aimee Lee S Houde
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada, V9T 6N7
| | - Arash Akbarzadeh
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada, V9T 6N7
- Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, PO Box 3995, Bandar Abbas, Iran
| | - Oliver P Günther
- Günther Analytics, 402-5775 Hampton Place, Vancouver, BC, Canada, V6T 2G6
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada, V9T 6N7
| | - David A Patterson
- School of Resource and Environmental Management, Fisheries and Oceans Canada, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Anthony P Farrell
- Department of Zoology and Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Scott G Hinch
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada, V9T 6N7
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31
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Huang J, Li Y, Liu Z, Kang Y, Wang J. Transcriptomic responses to heat stress in rainbow trout Oncorhynchus mykiss head kidney. FISH & SHELLFISH IMMUNOLOGY 2018; 82:32-40. [PMID: 30077801 DOI: 10.1016/j.fsi.2018.08.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/24/2018] [Accepted: 08/01/2018] [Indexed: 05/20/2023]
Abstract
Rainbow trout (Oncorhynchus mykiss) are widely cultured throughout the word for commercial aquaculture. However, as a cold-water species, rainbow trout are highly susceptible to heat stress, which may cause pathological signs or diseases by alleviating the immune roles and then lead to mass mortality. Understanding the molecular mechanisms that occur in the rainbow trout in response to heat stress will be useful to decrease heat stress-related morbidity and mortality in trout aquaculture. In the present study, we conducted transcriptome analysis of head kidney tissue in rainbow trout under heat-stress (24 °C) and control (18 °C) conditions, to identify heat stress-induced genes and pathways. More than 281 million clean reads were generated from six head kidney libraries. Using an adjusted P-value of P < 0.05 as the threshold, a total of 443 differentially expressed genes (DEGs) were identified, including members of the HSP90, HSP70, HSP60, and HSP40 family and several cofactors or cochaperones. The RNA-seq results were confirmed by RT-qPCR. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis of DEGs were performed. Many genes involved in maintaining homeostasis or adapting to stress and stimuli were highly induced in response to high temperature. The most significantly enriched pathway was "Protein processing in endoplasmic reticulum (ER)", a quality control system that ensures correct protein folding or degradation of misfolded polypeptides by ER-associated degradation. Other signaling pathways involved in regulation of immune system and post-transcriptional regulation of spliceosome were also critical for thermal adaptation. These findings improve our understanding of the molecular mechanisms of heat stress responses and are useful to develop strategies for the improvement of rainbow trout survival rate during summer high-temperature period.
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Affiliation(s)
- Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yongjuan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China; College of Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Yujun Kang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jianfu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
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32
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Chen XL, Lui EY, Ip YK, Lam SH. RNA sequencing, de novo assembly and differential analysis of the gill transcriptome of freshwater climbing perch Anabas testudineus after 6 days of seawater exposure. JOURNAL OF FISH BIOLOGY 2018; 93:215-228. [PMID: 29931780 DOI: 10.1111/jfb.13653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 05/13/2018] [Indexed: 06/08/2023]
Abstract
To obtain transcriptomic insights into branchial responses to salinity challenge in Anabas testudineus, this study employed RNA sequencing (RNA-Seq) to analyse the gill transcriptome of A. testudineus exposed to seawater (SW) for 6 days compared with the freshwater (FW) control group. A combined FW and SW gill transcriptome was de novo assembled from 169.9 million 101 bp paired-end reads. In silico validation employing 17 A. testudineus Sanger full-length coding sequences showed that 15/17 of them had greater than 80% of their sequences aligned to the de novo assembled contigs where 5/17 had their full-length (100%) aligned and 9/17 had greater than 90% of their sequences aligned. The combined FW and SW gill transcriptome was mapped to 13,780 unique human identifiers at E-value ≤1.0E-20 while 952 and 886 identifiers were determined as up and down-regulated by 1.5 fold, respectively, in the gills of A. testudineus in SW when compared with FW. These genes were found to be associated with at least 23 biological processes. A larger proportion of genes encoding enzymes and transporters associated with molecular transport, energy production, metabolisms were up-regulated, while a larger proportion of genes encoding transmembrane receptors, G-protein coupled receptors, kinases and transcription regulators associated with cell cycle, growth, development, signalling, morphology and gene expression were relatively lower in the gills of A. testudineus in SW when compared with FW. High correlation (R = 0.99) was observed between RNA-Seq data and real-time quantitative PCR validation for 13 selected genes. The transcriptomic sequence information will facilitate development of molecular resources and tools while the findings will provide insights for future studies into branchial iono-osmoregulation and related cellular processes in A. testudineus.
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Affiliation(s)
- Xiu L Chen
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Eei Y Lui
- NUS Environmental Research Institute, National University of Singapore, Singapore
| | - Yuen K Ip
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Siew H Lam
- Department of Biological Sciences, National University of Singapore, Singapore
- NUS Environmental Research Institute, National University of Singapore, Singapore
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33
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Si Y, Wen H, Li Y, He F, Li J, Li S, He H. Liver transcriptome analysis reveals extensive transcriptional plasticity during acclimation to low salinity in Cynoglossus semilaevis. BMC Genomics 2018; 19:464. [PMID: 29914359 PMCID: PMC6006554 DOI: 10.1186/s12864-018-4825-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 05/24/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Salinity is an important abiotic stress that influences the physiological and metabolic activity, reproduction, growth and development of marine fish. It has been suggested that half-smooth tongue sole (Cynoglossus semilaevis), a euryhaline fish species, uses a large amount of energy to maintain osmotic pressure balance when exposed to fluctuations in salinity. To delineate the molecular response of C. semilaevis to different levels of salinity, we performed RNA-seq analysis of the liver to identify the genes and molecular and biological processes involved in responding to salinity changes. RESULTS The present study yielded 330.4 million clean reads, of which 83.9% were successfully mapped to the reference genome of C. semilaevis. One hundred twenty-eight differentially expressed genes (DEGs), including 43 up-regulated genes and 85 down-regulated genes, were identified. These DEGs were highly represented in metabolic pathways, steroid biosynthesis, terpenoid backbone biosynthesis, butanoate metabolism, glycerolipid metabolism and the 2-oxocarboxylic acid metabolism pathway. In addition, genes involved in metabolism, osmoregulation and ion transport, signal transduction, immune response and stress response, and cytoskeleton remodeling were affected during acclimation to low salinity. Genes acat2, fdps, hmgcr, hmgcs1, mvk, pmvk, ebp, lss, dhcr7, and dhcr24 were up-regulated and abat, ddc, acy1 were down-regulated in metabolic pathways. Genes aqp10 and slc6a6 were down-regulated in osmoregulation and ion transport. Genes abat, fdps, hmgcs1, mvk, pmvk and dhcr7 were first reported to be associated with salinity adaptation in teleosts. CONCLUSIONS Our results revealed that metabolic pathways, especially lipid metabolism were important for salinity adaptation. The candidate genes identified from this study provide a basis for further studies to investigate the molecular mechanism of salinity adaptation and transcriptional plasticity in marine fish.
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Affiliation(s)
- Yufeng Si
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, People's Republic of China
| | - Haishen Wen
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, People's Republic of China.
| | - Yun Li
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, People's Republic of China.
| | - Feng He
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, People's Republic of China
| | - Jifang Li
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, People's Republic of China
| | - Siping Li
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, People's Republic of China
| | - Huiwen He
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, People's Republic of China
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Metzger DCH, Schulte PM. Similarities in temperature-dependent gene expression plasticity across timescales in threespine stickleback (Gasterosteus aculeatus). Mol Ecol 2018; 27:2381-2396. [PMID: 29654710 DOI: 10.1111/mec.14591] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/16/2018] [Accepted: 03/26/2018] [Indexed: 12/22/2022]
Abstract
Phenotypic plasticity occurs at a variety of timescales, but little is known about the degree to which plastic responses at different timescales are associated with similar underlying molecular processes, which is critical for assessing the effects of plasticity on evolutionary trajectories. To address this issue, we identified differential gene expression in response to developmental temperature in the muscle transcriptome of adult threespine stickleback (Gasterosteus aculeatus) exposed to 12, 18 and 24°C until hatch and then held at 18°C for 9 months and compared these results to differential gene expression in response to adult thermal acclimation in stickleback developed at 18°C and then acclimated to 5 and 25°C as adults. Adult thermal acclimation affected the expression of 7,940 and 7,015 genes in response to cold and warm acclimation, respectively, and 4,851 of these genes responded in both treatments. In contrast, the expression of only 33 and 29 genes was affected by cold and warm development, respectively. The majority of the genes affected by developmental temperature were also affected by adult acclimation temperature. Many genes that were differentially expressed as a result of adult acclimation were associated with previously identified temperature-dependent effects on DNA methylation patterns, suggesting a role of epigenetic mechanisms in regulating gene expression plasticity during acclimation. Taken together, these results demonstrate similarities between the persistent effects of developmental plasticity on gene expression and the effects of adult thermal acclimation, emphasizing the potential for mechanistic links between plasticity acting at these different life stages.
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Affiliation(s)
- David C H Metzger
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Patricia M Schulte
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. Population Genomics: Advancing Understanding of Nature. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_60] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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