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Barkan R, Cooke I, Watson SA, Strugnell JM. Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis). BMC Genomics 2025; 26:474. [PMID: 40361012 PMCID: PMC12070547 DOI: 10.1186/s12864-025-11680-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Accepted: 05/07/2025] [Indexed: 05/15/2025] Open
Abstract
BACKGROUND As climate change causes marine heat waves to become more intense and frequent, marine species increasingly suffer from heat stress. This stress can result in reduced growth, disrupted breeding cycles, vulnerability to diseases and pathogens, and increased mortality rates. Abalone (genus Haliotis) are an ecologically significant group of marine gastropods and are among the most highly valued seafood products. However, heat stress events have had devastating impacts on both farmed and wild populations. Members of this genus are among the most susceptible marine species to climate change impacts, with over 40% of all abalone species listed as threatened with extinction. This has motivated researchers to explore the genetics linked to heat stress in abalone. A substantial portion of publicly available studies has employed transcriptomic approaches to investigate abalone genetic response to heat stress. However, to date, no meta-analysis has been conducted to determine the common response to heat stress (i.e. the core response) across the genus. This study uses a standardized bioinformatic pipeline to reanalyze and compare publicly available RNA-seq datasets from different heat stress studies on abalone. RESULTS Nine publicly available RNA-seq datasets from nine different heat-stress studies on abalone from seven different abalone species and three hybrids were included in the meta-analysis. We identified a core set of 74 differentially expressed genes (DEGs) in response to heat stress in at least seven out of nine studies. This core set of DEGs mainly included genes associated with alternative splicing, heat shock proteins (HSPs), Ubiquitin-Proteasome System (UPS), and other protein folding and protein processing pathways. CONCLUSIONS The detection of a consistent set of genes that respond to heat stress across various studies, despite differences in experimental design (e.g. stress intensity, species studied-geographical distribution, preferred temperature range, etc.), strengthens our proposal that these genes are key elements of the heat stress response in abalone. The identification of the core response to heat stress in abalone lays an important foundation for future research. Ultimately, this study will aid conservation efforts and aquaculture through the identification of resilient populations, genetic-based breeding programs, possible manipulations such as early exposure to stress, gene editing and the use of immunostimulants to enhance thermal tolerance.
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Affiliation(s)
- Roy Barkan
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia.
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
| | - Ira Cooke
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, Australia
| | - Sue-Ann Watson
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Biodiversity and Geosciences Program, Queensland Museum Tropics, Queensland Museum, Townsville, QLD, Australia
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
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Fuller SA, Abernathy JW, Sankappa NM, Beck BH, Rawles SD, Green BW, Rosentrater KA, McEntire ME, Huskey G, Webster CD. Hepatic transcriptome analyses of juvenile white bass ( Morone chrysops) when fed diets where fish meal is partially or totally replaced by alternative protein sources. Front Physiol 2024; 14:1308690. [PMID: 38288350 PMCID: PMC10822904 DOI: 10.3389/fphys.2023.1308690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/26/2023] [Indexed: 01/31/2024] Open
Abstract
White bass (Morone chrysops) are a popular sportfish throughout the southern United States, and one parent of the commercially-successful hybrid striped bass (M. chrysops ♂ x M. saxatilis ♀). Currently, white bass are cultured using diets formulated for other carnivorous fish, such as largemouth bass (Micropterus salmoides) or hybrid striped bass and contain a significant percentage of marine fish meal. Since there are no studies regarding the utilization of alternative proteins in this species, we evaluated the global gene expression of white bass fed diets in which fish meal was partially or totally replaced by various combinations of soybean meal, poultry by-product meal, canola meal, soy protein concentrate, wheat gluten, or a commercial protein blend (Pro-Cision™). Six isonitrogenous (40% protein), isolipidic (11%), and isocaloric (17.1 kJ/g) diets were formulated to meet the known nutrient and energy requirements of largemouth bass and hybrid striped bass using nutrient availability data for most of the dietary ingredients. One of the test diets consisted exclusively of plant protein sources. Juvenile white bass (40.2 g initial weight) were stocked into a flow-through aquaculture system (three tanks/diet; 10 fish/tank) and fed the test diets twice daily to satiation for 60 days. RNA sequencing and bioinformatic analyses revealed significant differentially expressed genes between all test diets when compared to fish meal control. A total of 1,260 differentially expressed genes were identified, with major ontology relating to cell cycle and metabolic processes as well as immune gene functions. This data will be useful as a resource for future refinements to moronid diet formulation, as marine fish meal becomes limiting and plant ingredients are increasingly added as a reliable protein source.
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Affiliation(s)
- S. Adam Fuller
- USDA-ARS Harry K. Dupree Stuttgart National Aquaculture Research Center (HKDSNARC), Stuttgart, AR, United States
| | - Jason W. Abernathy
- USDA-ARS Aquatic Animal Health Research Unit (AAHRU), Auburn, AL, United States
| | - Nithin Muliya Sankappa
- USDA-ARS Aquatic Animal Health Research Unit (AAHRU), Auburn, AL, United States
- Oak Ridge Institute for Science and Education (ORISE), ARS Research Participation Program, Oak Ridge, TN, United States
| | - Benjamin H. Beck
- USDA-ARS Aquatic Animal Health Research Unit (AAHRU), Auburn, AL, United States
| | - Steven D. Rawles
- USDA-ARS Harry K. Dupree Stuttgart National Aquaculture Research Center (HKDSNARC), Stuttgart, AR, United States
| | - Bartholomew W. Green
- USDA-ARS Harry K. Dupree Stuttgart National Aquaculture Research Center (HKDSNARC), Stuttgart, AR, United States
| | - Kurt A. Rosentrater
- Iowa State University, Agricultural and Biosystems Engineering, Ames, IA, United States
| | - Matthew E. McEntire
- USDA-ARS Harry K. Dupree Stuttgart National Aquaculture Research Center (HKDSNARC), Stuttgart, AR, United States
| | - George Huskey
- USDA-ARS Harry K. Dupree Stuttgart National Aquaculture Research Center (HKDSNARC), Stuttgart, AR, United States
| | - Carl D. Webster
- USDA-ARS Harry K. Dupree Stuttgart National Aquaculture Research Center (HKDSNARC), Stuttgart, AR, United States
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Seo JW, Ham DY, Lee JG, Kim MJ, Yu CY, Seong ES. The effect of different LED wavelengths on the components and biosynthesis of isoflavonoid in sprout Astragalus membranaceus. PROTOPLASMA 2024; 261:103-110. [PMID: 37524894 DOI: 10.1007/s00709-023-01883-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/14/2023] [Indexed: 08/02/2023]
Abstract
An artificial light source is the optimal element for studying the usability of the medicinal plant Astragalus membranaceus as a sprout vegetable. Based on artificial light source conditions, formononetin (FO) level was the highest (2.6 mg/L) in A. membranaceus exposed to white light emitting diode (LED) light, and calycosin (CA) level was the highest (3.09 mg/L) in the plant exposed to red LED light. According to the publicly available transcriptome data of LED-exposed sprout A. membranaceus LED, reference genes related to the content enhancement of FO, an isoflavone compound, and those related to the content enhancement of CA were selected. The expression patterns of these genes were assayed using qPCR. Among the genes related to FO enhancement, Gene-225190T showed the highest mRNA levels in cells of LED-white light-exposed sprout A. membranaceus; among the genes related to CA enhancement, Gene_042770T showed the highest expression under red LED light. Most genes related to the overall biosynthesis regulation of flavonoids of the upper concept of isoflavone were highly expressed in response to red LED light, and the transcriptional level of 4CL in response to red LED light was the highest. Based on these results, the artificial light sources that regulated the FO and CA contents in sprouts A. membranaceus were white and red LED lights, and the selected reference genes were capable of regulating isoflavone biosynthesis.
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Affiliation(s)
- Ji Won Seo
- Interdisciplinary Program in Smart Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Da Ye Ham
- Interdisciplinary Program in Smart Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Jae Geun Lee
- Research Institute of Biotechnology, Hwajinbiocosmetic, Chuncheon, 24232, Republic of Korea
| | - Myong Jo Kim
- Division of Bioresource Sciences, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Chang Yeon Yu
- Division of Bioresource Sciences, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Eun Soo Seong
- Division of Bioresource Sciences, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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Gurr SJ, Trigg SA, Vadopalas B, Roberts SB, Putnam HM. Acclimatory gene expression of primed clams enhances robustness to elevated pCO 2. Mol Ecol 2022; 31:5005-5023. [PMID: 35947503 DOI: 10.1111/mec.16644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022]
Abstract
Sub-lethal exposure to environmental challenges may enhance ability to cope with chronic or repeated change, a process known as priming. In a previous study, pre-exposure to seawater enriched with pCO2 improved growth and reduced antioxidant capacity of juvenile Pacific geoduck Panopea generosa, suggesting that transcriptional shifts may drive phenotypic modifications post-priming. To this end, juvenile clams were sampled and TagSeq gene expression data analyzed after 1) a 110-day acclimation under ambient (921 μatm, naïve) and moderately-elevated pCO2 (2870 μatm, pre-exposed); then following 2) a second 7-day exposure to three pCO2 treatments (ambient: 754 μatm; moderately-elevated: 2750 μatm; severely-elevated: 4940 μatm), a 7-day return to ambient pCO2 , and a third 7-day exposure to two pCO2 treatments (ambient: 967 μatm; moderately-elevated: 3030 μatm). Pre-exposed geoducks frontloaded genes for stress and apoptosis/innate immune response, homeostatic processes, protein degradation, and transcriptional modifiers. Pre-exposed geoducks were also responsive to subsequent encounters, with gene sets enriched for mitochondrial recycling and immune defense under elevated pCO2 and energy metabolism and biosynthesis under ambient recovery. In contrast, gene sets with higher expression in naïve clams were enriched for fatty-acid degradation and glutathione components, suggesting naïve clams could be depleting endogenous fuels, with unsustainable energetic requirements if changes in carbonate chemistry persist. Collectively, our transcriptomic data indicates pCO2 priming during post-larval periods could, via gene expression regulation, enhance robustness in bivalves to environmental change. Such priming approaches may be beneficial for aquaculture, as seafood demand intensifies concurrent with increasing climate change in marine systems.
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Affiliation(s)
- Samuel J Gurr
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Shelly A Trigg
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA, USA
| | | | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
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Pedler RL, Harris JO, Thomson NL, Buss JJ, Stone DAJ, Handlinger JH. Development of a semi-quantitative scoring protocol for gill lesion assessment in greenlip abalone Haliotis laevigata held at elevated water temperature. DISEASES OF AQUATIC ORGANISMS 2022; 150:37-51. [PMID: 35796510 DOI: 10.3354/dao03673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Water temperatures that exceed thermal optimal ranges (~19 to 22°C for greenlip abalone Haliotis laevigata, depending on stock genetics) can be associated with abalone mortalities. We assessed histopathological changes in H. laevigata gills held in control (22°C) or elevated (25°C) water temperature conditions for 47 d by developing a new scoring protocol that incorporates histopathological descriptions and relative score summary. Lesions were allocated to 1 of 3 reaction patterns, (1) epithelial, (2) circulatory or (3) inflammatory, and scored based on their prevalence in gill leaflets. Indices for each reaction pattern were calculated and combined to provide an overall gill index. H. laevigata held in 25°C water temperature had significantly more epithelial lifting and hemolymph channel enlargement and significantly higher gill and circulatory reaction pattern indices than H. laevigata held in 22°C water temperature. One H. laevigata had a proliferation of unidentified cells in the v-shaped skeletal rod of a gill leaflet. The unidentified cells contained enlarged nuclei, a greater nucleus:cytoplasm ratio and, in some cases, mitotic figures. This cell population could represent a region of hematopoiesis in response to hemocyte loss or migration to a lesion. Without thorough diagnostic testing, the origin of these larger cells cannot be confirmed. The new scoring protocol developed will allow the standard quantification of gill lesions for H. laevigata, specifically for heat-related conditions, and could further be adapted for other Haliotis spp.
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Affiliation(s)
- R L Pedler
- College of Science and Engineering, Flinders University, Bedford Park, 5042 South Australia, Australia
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Nguyen TV, Alfaro A, Frost E, Chen D, Beale DJ, Mundy C. Investigating the biochemical effects of heat stress and sample quenching approach on the metabolic profiling of abalone (Haliotis iris). Metabolomics 2021; 18:7. [PMID: 34958425 DOI: 10.1007/s11306-021-01862-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Ocean temperatures have been consistently increasing due to climate change, and the frequency of heatwave events on shellfish quality is a growing concern worldwide. Typically, shellfish growing areas are in remote or difficult to access locations which makes in-field sampling and sample preservation of shellfish heat stress difficult. As such, there is a need to investigate in-field sampling approaches that facilitate the study of heat stress in shellfish. OBJECTIVES This study aims to apply a gas chromatography-mass spectrometry (GC-MS) based metabolomics approach to examine molecular mechanisms of heat stress responses in shellfish using abalone as a model, and compare the effects of different quenching protocols on abalone metabolic profiles. METHODS Twenty adult Haliotis iris abalone were exposed to two temperatures (14 °C and 24 °C) for 24 h. Then, haemolymph and muscle tissues of each animal were sampled and quenched with 4 different protocols (liquid nitrogen, dry ice, cold methanol solution and normal ice) which were analyzed via GC-MS for central carbon metabolites. RESULTS The effects of different quenching protocols were only observed in muscle tissues in which the cold methanol solution and normal ice caused some changes in the observed metabolic profiles, compared to dry ice and liquid nitrogen. Abalone muscle tissues were less affected by thermal stress than haemolymph. There were 10 and 46 compounds significantly influenced by thermal stress in muscle and haemolymph, respectively. The changes of these metabolite signatures indicate oxidative damage, disturbance of amino acid and fatty acid metabolism, and a shift from aerobic metabolism to anaerobic pathways. CONCLUSIONS The study provided insights into the heat response of abalone, which could be useful for understanding the effects of marine heatwaves and summer mortality events on abalone. Dry ice appeared to be a suitable protocol, and safer in-field alternative to liquid nitrogen, for quenching of abalone tissues.
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Affiliation(s)
- Thao V Nguyen
- Aquaculture Biotechnology Research Group, Faculty of Health and Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Andrea Alfaro
- Aquaculture Biotechnology Research Group, Faculty of Health and Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand.
| | - Emily Frost
- Aquaculture Biotechnology Research Group, Faculty of Health and Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Donglin Chen
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecoscience Precinct, Dutton Park, QLD, Australia
| | - Craig Mundy
- IMAS Fisheries and Aquaculture Centre, College of Science and Engineering, University of Tasmania, Taroona, TAS, Australia
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Tripp-Valdez MA, Cicala F, Galindo-Sánchez CE, Chacón-Ponce KD, López-Landavery E, Díaz F, Re-Araujo D, Lafarga-De la Cruz F. Growth Performance and Transcriptomic Response of Warm-Acclimated Hybrid Abalone Haliotis rufescens (♀) × H. corrugata (♂). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:62-76. [PMID: 33040235 DOI: 10.1007/s10126-020-10002-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 09/28/2020] [Indexed: 06/11/2023]
Abstract
Along the Pacific coast of the Baja California Peninsula (Mexico), abalone represents one of the most lucrative fisheries. As wild populations are currently depleted, abalone farm production aims to balance the decreasing populations with the increasing demand. The Mexican abalone aquaculture is almost entirely based on red abalone (Haliotis rufescens). However, the increasing frequency of extreme temperature events is hampering this activity. The use interspecific hybrids can potentially improve abalone culture, as species have differences in their thermal tolerance. Therefore, the hybrid progeny between H. rufescens (♀) and pink abalone H. corrugata (♂), a temperate and a warmer water abalone species, respectively, will naturally support higher temperature. To test this hypothesis, growth rate, mortality and metabolic rate of both pure (RR) and hybrid abalone (RP) were assessed under the H. rufescens' optimum (18 °C) and thermally stressed (22 °C) conditions. To unveil the molecular pathways involved in the heat response, transcriptional profiling of both crosses was also investigated. At high temperature, we observed constrained growth and survival in RR while RP showed a significant increase in both rates, supporting the improved performance of the hybrid compared. These results match with the transcriptional profiling of hybrids showing higher expression of genes involved in growth and calcification, whereas in the pure red progeny, the transcriptional profile was mainly associated with the regulation of necroptosis process. Our results may contribute to propose new management plans to increase farm abalone production in Baja California.
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Affiliation(s)
- M A Tripp-Valdez
- Departamento de Acuicultura, Centro de Investigación Científica y de Educación Superior de Ensenada, B. C. Carretera Tijuana-Ensenada 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | - F Cicala
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, B. C. Carretera Tijuana-Ensenada 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | - C E Galindo-Sánchez
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, B. C. Carretera Tijuana-Ensenada 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | - K D Chacón-Ponce
- Departamento de Acuicultura, Centro de Investigación Científica y de Educación Superior de Ensenada, B. C. Carretera Tijuana-Ensenada 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | - E López-Landavery
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, B. C. Carretera Tijuana-Ensenada 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | - F Díaz
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, B. C. Carretera Tijuana-Ensenada 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | - D Re-Araujo
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, B. C. Carretera Tijuana-Ensenada 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | - F Lafarga-De la Cruz
- Departamento de Acuicultura, Centro de Investigación Científica y de Educación Superior de Ensenada, B. C. Carretera Tijuana-Ensenada 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, Baja California, Mexico.
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Zhu ZX, Jiang DL, Li BJ, Qin H, Meng ZN, Lin HR, Xia JH. Differential Transcriptomic and Metabolomic Responses in the Liver of Nile Tilapia (Oreochromis niloticus) Exposed to Acute Ammonia. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:488-502. [PMID: 31076921 DOI: 10.1007/s10126-019-09897-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
Ammonia is toxic to aquatic animal. Currently, only limited works were reported on the responses of aquatic animals after ammonia exposure using "omics" technologies. Tilapia suffers from the stress of ammonia-nitrogen during intensive recirculating aquaculture. Optimizing ammonia stress tolerance has become an important issue in tilapia breeding. The molecular and biochemical mechanisms of ammonia-nitrogen toxicity have not been understood comprehensively in tilapia yet. In this study, using RNA-seq and gas chromatograph system coupled with a Pegasus HT time-of-flight mass spectrometer (GC-TOF-MS) techniques, we investigated differential expressed genes (DEGs) and metabolomes in the liver at 6 h post-challenges (6 hpc) and 24 h post-challenges (24 hpc) under high concentration of ammonia-nitrogen treatment. We detected 2258 DEGs at 6 hpc and 315 DEGs at 24 hpc. Functional enrichment analysis indicated that DEGs were significantly associated with cholesterol biosynthesis, steroid and lipid metabolism, energy conservation, and mitochondrial tissue organization. Metabolomic analysis detected 31 and 36 metabolites showing significant responses to ammonia-nitrogen stress at 6 and 24 hpc, respectively. D-(Glycerol 1-phosphate), fumaric acid, and L-malic acid were found significantly down-regulated at both 6 and 24 hpc. The integrative analysis of transcriptomics and metabolomics suggested considerable alterations and precise control of gene expression at both physiological and molecular levels in response to the stress of ammonia-nitrogen in tilapia.
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Affiliation(s)
- Zong Xian Zhu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Dan Li Jiang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Hui Qin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Zi Ning Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China.
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Tripp-Valdez MA, Harms L, Pörtner HO, Sicard MT, Lucassen M. De novo transcriptome assembly and gene expression profile of thermally challenged green abalone (Haliotis fulgens: Gastropoda) under acute hypoxia and hypercapnia. Mar Genomics 2019; 45:48-56. [DOI: 10.1016/j.margen.2019.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/25/2019] [Accepted: 01/26/2019] [Indexed: 12/19/2022]
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Silliman K. Population structure, genetic connectivity, and adaptation in the Olympia oyster ( Ostrea lurida) along the west coast of North America. Evol Appl 2019; 12:923-939. [PMID: 31080505 PMCID: PMC6503834 DOI: 10.1111/eva.12766] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/28/2018] [Accepted: 12/02/2018] [Indexed: 01/02/2023] Open
Abstract
Effective management of threatened and exploited species requires an understanding of both the genetic connectivity among populations and local adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from Baja California to the central coast of Canada, has a long history of population declines due to anthropogenic stressors. For such coastal marine species, population structure could follow a continuous isolation-by-distance model, contain regional blocks of genetic similarity separated by barriers to gene flow, or be consistent with a null model of no population structure. To distinguish between these hypotheses in O. lurida, 13,424 single nucleotide polymorphisms (SNPs) were used to characterize rangewide population structure, genetic connectivity, and adaptive divergence. Samples were collected across the species range on the west coast of North America, from southern California to Vancouver Island. A conservative approach for detecting putative loci under selection identified 235 SNPs across 129 GBS loci, which were functionally annotated and analyzed separately from the remaining neutral loci. While strong population structure was observed on a regional scale in both neutral and outlier markers, neutral markers had greater power to detect fine-scale structure. Geographic regions of reduced gene flow aligned with known marine biogeographic barriers, such as Cape Mendocino, Monterey Bay, and the currents around Cape Flattery. The outlier loci identified as under putative selection included genes involved in developmental regulation, sensory information processing, energy metabolism, immune response, and muscle contraction. These loci are excellent candidates for future research and may provide targets for genetic monitoring programs. Beyond specific applications for restoration and management of the Olympia oyster, this study lends to the growing body of evidence for both population structure and adaptive differentiation across a range of marine species exhibiting the potential for panmixia. Computational notebooks are available to facilitate reproducibility and future open-sourced research on the population structure of O. lurida.
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Chen N, Huang Z, Lu C, Shen Y, Luo X, Ke C, You W. Different Transcriptomic Responses to Thermal Stress in Heat-Tolerant and Heat-Sensitive Pacific Abalones Indicated by Cardiac Performance. Front Physiol 2019; 9:1895. [PMID: 30687115 PMCID: PMC6334008 DOI: 10.3389/fphys.2018.01895] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022] Open
Abstract
The Pacific abalone Haliotis discus hannai is one of the most economically important mollusks in China. Even though it has been farmed in southern China for almost 20 years, summer mortality remains the most challengeable problem for Pacific abalone aquaculture recently. Here, we determined the different heat tolerance ability for five selective lines of H. discus hannai by measuring the cardiac performance and Arrhenius breakpoint temperature (ABT). The Red line (RL) and Yangxia line (YL) were determined as the most heat-sensitive and most heat-tolerant line, respectively. Heart rates for RL were significantly lower than those of the YL at the same temperature (p < 0.05). The differentially expressed genes (DEGs), which were enriched in several pathways including cardiac muscle contraction, glutathione metabolism and oxidative phosphorylation, were identified between RL and YL at control temperature (20°C) and heat stress temperature (28.5°C, the ABT of the RL) by RNA-seq method. In the RL, 3370 DEGs were identified between the control and the heat-stress temperature, while only 1351 DEGs were identified in YL between these two temperature tests. Most of these DEGs were enriched in the pathways such as protein processing in endoplasmic reticulum, nucleotide binding and oligomerization domain (NOD) like receptor signaling, and ubiquitin mediated proteolysis. Notably, the most heat-tolerant line YL used an effective heat-protection strategy based on moderate transcriptional changes and regulation on the expression of key genes.
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Affiliation(s)
- Nan Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Chengkuan Lu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yawei Shen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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12
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Fang Z, Sun Y, Zhang X, Wang G, Li Y, Wang Y, Zhang Z. Responses of HSP70 Gene to Vibrio parahaemolyticus Infection and Thermal Stress and Its Transcriptional Regulation Analysis in Haliotis diversicolor. Molecules 2019; 24:E162. [PMID: 30609869 PMCID: PMC6337134 DOI: 10.3390/molecules24010162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/04/2018] [Accepted: 12/17/2018] [Indexed: 02/08/2023] Open
Abstract
Heat-shock protein 70 (HSP70) is a molecular chaperone that plays critical roles in cell protein folding and metabolism, which helps to protect cells from unfavorable environmental stress. Haliotis diversicolor is one of the most important economic breeding species in the coastal provinces of south China. To date, the expression and transcriptional regulation of HSP70 in Haliotis diversicolor (HdHSP70) has not been well characterized. In this study, the expression levels of HdHSP70 gene in different tissues and different stress conditions were detected. The results showed that the HdHSP70 gene was ubiquitously expressed in sampled tissues and was the highest in hepatopancreas, followed by hemocytes. In hepatopancreas and hemocytes, the HdHSP70 gene was significantly up-regulated by Vibrio parahaemolyticus infection, thermal stress, and combined stress (Vibrio parahaemolyticus infection and thermal stress combination), indicating that HdHSP70 is involved in the stress response and the regulation of innate immunity. Furthermore, a 2383 bp of 5'-flanking region sequence of the HdHSP70 gene was cloned, and it contains a presumed core promoter region, a CpG island, a (TG)39 simple sequence repeat (SSR), and many potential transcription factor binding sites. The activity of HdHSP70 promoter was evaluated by driving the expression of luciferase gene in HEK293FT cells. A series of experimental results indicated that the core promoter region is located between -189 bp and +46 bp, and high-temperature stress can increase the activity of HdHSP70 promoter. Sequence-consecutive deletions of the luciferase reporter gene in HEK293FT cells revealed two possible promoter activity regions. To further identify the binding site of the key transcription factor in the two regions, two expression vectors with site-directed mutation were constructed. The results showed that the transcriptional activity of NF-1 site-directed mutation was significantly increased (p < 0.05), whereas the transcriptional activity of NF-κB site-directed mutation was significantly reduced. These results suggest that NF-1 and NF-κB may be two important transcription factors that regulate the expression of HdHSP70 gene.
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Affiliation(s)
- Zhiqiang Fang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China.
| | - Yulong Sun
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xin Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Guodong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China.
| | - Yuting Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China.
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China.
| | - Ziping Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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13
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Sandoval‐Castillo J, Robinson NA, Hart AM, Strain LWS, Beheregaray LB. Seascape genomics reveals adaptive divergence in a connected and commercially important mollusc, the greenlip abalone (
Haliotis laevigata
), along a longitudinal environmental gradient. Mol Ecol 2018; 27:1603-1620. [DOI: 10.1111/mec.14526] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 12/05/2017] [Accepted: 12/15/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Jonathan Sandoval‐Castillo
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide SA Australia
| | - Nick A. Robinson
- Nofima Ås Norway
- Sustainable Aquaculture Laboratory School of BioSciences University of Melbourne Parkville Vic Australia
| | - Anthony M. Hart
- Western Australian Fisheries and Marine Research Laboratories Department of Fisheries Western Australia Hillarys WA Australia
| | - Lachlan W. S. Strain
- Western Australian Fisheries and Marine Research Laboratories Department of Fisheries Western Australia Hillarys WA Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide SA Australia
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