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Kim DH, Kim MS, Lee JS, Yoon DS, Lee JS. Genome-wide identification of 769 G protein-coupled receptor (GPCR) genes from the marine medaka Oryzias melastigma. MARINE POLLUTION BULLETIN 2024; 207:116868. [PMID: 39173477 DOI: 10.1016/j.marpolbul.2024.116868] [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: 06/18/2024] [Revised: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024]
Abstract
The marine medaka Oryzias melastigma is a useful fish model for marine and estuarine ecotoxicology studies and can be applied to field-based population genomics because of its distribution in Asian estuaries and other coastal areas. We identified 769 full-length G protein-coupled receptor genes in the O. melastigma genome and classified them into five distinct classes. A phylogenetic comparison of GPCR genes in O. melastigma to humans and two other small fish species revealed a high-level orthological relationship. Purinergic and chemokine receptors were highly differentiated in humans whereas significant differentiation of chemosensory receptors was evident in fish species. Our results suggest that the GPCR gene families among the species used in this study exhibit evidence of sporadic evolutionary processes. These results may help improve our understanding of the advanced repertoires of GPCR and expand our knowledge of physiological mechanisms of fish in response to various environmental stimuli.
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Affiliation(s)
- Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jin-Sol Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Deok-Seo Yoon
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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2
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Zeb R, Yin X, Chen F, Wang KJ. Sex-specific divergent responses of marine medaka (Oryzias melastigma) towards long-term benzo[a]pyrene exposure revealed stronger resilience and recoverability in female fish. CHEMOSPHERE 2024; 364:143077. [PMID: 39134182 DOI: 10.1016/j.chemosphere.2024.143077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 07/29/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024]
Abstract
Benzo[a]pyrene (BaP), a representative five-membered polycyclic aromatic hydrocarbon, has been extensively studied as a pollutant for decades. Despite this, sex-specific responses to BaP exposure remain poorly understood. This study employed a life-cycle exposure approach to investigate the effects of prolonged BaP exposure on marine medaka (Oryzias melastigma), highlighting sex-specific responses. After a 90-day exposure period, significant variations in biometric measurements and oxidative stress markers were observed between male and female fish. BaP exposure resulted in weak detoxification defense in males, while females exhibited an opposite response. Transcriptomic analysis revealed 13 significantly enriched pathways in males and 11 in females, with varying numbers of differentially expressed genes between the sexes, highlighting distinct biological responses. Host resistance assay showed higher mortality rates among BaP-exposed males, and suppressed immune gene expressions and lysozyme activity, while females demonstrated enhanced immune genes and lysozyme activity post-challenge, indicating a more resilient defense response. Furthermore, after a one-month depuration period following BaP exposure, male medaka demonstrated slower recoverability compared to females. These findings underscore sex-specific effects of BaP exposure on fish, with females displaying stronger resilience. Understanding these distinctions are crucial for accurately assessing the impact of environmental pollutants on the aquatic population and ecosystem maintenance.
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Affiliation(s)
- Rabia Zeb
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China.
| | - Xiaohan Yin
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China.
| | - Fangyi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China.
| | - Ke-Jian Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China.
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3
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Liu M, Li J, Li J, Zhou B, Lam PKS, Hu C, Chen L. Developmental cardiotoxicity of 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT) in marine medaka (Oryzias melastigma). JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133176. [PMID: 38070264 DOI: 10.1016/j.jhazmat.2023.133176] [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: 10/17/2023] [Revised: 11/15/2023] [Accepted: 12/02/2023] [Indexed: 02/08/2024]
Abstract
The application of 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT) as an antifouling biocide causes high toxicity to non-target marine organisms. To examine the developmental cardiotoxicity and mechanisms of DCOIT, we concurrently performed sub-chronic exposure and life-cycle exposure experiments using marine medaka embryos. After sub-chronic exposure to DCOIT at 1, 3, 10, and 33 μg/L, cardiac defects were caused by upregulation of cardiac gene transcriptions, decreasing heart size, and accelerating heartbeat. Hyperthyroidism in medaka larvae was identified as the cause of developmental cardiotoxicity of DCOIT sub-chronic exposure. In addition, parental life-cycle exposure to 1, 3, and 10 μg/L DCOIT led to transgenerational impairment of cardiogenesis in offspring medaka. A crossbreeding strategy discriminated a concentration-dependent mechanism of transgenerational cardiotoxicity. At 1 μg/L, the DCOIT-exposed female parent transferred a significantly higher amount of triiodothyronine (T3) hormone to offspring, corresponding to an accelerated heart rate. However, DCOIT at higher exposure concentrations modified the methylome imprinting in larval offspring, which was associated with cardiac dysfunction. Overall, the findings provide novel insights into the developmental cardiotoxicity of DCOIT. The high risks of DCOIT-even at environmentally realistic concentrations-raise concerns about its applicability as an antifoulant in a marine environment.
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Affiliation(s)
- Mengyuan Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiali Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingsheng Zhou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Paul K S Lam
- Department of Science, School of Science and Technology, Hong Kong Metropolitan University, Kowloon, Hong Kong, China
| | - Chenyan Hu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430072, China
| | - Lianguo Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Li X, Luo J, Han C, Lu X. Nanoplastics enhance the intestinal damage and genotoxicity of sulfamethoxazole to medaka juveniles (Oryzias melastigma) in coastal environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 894:164943. [PMID: 37329919 DOI: 10.1016/j.scitotenv.2023.164943] [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: 04/10/2023] [Revised: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
Antibiotics and nanoplastics are widely detected in the coastal ecosystem. However, the transcriptome mechanism elucidating the effect of antibiotics and nanoplastics co-exposure on the gene expression of aquatic organisms in coastal environment is still unclear. Here, single and joint effects of sulfamethoxazole (SMX) and polystyrene nanoplastics (PS-NPs) on the intestinal health and gene expression of medaka juveniles (Oryzias melastigma), which live in coastal environment, were investigated. The SMX and PS-NPs co-exposure decreased intestinal microbiota diversity compared to the PS-NPs, and caused more adverse effect on the intestinal microbiota composition and intestinal damage compared to the SMX, indicating that PS-NPs might enhance the toxicity of SMX on the medaka intestine. The increased abundance of Proteobacteria in the intestine was observed in the co-exposure group, which might induce the intestinal epithelium damage. In addition, the differentially expressed genes (DEGs) were mainly involved in the drug metabolism-other enzymes, drug metabolism-cytochrome P450, metabolism of xenobiotics by cytochrome P450 pathways in visceral tissue after the co-exposure. The expression of the host immune system genes (e.g., ifi30) could be associated with the increased pathogens in intestinal microbiota. This study is useful for understanding the toxicity effect of antibiotics and NPs on aquatic organisms in coastal ecosystem.
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Affiliation(s)
- Xue Li
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jiwei Luo
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou 570228, China
| | - Chenglong Han
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xueqiang Lu
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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5
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Liu QY, Chen ZM, Li DW, Li AF, Ji Y, Li HY, Yang WD. Toxicity and potential underlying mechanism of Karenia selliformis to the fish Oryzias melastigma. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 262:106643. [PMID: 37549486 DOI: 10.1016/j.aquatox.2023.106643] [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: 05/09/2023] [Revised: 07/18/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023]
Abstract
Karenia selliformis can produce toxins such as gymnodimines, and form microalgal blooms causing massive mortality of marine life such as fish and shellfish, and resulting in serious economic losses. However, there are a few of studies on the toxic effects of K. selliformis on marine organisms and the underlying mechanisms, and it is not clear whether the toxins produced by K. selliformis affect fish survival through the food chain. In this study, a food chain was simulated and composed by K. selliformis-brine shrimp-marine medaka to investigate the possibility of K. selliformis toxicity transmission through the food chain, in which fish behavior, histopathology and transcriptomics changes were observed after direct or indirect exposure (through the food chain) of K. selliformis. We found that both direct and indirect exposure of K. selliformis could affect the swimming behavior of medaka, manifested as decreased swimming performance and increased "frozen events". Meanwhile, exposure to K. selliformis caused pathological damage to the intestine and liver tissues of medaka to different degree. The effect of direct exposure to K. selliformis on swimming behavior and damage to fish tissues was more severe. In addition, K. selliformis exposure induced significant changes in the expression of genes related to energy metabolism, metabolic detoxification and immune system in medaka. These results suggest that toxins produced by K. selliformis can be transferred through the food chain, and that K. selliformis can destroy the intestinal integrity of medaka and increase the absorption of toxins, leading to energy metabolism disorders in fish, affecting the metabolic detoxification capacity of the liver. Our finding provides novel insight into the toxicity of K. selliformis to marine fish.
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Affiliation(s)
- Qin-Yuan Liu
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Zi-Min Chen
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Da-Wei Li
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Ai-Feng Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Ying Ji
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Hong-Ye Li
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Wei-Dong Yang
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China.
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6
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Huang Z, Gao J, Chen Y, Huan Z, Liu Y, Zhou T, Dong Z. Toxic effects of bisphenol AF on the embryonic development of marine medaka (Oryzias melastigma). ENVIRONMENTAL TOXICOLOGY 2023; 38:1445-1454. [PMID: 36929865 DOI: 10.1002/tox.23779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/01/2023] [Accepted: 03/05/2023] [Indexed: 05/18/2023]
Abstract
Bisphenol AF (BPAF), an emerging environmental endocrine disruptor, has been detected in surface waters worldwide and has adverse effects on aquatic organisms. The accumulation of BPAF in oceans and its potential toxic effect on marine organisms are important concerns. In this study, the effects of BPAF (10, 100, 1, and 5 mg/L) on marine medaka (Oryzias melastigma) were evaluated, including effects on the survival rate, heart rate, hatchability, morphology, and gene expression in embryos. The survival rate of marine medaka embryos was significantly lower after treatment with 5 mg/L BPAF than in the solvent control group. Exposure to 1 mg/L and 5 mg/L BPAF significantly reduced hatchability. Low-dose BPAF (10 μg/L) significantly accelerated the heart rate of embryos, while high-dose BPAF (5 mg/L) significantly decreased the heart rate. BPAF exposure also resulted in notochord curvature, pericardial edema, yolk sac cysts, cardiovascular bleeding, and caudal curvature in marine medaka. At the molecular level, BPAF exposure affected the transcript levels of genes involved in the thyroid system (dio1, dio3a, trhr2, tg, and thra), cardiovascular system (gata4, atp2a1, and cacna1da), nervous system (elavl3 and gap43), and antioxidant and inflammatory systems (sod, pparβ, and il-8) in embryos. These results indicate that BPAF exposure can alter the expression of functional genes, induce abnormal development, and reduce the hatching and survival rates in marine medaka embryos. Overall, BPAF can adversely affect the survival and development of marine medaka embryos, and BPAF may not be an ideal substitute for BPA.
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Affiliation(s)
- Zeyin Huang
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, China
| | - Jiahao Gao
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, China
| | - Yuebi Chen
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, China
| | - Zhang Huan
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, China
| | - Yue Liu
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, China
| | - Tianyang Zhou
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, China
| | - Zhongdian Dong
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang, China
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7
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Wang Y, Guo J, Jia X, Luo X, Zhou Y, Mao X, Fan X, Hu H, Zhu H, Jia C, Guo X, Cheng L, Li X, Zhang Z. Genome and transcriptome of Chinese medaka (Oryzias sinensis) and its uses as a model fish for evaluating estrogenicity of surface water. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120724. [PMID: 36427818 DOI: 10.1016/j.envpol.2022.120724] [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: 07/21/2022] [Revised: 11/13/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Ecological toxicity assessments of contaminants in aquatic environments are of great concern. However, a dilemma in ecological toxicity assessments often arises when linking the effects found in model animals in the laboratory and the phenomena observed in wild fishes in the field due to species differences. Chinese medaka (Oryzias sinensis), widely distributed in East Asia, is a satisfactory model animal to assess aquatic environment in China. Here, we domesticated this species and assembled its genome (814 Mb) using next-generation sequencing (NGS). A total of 21,922 high-confidence genes with 41,306 transcripts were obtained and annotated, and their expression patterns in tissues were determined by RNA-sequencing. Six mostly sensitive biomarker genes, including vtg1, vtg3, vtg6, zp3a.2, zp2l1, and zp2.3 to estrogen exposure were screened and validated in the fish exposed to concentrations of estrone (E1), 17β-estradiol (E2), and estriol (E3) under laboratory condition. Field investigations were then performed to evaluating the gene expression of biomarkers in wild Chinese medaka and levels of E1, E2, and E3 in the fish habitats. It was found that in 40 sampling sites, the biomarker genes were obviously highly expressed in the wild fish from about half sites, and the detection frequencies of E1, E2, and E3, were 97.5%, 42.5%, and 45% with mean concentrations of 82.48, 43.17, 52.69 ng/L, respectively. Correlation analyses of the biomarker gene expressions in the fish with the estrogens levels which were converted to EEQs showed good correlation, indicating that the environmental estrogens and estrogenicity of the surface water might adversely affect wild fishes. Finally, histologic examination of gonads in male wild Chinese medaka was performed and found the presence of intersex in the fish. This study facilitated the uses of Chinese medaka as a model animal for ecotoxicological studies.
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Affiliation(s)
- Yue Wang
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Jilong Guo
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Xiaojing Jia
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Xiaozhe Luo
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Ying Zhou
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Xingtai Mao
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Xiaolin Fan
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Hongxia Hu
- Fisheries Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100068, China
| | - Hua Zhu
- Fisheries Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100068, China
| | - Chengxia Jia
- Fisheries Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100068, China
| | - Xuan Guo
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Lan Cheng
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Xiqing Li
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Zhaobin Zhang
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China.
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Ye Z, Huang L, Zhao Q, Zhang W, Zhang L. Key genes for arsenobetaine synthesis in marine medaka (Oryzias melastigma) by transcriptomics. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 253:106349. [PMID: 36395554 DOI: 10.1016/j.aquatox.2022.106349] [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: 10/04/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Marine fish undergo detoxification to overcome As stress, forming non-toxic metabolites arsenobetaine (AsB). Genes associated with AsB synthesis remain unknown. Therefore, in this study, we explored the key genes involved in the synthesis of AsB by transcriptomic analysis in marine medaka (Oryzias melastigma), and then screened candidate genes related to AsB synthesis. In the liver, 40 genes were up-regulated and 23 genes were down-regulated, whereas in muscle, 83 genes were up-regulated and 331 genes were down-regulated. We revealed that bhmt, mat2aa, and gstt1a can play a significant role in the glutathione and methionine metabolic pathway. These three genes can affect the conversion of arsenocholine (AsC) to AsB by the vitro gene transformation experiments of E. coli BL21(DE3). E. coli BL21-bhmt overexpressing bhmt resulted in more oxidation of precursor AsC to AsB. Furthermore, the AsB concentration was decreased after E. coli BL21 overexpressing mat2aa and gstt1a, which were down-regulated in marine medaka. Therefore, we concluded that bhmt, mat2aa, and gstt1a are involved in AsB synthesis. Overall, this is the first report on transcriptome screening and identification of key genes for AsB synthesis in marine medaka. We provided important insights to reveal the mystery of AsB synthesis in marine fish.
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Affiliation(s)
- Zijun Ye
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Liping Huang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Qianyu Zhao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Wei Zhang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China.
| | - Li Zhang
- Key laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
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9
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Wang M, Wang WX. Meeting Zn Needs during Medaka Eye Development: Nanoscale Visualization of Retina by Expansion Microscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15780-15790. [PMID: 36266765 DOI: 10.1021/acs.est.2c06479] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fish eyes require high Zn levels to support their early development. Although numerous studies have been conducted on the nutritional and toxic effects of Zn on the eye, the Zn requirement for retinal cell development is still debatable. Moreover, due to the complexity of the retinal structure, it is difficult to clearly visualize each retinal layer and accurately separate cell morphology in vivo by conventional methods. In the present study, we for the first time have achieved nanoscale imaging of retinal anatomy affected by dietary and waterborne Zn exposure by novel expansion microscopy. We demonstrated that the fish retina showed different developmental strategies in response to dietary and aqueous Zn exposures. Excess dietary Zn produced toxicity to retinal photoreceptor cells, resulting in a reduction in cell number and cell area, and this toxicity became severe with biological development. In contrast, waterborne Zn in the natural environment probably failed to meet the Zn requirements of retinal development. Overall, our results indicated that during early development, the Zn requirement of the fish eyes was sensitive, and oversupplementation led to impaired photoreceptor cell development. Our study has provided new perspectives using the powerful and novel expansion microscopy technique in toxicity assessment, enabling ultra-clear visualization of small but complex organ development.
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Affiliation(s)
- Mengyu Wang
- School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong 518057, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong 518057, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
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10
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He S, Yu D, Li P, Zhang M, Xing S, Liu B, Sun C, Liu L, Li ZH. A new perspective on endocrine disrupting effects of triphenyltin on marine medaka: From brain transcriptome, gut content metabolome and behavior. CHEMOSPHERE 2022; 307:136190. [PMID: 36030938 DOI: 10.1016/j.chemosphere.2022.136190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/10/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Triphenyltin (TPT) is an endocrine contaminant that is often detected in the environment. However, the mechanism of the effects of TPT on biological systems is not fully understood. Here we exposed marine medaka (Oryzias melastigma) to TPT for 21 days. Brain transcriptome, intestinal content metabolism group, and behavior analysis were carried out. Through the comprehensive analysis of multiomics for the in-depth understanding of the ways related to health improvement, we determined that the glycine-serine-threonine metabolic axis was most perturbed by TPT. Through behavioral analysis, it was found that there was behavioral hyperactivity in the exposed group; behavioral hyperactivity may be caused by the interference of TPT with the neuroendocrine system. In order to gain a full understanding of the impacts of TPT on human health, transcriptomic screening of differential genes and an impartial attitude based on bioinformatics were used. Gene-disease interaction analysis using the Comparative Toxicogenomics Database (CTD) revealed the possible effects of TPT on human health. Finally, based on these findings, the relevant adverse outcome pathway (AOP), which is the "epigenetic modification of PPARG leading to adipogenesis," was identified from AOP Wiki. Further research is required to validate the potential AOP of TPT.
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Affiliation(s)
- Shuwen He
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Daode Yu
- Marine Biology Institute of Shandong Province, Qingdao, Shandong, 266104, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Min Zhang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Shaoying Xing
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Bin Liu
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Cuici Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China.
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11
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Transcriptomic Analysis in Marine Medaka Gill Reveals That the Hypo-Osmotic Stress Could Alter the Immune Response via the IL17 Signaling Pathway. Int J Mol Sci 2022; 23:ijms232012417. [PMID: 36293271 PMCID: PMC9604416 DOI: 10.3390/ijms232012417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/03/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022] Open
Abstract
Fish gills are the major osmoregulatory tissue that contact the external water environment and have developed an effective osmoregulatory mechanism to maintain cellular function. Marine medaka (Oryzias melastigma) has the ability to live in both seawater and fresh water environments. The present study performed a seawater (SW) to 50% seawater (SFW) transfer, and the gill samples were used for comparative transcriptomic analysis to study the alteration of hypo-osmotic stress on immune responsive genes in this model organism. The result identified 518 differentiated expressed genes (DEGs) after the SW to SFW transfer. Various pathways such as p53 signaling, forkhead box O signaling, and the cell cycle were enriched. Moreover, the immune system was highlighted as one of the top altered biological processes in the enrichment analysis. Various cytokines, chemokines, and inflammatory genes that participate in the IL-17 signaling pathway were suppressed after the SW to SFW transfer. On the other hand, some immunoglobulin-related genes were up-regulated. The results were further validated by real-time qPCR. Taken together, our study provides additional gill transcriptome information in marine medaka; it also supports the notion that osmotic stress could influence the immune responses in fish gills.
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12
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Chen JC, Fang C, Zheng RH, Chen ML, Kim DH, Lee YH, Bailey C, Wang KJ, Lee JS, Bo J. Environmentally relevant concentrations of microplastics modulated the immune response and swimming activity, and impaired the development of marine medaka Oryzias melastigma larvae. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113843. [PMID: 36068765 DOI: 10.1016/j.ecoenv.2022.113843] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/17/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Microplastics (MPs), due to their impacts on the ecosystem and their integration into the food web either through trophic transfer or ingestion directly from the ambient environment, are an emerging class of environmental contaminants posing a great threat to marine organisms. Most reports on the toxic effects of MPs exclusively focus on bioaccumulation, oxidative stress, pathological damage, and metabolic disturbance in fish. However, the collected information on fish immunity in response to MPs is poorly defined. In particular, little is known regarding mucosal immunity and the role of mucins. In this study, marine medaka (Oryzias melastigma) larvae were exposed to 6.0 µm beads of polystyrene microplastics (PS-MPs) at three environmentally relevant concentrations (102 particles/L, 104 particles/L, and 106 particles/L) for 14 days. The experiment was carried out to explore the developmental and behavioural indices, the transcriptional profiles of mucins, pro-inflammatory, immune, metabolism and antioxidant responses related genes, as well as the accumulation of PS-MPs in larvae. The results revealed that PS-MPs were observed in the gastrointestinal tract, with a concentration- and exposure time-dependent manner. No significant difference in the larval mortality was found between the treatment groups and the control, whereas the body length of larvae demonstrated a significant reduction at 106 particles/L on 14 days post-hatching. The swimming behaviour of the larvae became hyperactive under exposure to 104 and 106 particles/L PS-MPs. In addition, PS-MP exposure significantly up-regulated the mucin gene transcriptional levels of muc7-like and muc13-like, however down-regulated the mucin gene expression levels of heg1, muc2, muc5AC-like and muc13. The immune- and inflammation and metabolism-relevant genes (jak, stat-3, il-6, il-1β, tnf-а, ccl-11, nf-κb, and sod) were significantly induced by PS-MPs at 104 and 106 particles/L compared to the control. Taken together, this study suggests that PS-MPs induced inflammation response and might obstruct the immune functions and retarded the growth of the marine medaka larvae even at environmentally relevant concentrations.
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Affiliation(s)
- Jin-Can Chen
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Chao Fang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Rong-Hui Zheng
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Ming-Liang Chen
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Young-Hwan Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Christyn Bailey
- Fish Immunology and Pathology Laboratory, Animal Health Research Center (CISA-INIA), Madrid 28130, Spain
| | - Ke-Jian Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Bo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China.
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13
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Embryotoxicity of Polystyrene Microspheres of Different Sizes to the Marine Medaka Oryzias melastigma (McClelland, 1839). WATER 2022. [DOI: 10.3390/w14121831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Polystyrene microplastics (PS-MPs) are potentially harmful to marine organisms, especially during the early developmental stages, although the underlying mechanism remains unclear. The present study evaluated the growth and morphological characteristics of marine medaka Oryzias melastigma (McClelland, 1839) embryos exposed to PS-MP. PS-MPs of three different sizes (0.05, 0.5, and 6.0 μm with a concentration of 106 particles/L) were subjected to waterborne exposure for 19 d. The hatching time and rate of embryos exposed to 0.5 and 6.0 μm PS-MPs were significantly lower than those of the control, while no significant difference was observed in the 0.05 μm treatment. No significant differences were observed in the mortality rate of the embryos, embryo diameter, and relevant gene expression levels, including il6, il8, il-1β, jak, stat-3, nf-κb, hif-1α, epo, cyp1a1, ahr, sod, cat, and gpx, but with the exception of vtg. Fluorescent PS-MPs were found on the embryo surfaces when the embryos were exposed to 0.5 and 6.0 μm PS-MPs, but no signals were detected inside embryos using confocal microscopy. Therefore, the results indicate that PS-MPs having a diameter of 6.0 μm can only attach to the surface or villus of embryos and not enter the embryos through the membrane pores, whereas PS-MPs with diameters of 0.05 and 0.5 μm cannot enter the embryos.
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14
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Integrated Omics Approaches Revealed the Osmotic Stress-Responsive Genes and Microbiota in Gill of Marine Medaka. mSystems 2022; 7:e0004722. [PMID: 35285678 PMCID: PMC9040874 DOI: 10.1128/msystems.00047-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This is the first study using the transcriptome and 16S rRNA gene sequencing to report the hypotonic responsive genes in gill cells and the compositions of gill microbiota in marine medaka. The overlapped glycosaminoglycan- and chitin-related pathways suggest host-bacterium interaction in fish gill during osmotic stress.
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15
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Tigano A, Jacobs A, Wilder AP, Nand A, Zhan Y, Dekker J, Therkildsen NO. Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation. Genome Biol Evol 2021; 13:evab098. [PMID: 33964136 PMCID: PMC8214408 DOI: 10.1093/gbe/evab098] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/21/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)-an established ecological model for studying the phenotypic effects of natural and artificial selection-and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is among the highest reported for a fish, or any vertebrate (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ∼23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.
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Affiliation(s)
- Anna Tigano
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Arne Jacobs
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
| | - Aryn P Wilder
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
- Conservation Genetics, San Diego Zoo Global, Escondido, California, USA
| | - Ankita Nand
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ye Zhan
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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16
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Feng S, Zeng Y, Cai Z, Wu J, Chan LL, Zhu J, Zhou J. Polystyrene microplastics alter the intestinal microbiota function and the hepatic metabolism status in marine medaka (Oryzias melastigma). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143558. [PMID: 33190902 DOI: 10.1016/j.scitotenv.2020.143558] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
To assess the potential effects of microplastics (MPs) on gut microbiome, a simple investigation of gut microbial structure is not sufficient, and the function and association of gut microbial structure with host health should also be taken into account. Here, the effects of two particle sizes (2 and 200 μm) of polystyrene MPs (PS-MPs) on the gut microbiota of medaka were evaluated following oral administration at 0.3 and 3.0 μg/mg for 28 days. No change in body length and gut histopathology damage were observed. However, the exposure to PS-MPs significantly decreased fish body weight and disrupted the liver anti-oxidative status. The PS-MPs caused a shift in the gut microbial structure of medaka accompanied by changes in community function, including significant environmental stress, increased carbon degradation/fixation activities, and partially modified nitrogen/phosphorus/sulfur metabolic abilities. Furthermore, the PS-MPs exposure disturbed the glycolipid/tyrosine/energy metabolism and the endocrine balance. A potential correlation between the gut microecology and host response to PS-MPs exposure was also observed. These results indicated that the PS-MPs may contribute to gut-liver axis disruption, which could be the underlying toxicological mechanisms of PS-MPs exposure. This work has improved our knowledge about the relationship between gut microbiota dysbiosis and host metabolic disorders following MPs exposure.
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Affiliation(s)
- Shibo Feng
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China
| | - Yanhua Zeng
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China
| | - Jiajun Wu
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China
| | - Leo Lai Chan
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China
| | - Jianming Zhu
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China
| | - Jin Zhou
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China.
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17
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Kang HM, Byeon E, Jeong H, Kim MS, Chen Q, Lee JS. Different effects of nano- and microplastics on oxidative status and gut microbiota in the marine medaka Oryzias melastigma. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124207. [PMID: 33199151 DOI: 10.1016/j.jhazmat.2020.124207] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/11/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
Plastic is regarded as a major environmental concern. In particular, nanoplastics and microplastics (NMPs) are attracting global attention due to their potential impact on aquatic organisms. Here, we examined the effects of NMPs (50 nm polystyrene microbead nanoplastics [NPs] and 45 µm microplastics [MPs]) on oxidative status and gut microbiota in the marine medaka Oryzias melastigma. The NP-exposed group exhibited stronger oxidative stress with higher activation levels of antioxidants compared to the MP-exposed group. However, the MP-exposed group demonstrated induction of intestinal damage (e.g., increased mucus ratio) with further alterations of gut microbiota, compared to the NP-exposed group. In particular, MPs caused more significant alterations of microbiota composition at both phylum and genus levels. Thus, in this study we show distinct toxicity pathways of NPs and MPs, an oxidative stress-mediated pathway (e.g., antioxidants) induced by NP exposure and dysbiosis of gut microbiota in association with immune dysfunction induced by MP exposure. Our results are helpful for expanding our knowledge about the impacts of NMPs as potentially harmful substances in the aquatic environment.
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Affiliation(s)
- Hye-Min Kang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea
| | - Eunjin Byeon
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Haksoo Jeong
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Qiqing Chen
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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18
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Ansai S, Mochida K, Fujimoto S, Mokodongan DF, Sumarto BKA, Masengi KWA, Hadiaty RK, Nagano AJ, Toyoda A, Naruse K, Yamahira K, Kitano J. Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes. Nat Commun 2021; 12:1350. [PMID: 33649298 PMCID: PMC7921647 DOI: 10.1038/s41467-021-21697-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Sexual selection drives rapid phenotypic diversification of mating traits. However, we know little about the causative genes underlying divergence in sexually selected traits. Here, we investigate the genetic basis of male mating trait diversification in the medaka fishes (genus Oryzias) from Sulawesi, Indonesia. Using linkage mapping, transcriptome analysis, and genome editing, we identify csf1 as a causative gene for red pectoral fins that are unique to male Oryzias woworae. A cis-regulatory mutation enables androgen-induced expression of csf1 in male fins. csf1-knockout males have reduced red coloration and require longer for mating, suggesting that coloration can contribute to male reproductive success. Contrary to expectations, non-red males are more attractive to a predatory fish than are red males. Our results demonstrate that integrating genomics with genome editing enables us to identify causative genes underlying sexually selected traits and provides a new avenue for testing theories of sexual selection.
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Affiliation(s)
- Satoshi Ansai
- grid.288127.60000 0004 0466 9350Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan ,grid.419396.00000 0004 0618 8593Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan ,grid.69566.3a0000 0001 2248 6943Present Address: Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi Japan
| | - Koji Mochida
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan ,grid.26091.3c0000 0004 1936 9959Department of Biology, Keio University, Yokohama, Kanagawa, Japan
| | - Shingo Fujimoto
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan ,grid.267625.20000 0001 0685 5104Present Address: Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa Japan
| | - Daniel F. Mokodongan
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan ,grid.249566.a0000 0004 0644 6054Present Address: Museum Zoologicum Bogoriense (MZB), Zoology Division of Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Indonesia
| | - Bayu Kreshna Adhitya Sumarto
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Kawilarang W. A. Masengi
- grid.412381.d0000 0001 0702 3254Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, Indonesia
| | - Renny K. Hadiaty
- grid.249566.a0000 0004 0644 6054Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Indonesia
| | - Atsushi J. Nagano
- grid.440926.d0000 0001 0744 5780Faculty of Agriculture, Ryukoku University, Ohtsu, Shiga, Japan
| | - Atsushi Toyoda
- grid.288127.60000 0004 0466 9350Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kiyoshi Naruse
- grid.419396.00000 0004 0618 8593Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kazunori Yamahira
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Jun Kitano
- grid.288127.60000 0004 0466 9350Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
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19
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Tang L, Liu M, Hu C, Zhou B, Lam PKS, Lam JCW, Chen L. Binary exposure to hypoxia and perfluorobutane sulfonate disturbs sensory perception and chromatin topography in marine medaka embryos. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115284. [PMID: 32781212 DOI: 10.1016/j.envpol.2020.115284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/23/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
Perfluorobutane sulfonate (PFBS), an environmental pollutant of emerging concern, is previously shown to dynamically interact with hypoxia on aquatic developmental toxicities. However, the molecular mechanisms underlying the interaction remain unknown. In this follow-up study, marine medaka embryos were exposed to 0 and 3.3 mg/L of PFBS under normoxia (6.9 mg/L) or hypoxia (1.7 mg/L) condition till 15 days post-fertilization. High-throughput transcriptomic sequencing was employed to filter differentially expressed genes and provide mechanistic insight into interactive action between hypoxia and PFBS. The results showed that hypoxia alone and the coexposure paradigm were similarly potent to modify transcriptional profiles, with the majority of genes significantly down-regulated. In contrast, transcriptional toxicity of PFBS was relatively milder. Functional annotation analyses found that hypoxia and coexposure groups mainly impacted phototransduction signaling by decreasing the transcriptions of cyclic nucleotide-gated (CNG) cation channels and retinol transport genes. However, this study demonstrated the first toxicological evidence that toxic effects of PFBS targeted the perception of chemical stimulus through olfactory and gustatory receptors. The addition of PFBS moderately exacerbated the toxic actions of hypoxia, which largely shaped the transcriptional pattern of coexposure group. In addition, gene interactive networks were constructed for hypoxia and coexposure groups, underlining the increased chromatin deacetylation and methylation to epigenetically repress genome-wide transcriptional initiation. Overall, PFBS and hypoxia interact to interrupt the embryonic development of sensory systems, which may compromise the individual fitness and survival, especially during early life stages when precocious perception of food and escape from predators are essential.
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Affiliation(s)
- Lizhu Tang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengyuan Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chenyan Hu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, 430072, China
| | - Bingsheng Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Paul K S Lam
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, SAR, Hong Kong, China
| | - James C W Lam
- Department of Science and Environmental Studies, The Education University of Hong Kong, SAR, Hong Kong, China
| | - Lianguo Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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20
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Liang P, Saqib HSA, Ni X, Shen Y. Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma). BMC Genomics 2020; 21:640. [PMID: 32938378 PMCID: PMC7493909 DOI: 10.1186/s12864-020-07042-7] [Citation(s) in RCA: 5] [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: 02/03/2020] [Accepted: 08/31/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters. RESULTS In this study, we reported a high-quality and accurate de novo genome assembly of marine medaka through the integration of single-molecule sequencing, Illumina paired-end sequencing, and 10X Genomics linked-reads. The 844.17 Mb assembly is estimated to cover more than 98% of the genome and is more continuous with fewer gaps and errors than the previous genome assembly. Comparison of O. melastigma with closely related species showed significant expansion of gene families associated with DNA repair and ATP-binding cassette (ABC) transporter pathways. We identified 274 genes that appear to be under significant positive selection and are involved in DNA repair, cellular transportation processes, conservation and stability of the genome. The positive selection of genes and the considerable expansion in gene numbers, especially related to stimulus responses provide strong supports for adaptations of O. melastigma under varying environmental stresses. CONCLUSIONS The highly contiguous marine medaka genome and comparative genomic analyses will increase our understanding of the underlying mechanisms related to its extraordinary adaptation capability, leading towards acceleration in the ongoing and future investigations in marine ecotoxicology.
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Affiliation(s)
- Pingping Liang
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Hafiz Sohaib Ahmed Saqib
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaomin Ni
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
- Fudan University, Shanghai, 200240, China
| | - Yingjia Shen
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China.
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21
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Lai KP, Tam N, Wang SY, Lin X, Chan TF, Au DWT, Wu RSS, Kong RYC. Hypoxia causes sex-specific hepatic toxicity at the transcriptome level in marine medaka (Oryzias melastigma). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 224:105520. [PMID: 32480175 DOI: 10.1016/j.aquatox.2020.105520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 05/03/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
Hypoxia, a low environmental oxygen level, is a common problem in the ocean globally. Hypoxia has been known to cause disruption to the endocrine system of marine organisms in both laboratory and field studies. Our previous studies have demonstrated the sex-specific response to hypoxia in the neural and reproductive systems of marine fish. In the current report, we aim to study the sex-specific hepatic response of fish at the transcriptome level to hypoxic stress. By using a comparative transcriptome analysis, followed by a systematic bioinformatics analysis including Database for Annotation, Visualization and Integrated Discovery (DAVID) and Ingenuity Pathway Analysis (IPA), we found that hypoxia altered expression of genes related to cell proliferation and apoptosis of hepatocytes, which are associated with human pathologies, such as liver inflammation hepatic steatosis and steatohepatitis. Furthermore, we observed sex-specific responses in the livers of fish through different cell signaling pathways. In female fish, hypoxia causes dysregulation of expression of genes related to impairment in endoplasmic reticulum structure and liver metabolism. In male fish, genes associated with redox homeostasis and fatty acid metabolism were altered by hypoxic stress. The findings of this study support the notion that hypoxia could cause sex-specific changes (hepatic toxicity and changes) in marine fish.
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Affiliation(s)
- Keng Po Lai
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, PR China; Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, PR China; Department of Chemistry, City University of Hong Kong, Hong Kong, PR China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, PR China.
| | - Nathan Tam
- Department of Chemistry, City University of Hong Kong, Hong Kong, PR China
| | - Simon Yuan Wang
- Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, Massachusetts, 02115, United States; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, 02115, United States
| | - Xiao Lin
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, PR China
| | - Ting Fung Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, PR China
| | - Doris Wai Ting Au
- Department of Chemistry, City University of Hong Kong, Hong Kong, PR China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, PR China
| | - Rudolf Shiu Sun Wu
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, PR China; Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, PR China
| | - Richard Yuen Chong Kong
- Department of Chemistry, City University of Hong Kong, Hong Kong, PR China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, PR China.
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22
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Ni X, Wan L, Liang P, Zheng R, Lin Z, Chen R, Pei M, Shen Y. The acute toxic effects of hexavalent chromium on the liver of marine medaka (Oryzias melastigma). Comp Biochem Physiol C Toxicol Pharmacol 2020; 231:108734. [PMID: 32151776 DOI: 10.1016/j.cbpc.2020.108734] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
Chromium is toxic to marine animals and can cause damage to many of their organs, including the liver. To test the toxicity of chromium on marine organisms, we exposed the liver of the marine medaka (Oryzias melastigma) with hexavalent chromium [Cr(VI)]. Our results show that Cr enrichment in the liver demonstrates a positive correlation to the exposure concentration. With the increase of Cr(VI) concentration, pathological changes including nuclear migration, cell vacuolization, blurred intercellular gap, nuclear condensation, become noticeable. To further study changes in gene expression in the liver after Cr(VI) exposure, we used RNA-seq to compare expression profiles before and after Cr(VI) exposure. After acute Cr(VI) exposure (2.61 mg/l) for 96 h, 5862 transcripts significantly changed. It is the first time that the PPAR pathway was found to respond sensitively to Cr(VI) exposure in fish. Finally, combined with other published study, we found that there may be some difference between Cr(VI) toxicity in seawater fish and freshwater fish, due to degree of oxidative stress, distribution patterns and detailed Cr(VI) toxicological mechanisms. Not only does our study explore the mechanisms of Cr(VI) toxicity on the livers of marine medaka, it also points out different Cr(VI) toxicity levels and potential mechanisms between seawater fish and freshwater fish.
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Affiliation(s)
- Xiaomin Ni
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University), Ministry of Education, Xiamen University, Xiamen, Fujian 361005, China; Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen, Fujian 361005, China; Fudan University, Shanghai 200240, China.
| | - Lei Wan
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University), Ministry of Education, Xiamen University, Xiamen, Fujian 361005, China; Bellastem Biotechnology Limited, Weifang, Shandong 261503, China
| | - Pingping Liang
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University), Ministry of Education, Xiamen University, Xiamen, Fujian 361005, China; Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen, Fujian 361005, China
| | - Ruping Zheng
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University), Ministry of Education, Xiamen University, Xiamen, Fujian 361005, China; Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen, Fujian 361005, China
| | - Zeyang Lin
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University), Ministry of Education, Xiamen University, Xiamen, Fujian 361005, China; Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen, Fujian 361005, China
| | - Ruichao Chen
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University), Ministry of Education, Xiamen University, Xiamen, Fujian 361005, China; College of Urban and Environmental Sciences, Peking University, Beijing 100089, China
| | - Mengke Pei
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University), Ministry of Education, Xiamen University, Xiamen, Fujian 361005, China; School of Environmental Science & Engineering, Shanghai Jiao Tong University, 200240, China
| | - Yingjia Shen
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University), Ministry of Education, Xiamen University, Xiamen, Fujian 361005, China; Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen, Fujian 361005, China.
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23
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Lee BY, Park JC, Kim MS, Choi BS, Kim DH, Lim JS, Yum S, Hwang UK, Nah GJ, Lee JS. The genome of the Java medaka (Oryzias javanicus): Potential for its use in marine molecular ecotoxicology. MARINE POLLUTION BULLETIN 2020; 154:111118. [PMID: 32319931 DOI: 10.1016/j.marpolbul.2020.111118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
The Java medaka (Oryzias javanicus) is distributed in tropical brackish water and is considered as an ecotoxicological experimental organism for assessing diverse pollutions and global climate change effects in the ocean. In this study, we sequenced and assembled the genome of O. javanicus using the Oxford Nanopore technique and anchored the scaffolds to the 24 genetic linkage map of a sister species Oryzias melastigma. The assembled genome consisted of 773 scaffolds including 24 LG-based scaffolds, and the estimated genome length was 846.3 Mb (N50 = 19.3 Mb), containing 24,498 genes. As detoxification processes are crucial in aquatic organisms, antioxidant-related genes including glutathione S-transferases, superoxide dismutase, catalase, and glutathione peroxidase were identified in this study. In the genome of O. javanicus, a total of 21 GSTs, 4 SODs, 1 CAT, and 7 GPxs were identified and showed high similarities between sister species O. melastigma and Oryzias latipes. In addition, despite having 8 classes of cytosolic GSTs family, medaka showed no presence of GST pi and sigma classes, which are predominantly found in carp and salmon, but not in neoteleostei. This study adds another set to genome-library of Oryzias spp. and is a useful resource for better understanding of the molecular ecotoxicology.
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Affiliation(s)
- Bo-Young Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | | | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jong-Sung Lim
- NICEM, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Seungshic Yum
- Risk Assessment Research Center, Korea Institute of Ocean Science and Technology (KIOST), Geoje 53201, South Korea
| | - Un-Ki Hwang
- Marine Ecological Risk Assessment Center, West Sea Fisheries Research Institute, National Institute of Fisheries Science, Incheon 46083, South Korea
| | - Gyoung Ju Nah
- NICEM, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea.
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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24
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Jeong CB, Kang HM, Hong SA, Byeon E, Lee JS, Lee YH, Choi IY, Bae S, Lee JS. Generation of albino via SLC45a2 gene targeting by CRISPR/Cas9 in the marine medaka Oryzias melastigma. MARINE POLLUTION BULLETIN 2020; 154:111038. [PMID: 32174491 DOI: 10.1016/j.marpolbul.2020.111038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 02/28/2020] [Accepted: 03/01/2020] [Indexed: 05/22/2023]
Abstract
To produce albinism in the marine medaka Oryzias melastigma, we disrupted the solute carrier family 45 (SLC45a2) gene by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 with a single guide RNA (sgRNA). Selected sgRNAs were able to target a SLC45a2 gene as confirmed by genotyping and heteroduplex mobility assay (HMA). Of the survived embryos after injection, 54.2% and 60.0% embryos exhibited albinism phenotype by sgRNA1 and sgRNA2, respectively. Deep sequencing at the on-target sites showed different insertion and deletion (indel) mutation profiles near the DNA cleavage sites, indicating high efficacy of producing SLC45a2 knock-out mutants by this method. Moreover, HMA at the potential off-target sites revealed that off-target activity would be induced at a low rate, or not induced at all. This albino marine medaka will be a good model for marine molecular ecotoxicology in establishment of diverse in vivo endpoints, and the application of this efficient gene targeting method in the marine medaka would be useful tool for mechanistic approaches.
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Affiliation(s)
- Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea; Department of Marine Science, College of Nature Science, Incheon National University, Incheon 22012, South Korea
| | - Hye-Min Kang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Sung-Ah Hong
- Department of Chemistry, College of Nature Sciences, Hanyang University, Seoul 04763, South Korea
| | - Eunjin Byeon
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jin-Sol Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Young Hwan Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, South Korea
| | - Sangsu Bae
- Department of Chemistry, College of Nature Sciences, Hanyang University, Seoul 04763, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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25
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Construction of High-Resolution RAD-Seq Based Linkage Map, Anchoring Reference Genome, and QTL Mapping of the Sex Chromosome in the Marine Medaka Oryzias melastigma. G3-GENES GENOMES GENETICS 2019; 9:3537-3545. [PMID: 31530635 PMCID: PMC6829124 DOI: 10.1534/g3.119.400708] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Medaka (Oryzias sp.) is an important fish species in ecotoxicology and considered as a model species due to its biological features including small body size and short generation time. Since Japanese medaka Oryzias latipes is a freshwater species with access to an excellent genome resource, the marine medaka Oryzias melastigma is also applicable for the marine ecotoxicology. In genome era, a high-density genetic linkage map is a very useful resource in genomic research, providing a means for comparative genomic analysis and verification of de novo genome assembly. In this study, we developed a high-density genetic linkage map for O. melastigma using restriction-site associated DNA sequencing (RAD-seq). The genetic map consisted of 24 linkage groups with 2,481 single nucleotide polymorphism (SNP) markers. The total map length was 1,784 cM with an average marker space of 0.72 cM. The genetic map was integrated with the reference-assisted chromosome assembly (RACA) of O. melastigma, which anchored 90.7% of the assembled sequence onto the linkage map. The values of complete Benchmarking Universal Single-Copy Orthologs were similar to RACA assembly but N50 (23.74 Mb; total genome length 779.4 Mb; gap 5.29%) increased to 29.99 Mb (total genome length 778.7 Mb; gap 5.2%). Using MapQTL analysis with SNP markers, we identified a major quantitative trait locus for sex traits on the Om10. The integration of the genetic map with the reference genome of marine medaka will serve as a good resource for studies in molecular toxicology, genomics, CRISPR/Cas9, and epigenetics.
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26
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Ge H, Lin K, Shen M, Wu S, Wang Y, Zhang Z, Wang Z, Zhang Y, Huang Z, Zhou C, Lin Q, Wu J, Liu L, Hu J, Huang Z, Zheng L. De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C. Mol Ecol Resour 2019; 19:1461-1469. [PMID: 31325912 PMCID: PMC6899872 DOI: 10.1111/1755-0998.13064] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 01/02/2023]
Abstract
The red-spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and South-East Asia and is a threatened species. The species is also considered a good model for studies of sex inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of E. akaara by taking advantage of long-read single-molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi-C. A red-spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96-fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudochromosomes covering approximately 95.55% of the genome assembly with Hi-C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 noncoding RNAs. Furthermore, combined with several RNA-seq data sets, 23,808 (99.5%) genes were functionally annotated from a total of 23,923 predicted protein-coding sequences. The high-quality chromosome-level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red-spotted grouper in the future.
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Affiliation(s)
- Hui Ge
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
| | - Kebing Lin
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
| | - Mi Shen
- Nextomics Biosciences InstituteWuhanChina
| | - Shuiqing Wu
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
| | - Ziping Zhang
- College of Animal SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
| | - Yong Zhang
- Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic AnimalsSun Yat‐Sen UniversityGuangzhouChina
| | - Zhen Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic AdministrationFujian Normal UniversityFuzhouChina
| | - Chen Zhou
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
| | - Qi Lin
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
| | - Jianshao Wu
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
| | - Lei Liu
- Nextomics Biosciences InstituteWuhanChina
| | - Jiang Hu
- Nextomics Biosciences InstituteWuhanChina
| | - Zhongchi Huang
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
| | - Leyun Zheng
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
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27
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Chen L, Tsui MMP, Hu C, Wan T, Au DWT, Lam JCW, Lam PKS, Zhou B. Parental Exposure to Perfluorobutanesulfonate Impairs Offspring Development through Inheritance of Paternal Methylome. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:12018-12025. [PMID: 31539238 DOI: 10.1021/acs.est.9b03865] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Perfluorobutanesulfonate (PFBS), an environmental pollutant of emerging concern, significantly impairs offspring development and overall health after parental exposure. However, the true inducer of offspring developmental defects among the complexity of parental influences remains unknown. In the present study, marine medaka (Oryzias melastigma) were exposed to environmentally realistic concentrations of PFBS (0, 1, 3, and 10 μg/L) for an entire life cycle. By mixing and mating control and exposed medaka (male or female), a crossbreeding strategy was employed to produce offspring eggs from various crossbreeds, with the aim of differentiating the maternal and paternal influences. Measurements of swimming performance in larval offspring showed that larvae of exposed male parents swam hyperactively in comparison to the control larvae. Contrasting trends in PFBS transfer and maternal factor transfer (e.g., proteins and lipids) to that of swimming behavior eliminated these two factors as major inducers of offspring developmental impairment. Inheritance of the exposed paternal methylome marks in offspring may be partially responsible for abnormal swimming behavior, although different toxic mechanisms may be involved depending on the exposure concentration. Overall, these findings suggest that inheritance of epigenetic modifications implicates a long-lasting threat of PFBS to the fitness and sustainability of fish populations.
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Affiliation(s)
- Lianguo Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology , Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072 , People's Republic of China
| | - Mirabelle M P Tsui
- State Key Laboratory of Marine Pollution , City University of Hong Kong , Kowloon, Hong Kong SAR , People's Republic of China
| | - Chenyan Hu
- School of Chemistry and Environmental Engineering , Wuhan Institute of Technology , Wuhan 430072 , People's Republic of China
| | - Teng Wan
- Department of Chemistry , City University of Hong Kong , Kowloon, Hong Kong SAR , People's Republic of China
| | - Doris W T Au
- Department of Chemistry , City University of Hong Kong , Kowloon, Hong Kong SAR , People's Republic of China
| | - James C W Lam
- State Key Laboratory of Marine Pollution , City University of Hong Kong , Kowloon, Hong Kong SAR , People's Republic of China
- Department of Science and Environmental Studies , The Education University of Hong Kong , Hong Kong SAR People's Republic of China
| | - Paul K S Lam
- State Key Laboratory of Marine Pollution , City University of Hong Kong , Kowloon, Hong Kong SAR , People's Republic of China
- Department of Chemistry , City University of Hong Kong , Kowloon, Hong Kong SAR , People's Republic of China
| | - Bingsheng Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology , Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072 , People's Republic of China
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28
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Hilgers L, Schwarzer J. The untapped potential of medaka and its wild relatives. eLife 2019; 8:46994. [PMID: 31287418 PMCID: PMC6615862 DOI: 10.7554/elife.46994] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/12/2019] [Indexed: 01/04/2023] Open
Abstract
The medaka is a fish that has served as a model organism for over a century, yet there is still much to learn about its life in the wild. Here we summarize the current knowledge, highlight recent progress and outline remaining gaps in our understanding of the natural history of medaka. It has also become clear over time that rather than being a single species, medaka comprises an entire species complex, so disentangling the species boundaries is an important goal for future research. Moreover, medaka and other ricefishes exhibit striking functional diversity, little of which has been investigated to date. As such, there are opportunities to use the resources developed for medaka to study other ricefishes, and to learn more about medaka itself in an evolutionary context.
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Affiliation(s)
- Leon Hilgers
- Zoological Research Museum Alexander Koenig, Bonn, Germany
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29
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Machado AM, Tørresen OK, Kabeya N, Couto A, Petersen B, Felício M, Campos PF, Fonseca E, Bandarra N, Lopes-Marques M, Ferraz R, Ruivo R, Fonseca MM, Jentoft S, Monroig Ó, da Fonseca RR, C Castro LF. " Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus. Genes (Basel) 2018; 9:E485. [PMID: 30304855 PMCID: PMC6210256 DOI: 10.3390/genes9100485] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/30/2022] Open
Abstract
Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25,579 bp and BUSCO completeness of 82.1% (Actinopterygii). The estimated size of the genome ranges between 655 and 850 Mb. Additionally, we generated a relatively high-level liver transcriptome. To deliver a proof of principle of the value of this dataset, we established the presence and function of enzymes (Elovl2, Elovl5, and Fads2) that have pivotal roles in the biosynthesis of long chain polyunsaturated fatty acids, essential nutrients particularly abundant in oily fish such as sardines. Our study provides the first omics dataset from a valuable economic marine teleost species, the European sardine, representing an essential resource for their effective conservation, management, and sustainable exploitation.
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Affiliation(s)
- André M Machado
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway.
| | - Naoki Kabeya
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo 113-8654, Japan.
| | - Alvarina Couto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Bent Petersen
- Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology, Kedah 08000, Malaysia.
| | - Mónica Felício
- Portuguese Institute for the Sea and Atmosphere, (IPMA), 1749-077 Lisbon, Portugal.
| | - Paula F Campos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Elza Fonseca
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, 4099-022 Porto, Portugal.
| | - Narcisa Bandarra
- Portuguese Institute for the Sea and Atmosphere, (IPMA), 1749-077 Lisbon, Portugal.
| | - Mónica Lopes-Marques
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Renato Ferraz
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4099-022 Porto, Portugal.
| | - Raquel Ruivo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Miguel M Fonseca
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway.
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630 Kristiansand, Norway.
| | - Óscar Monroig
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas (IATS-CSIC), 12595 Ribera de Cabanes, Spain.
| | - Rute R da Fonseca
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - L Filipe C Castro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, 4099-022 Porto, Portugal.
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30
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Ye RR, Peterson DR, Kitamura SI, Segner H, Seemann F, Au DWT. Sex-specific immunomodulatory action of the environmentalestrogen 17α-ethynylestradiol alongside with reproductive impairment in fish. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 203:95-106. [PMID: 30099325 DOI: 10.1016/j.aquatox.2018.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/25/2018] [Accepted: 07/25/2018] [Indexed: 06/08/2023]
Abstract
Estrogenic endocrine disrupting chemicals (EEDCs) are present ubiquitously in sediments and aquatic ecosystems worldwide. The detrimental impact of EEDCs on the reproduction of wildlife is widely recognized. Increasing evidence shows the immunosuppressive effects of EEDCs in vertebrates. Yet, no studies have considered concomitantly EEDC-induced impacts on reproductive impairment and immune suppression in vivo, which are deemed essential for risk assessment and environmental monitoring. In this study, EE2 was used as a representative EEDC, for parallel evaluation of EEDC-induced immune suppression (immune marker gene expression, leukocyte numbers, host resistance assay, and immune competence index) and reproductive impairment (estrogen responsive gene expression, fecundity, fertilization success, hatching success, and reproductive competence index) in an established fish model (marine medaka Oryzias melastigma), considering sex-specific induction and adaptation and recovery responses under different EE2 exposure scenarios. The findings in marine medaka reveal distinct sex differences in the EE2-mediated biological responses. For female fish, low concentration of exogenous EE2 (33 ng/L) could induce hormesis (immune enhancement), enable adaptation (restored reproduction) and even boost fish resistance to bacterial challenge after abatement of EE2. However, a prolonged exposure to high levels of EE2 (113 ng/L) not only impaired F0 immune function, but also perturbed females recovering from reproductive impairment, resulting in a persistent impact on the F1 generation output. Thus, for female fish, the exposure concentration of EE2 is more critical than the dose of EE2 in determining the impacts of EE2 on immune function and reproduction. Conversely, male fish are far more sensitive than females to the presence of low levels of exogenous EE2 in water and the EE2-mediated biological impacts are clearly dose-dependent. It is also evident in male fish that direct contact of EE2 is essential to sustain impairments of immune competence and reproductive output as well as deregulation of immune function genes in vivo. The immunomodulatory pathways altered by EE2 were deciphered for male and female fish, separately. Downregulation of hepatic tlr3 and c3 (in female) and tlr3, tlr5 and c3 (in male) may be indicative of impaired fish immune competence. Taken together, impaired immune competence in the EE2-exposed fish poses an immediate thread on the survival of F0 population. Impaired reproduction in the EE2-exposed fish can directly affect F1 output. Parallel evaluation of immune competence and reproduction are important considerations when assessing the risk of sublethal levels of EE2/EEDCs in aquatic environments.
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Affiliation(s)
- Roy R Ye
- State Key Laboratory in Marine Pollution, Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Drew R Peterson
- State Key Laboratory in Marine Pollution, Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Shin-Ichi Kitamura
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Japan
| | - Helmut Segner
- Centre for Fish and Wildlife Health, University of Bern, CH3012, Bern, Switzerland
| | - Frauke Seemann
- State Key Laboratory in Marine Pollution, Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong; Department of Life Sciences, Texas A&M University, Corpus Christi, TX, 78412, USA.
| | - Doris W T Au
- State Key Laboratory in Marine Pollution, Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong.
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