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Marjan P, Martyniuk CJ, Arlos MJ, Servos MR, Ruecker NJ, Munkittrick KR. Identifying transcriptomic indicators of tertiary treated municipal effluent in longnose dace (Rhinichthys cataractae) caged under semi-controlled conditions in experimental raceways. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171257. [PMID: 38417510 DOI: 10.1016/j.scitotenv.2024.171257] [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: 09/15/2023] [Revised: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
To evaluate effects of tertiary treated wastewater treatment plant effluent (MWWE) on transcriptomic responses in longnose dace (Rhinichthys cataractae; LND) we conducted a semi-controlled study in experimental raceways (Advancing Canadian Water Assets facility) imbedded in the Pine Creek treatment plant (Calgary, AB). LND collected from a reference site in the Bow River (REF) were caged in raceways containing either 5 % Pine Creek effluent (PC) or Bow River water (BR; control) over 28 d. Liver transcriptomes were analyzed in males and females sampled on days 7, 14 and 28 from BR and PC, and compared to REF fish on day 0. Concurrent with the caging, selected environmental substances of concern were analyzed in the BR and PC. Significantly different unigenes (SDUs) in females (vs males) within both BR and PC raceways increased over time and compared to REF fish. Moreover, SDUs in females and males within the same treatment (i.e., BR, PC) showed a temporal increase as well as compared to REF fish. Time was the dominant factor affecting SDUs, whereas sex and treatment had less of an impact on the transcriptome profiling. Gene Set Enrichment Analysis of BR vs PC over time revealed effects on genes involved in growth, metabolism of carbohydrates and lipids, and immune system on day 7; however, by day 28, 80-100 % of the transcripts localized to enriched biomarkers were associated with tissue immune responses in both sexes. Exposure to 5 % effluent had significant effects on female liver somatic index but no effects were observed on other phenotypic health indices in either sex. BR was used as the source of reference water, but analyses showed trace amounts of ESOCs. Analyses did not point towards definitive response patterns that could be used in field-based ecotoxicogenomic studies on the impacts of well-treated MWWE but suggested compromised adaptive immune responses.
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Affiliation(s)
- Patricija Marjan
- University of Calgary, Department of Biological Sciences, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada.
| | - Christopher J Martyniuk
- University of Florida, Department of Physiological Sciences, College of Veterinary Medicine, 2187 Mowry Rd., Gainesville, FL 32611, USA
| | - Maricor J Arlos
- University of Alberta, Civil and Environmental Engineering, 9211-116 Street NW, Edmonton, AB T6G 1H9, Canada
| | - Mark R Servos
- University of Waterloo, Department of Biology, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Norma J Ruecker
- The City of Calgary, Water Services, UEP-Water Resources, 2100, Station M, #35B, Calgary, AB T2P 2M5, Canada
| | - Kelly R Munkittrick
- University of Calgary, Department of Biological Sciences, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
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Huang Y, Luo P, Jiang FH, Gao HZ, Cui LF, Zhao Z. Molecular cloning, characterization and gene expression analysis of twelve interleukins in obscure puffer Takifugu obscurus. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 5:100103. [PMID: 37388236 PMCID: PMC10302539 DOI: 10.1016/j.fsirep.2023.100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023] Open
Abstract
Interleukins (ILs) are a subgroup of secreted cytokines, which are molecules involved in the intercellular regulation of the immune system. In this study, 12 IL homologs were cloned and functionally identified from obscure puffer Takifugu obscurus, and they were termed as ToIL-1β, ToIL-1, ToIL-6, ToIL-10, ToIL-11, ToIL-12, ToIL-17, ToIL-18, ToIL-20, ToIL-24, ToIL-27, and ToIL-34. Multiple alignment results showed that except for ToIL-24 and ToIL-27, other deduced ToIL proteins shared typical characteristics and structure with other known fish ILs. Phylogenetic analysis revealed that 12 ToILs were evolutionarily closely related to their counterparts in other selected vertebrates. Tissue distribution assay demonstrated that the mRNA transcripts of most ToIL genes were constitutively expressed in all tissues examined, with relatively high expression in immune tissues. Following Vibrio harveyi and Staphylococcus aureus infection, the expression levels of 12 ToILs in the spleen and liver were significantly upregulated, and their response over time varied. Taken together, these data were discussed accordingly with the ToIL expression and the immune response under the different situations tested. The results suggest that the 12 ToIL genes are involved in the antibacterial immune response in T. obscurus.
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Affiliation(s)
- Ying Huang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
| | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou 510301, China
| | - Fu-Hui Jiang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
| | - Hui-Ze Gao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
| | - Li-Fan Cui
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
| | - Zhe Zhao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
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Fajardo C, Santos P, Passos R, Vaz M, Azeredo R, Machado M, Fernández-Boo S, Baptista T, Costas B. Early Molecular Immune Responses of Turbot ( Scophthalmus maximus L.) Following Infection with Aeromonas salmonicida subsp. salmonicida. Int J Mol Sci 2023; 24:12944. [PMID: 37629124 PMCID: PMC10454659 DOI: 10.3390/ijms241612944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Turbot aquaculture production is an important economic activity in several countries around the world; nonetheless, the incidence of diseases, such furunculosis, caused by the etiological agent A. salmonicida subsp. salmonicida, is responsible for important losses to this industry worldwide. Given this perspective, this study aimed to evaluate early immune responses in turbot (S. maximus L.) following infection with A. salmonicida subsp. salmonicida. For this, 72 fish were individually weighed and randomly distributed into 6 tanks in a circulating seawater system. For the bacterial challenge, half of the individuals (3 tanks with 36 individuals) were infected using a peritoneal injection with the bacterial suspension, while the other half of individuals were injected with PBS and kept as a control group. Several factors linked to the innate immune response were studied, including not only haematological (white blood cells, red blood cells, haematocrit, haemoglobin, mean corpuscular volume, mean cell haemoglobin, mean corpuscular haemoglobin concentration, neutrophils, monocytes, lymphocytes, thrombocytes) and oxidative stress parameters, but also the analyses of the expression of 13 key immune-related genes (tnf-α, il-1β, il-8, pparα-1, acox1, tgf-β1, nf-kB p65, srebp-1, il-10, c3, cpt1a, pcna, il-22). No significant differences were recorded in blood or innate humoral parameters (lysozyme, anti-protease, peroxidase) at the selected sampling points. There was neither any evidence of significant changes in the activity levels of the oxidative stress indicators (catalase, glutathione S-transferase, lipid peroxidation, superoxide dismutase). In contrast, pro-inflammatory (tnf-α, il-1β), anti-inflammatory (il-10), and innate immune-related genes (c3) were up-regulated, while another gene linked with the lipid metabolism (acox1) was down-regulated. The results showed new insights about early responses of turbot following infection with A. salmonicida subsp. salmonicida.
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Affiliation(s)
- Carlos Fajardo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Porto, Portugal; (C.F.); (P.S.); (R.A.); (M.M.); (S.F.-B.)
- MARE—Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, 2520-620 Peniche, Portugal; (R.P.); (M.V.); (T.B.)
- Department of Biology, Faculty of Marine and Environmental Sciences, Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), University of Cadiz (UCA), 11510 Puerto Real, Spain
| | - Paulo Santos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Porto, Portugal; (C.F.); (P.S.); (R.A.); (M.M.); (S.F.-B.)
- MARE—Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, 2520-620 Peniche, Portugal; (R.P.); (M.V.); (T.B.)
- Department of Aquatic Production, School of Biomedicine and Biomedical Sciences, Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Ricardo Passos
- MARE—Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, 2520-620 Peniche, Portugal; (R.P.); (M.V.); (T.B.)
| | - Mariana Vaz
- MARE—Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, 2520-620 Peniche, Portugal; (R.P.); (M.V.); (T.B.)
| | - Rita Azeredo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Porto, Portugal; (C.F.); (P.S.); (R.A.); (M.M.); (S.F.-B.)
| | - Marina Machado
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Porto, Portugal; (C.F.); (P.S.); (R.A.); (M.M.); (S.F.-B.)
| | - Sergio Fernández-Boo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Porto, Portugal; (C.F.); (P.S.); (R.A.); (M.M.); (S.F.-B.)
| | - Teresa Baptista
- MARE—Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, 2520-620 Peniche, Portugal; (R.P.); (M.V.); (T.B.)
| | - Benjamin Costas
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Porto, Portugal; (C.F.); (P.S.); (R.A.); (M.M.); (S.F.-B.)
- Department of Aquatic Production, School of Biomedicine and Biomedical Sciences, Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
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Yang YC, Chen SN, Gan Z, Huang L, Li N, Wang KL, Nie P. Functional characterization of IL-18 receptor subunits, IL-18Rα and IL-18Rβ, and its natural inhibitor, IL-18 binding protein (IL-18BP) in rainbow trout Oncorhynchus mykiss. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 140:104610. [PMID: 36496012 DOI: 10.1016/j.dci.2022.104610] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
As an important proinflammation and immunomodulatory cytokine, IL-18 has been reported in several species of fish, but its receptor subunits, IL-18Rα and IL-18Rβ, and its decoy receptor, IL-18BP, have not been functionally characterized in fish. In the present study, IL-18Rα, IL-18Rβ and IL-18BP were cloned from rainbow trout Oncorhynchus mykiss, and they possess common conserved domains with their mammalian orthologues. In tested organs/tissues, IL-18Rα and IL-18Rβ exhibit basal expression levels, and IL-18BP has a pattern of constitutive expression. When transfected with different combinations of chimeric receptors in HEK293T cells, recombinant IL-18 (rIL-18) can induce the activation of NF-κB only when pcDNA3.1-IL-18Rα/IL-1R1 and pcDNA3.1-IL-18Rβ/IL-1RAP were both expressed. On the other hand, recombinant receptors, including rIL-18BP, rIL-18Rα-ECD-Fc and rIL-18Rβ-ECD-Fc can down-regulate significantly the activity of NF-κB, suggesting the participation of IL-18Rα, IL-18Rβ and IL-18BP in rainbow trout IL-18 signal transduction. Co-IP assays indicated that IL-18Rβ may form a complex with MyD88, IRAK4, IRAK1, TRAF6 and TAB2 in HEK293T cells, indicating that IL-18Rβ, in IL-18 signalling pathway, is associated with these signalling molecules. In conclusion, IL-18Rα, IL-18Rβ and IL-18BP in rainbow trout are conserved in function and signalling pathway with their mammalian orthologues.
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Affiliation(s)
- Yue Chong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Shan Nan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Zhen Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Lin Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Nan Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Kai Lun Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - P Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong Province, 266237, China; School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China.
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5
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Wang X, Xie Y, Hu W, Wei Z, Wei X, Yuan H, Yao H, Dunxue C. Transcriptome characterization and SSR discovery in the giant spiny frog Quasipaa spinosa. Gene 2022; 842:146793. [PMID: 35952842 DOI: 10.1016/j.gene.2022.146793] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 07/31/2022] [Accepted: 08/05/2022] [Indexed: 11/04/2022]
Abstract
The giant spiny frog Quasipaa spinosa (Amphibia: Ranidae) is a large unique frog species found mainly in southern China with a low amount of fat and high protein, and it has become one of the most important aquaculture animal species in China. To better understand its genetic background and screen potential molecular markers for artificial breeding and species conservation, we constructed an expression profile of Q. spinosa with high-throughput RNA sequencing and acquired potential SSR markers. Approximately 81.7 Gb of data and 93,887 unigenes were generated. The transcriptome contains 2085 (80.7 %) complete BUSCOs, suggesting that our assembly methods were effective and accurate.These unigenes were functionally classified using 7 functional databases, yielding 17,482 Pfam-, 12,752 Sting-, 17,526 KEGG-, 24,341 Swiss-Prot-, 28,604 Nr-, 16,287 GO- and 12,752 COG-annotated unigenes. Among several amphibian species, Q. spinosa unigenes had the highest number of hits to Xenopus tropicalis (35.25 %), followed by Xenopus laevis (12.68 %). 1417 unigenes were assigned to the immune system. In addition, a total of 33,019 candidate SSR markers were identified from the constructed library. Further tests with 20 loci and 118 large-scale breeding specimens gathered from four culture farms in China showed that 15 (75 %) loci were polymorphic, with the number of alleles per locus varying from 3 to 9 (mean of 4.3). The PIC values for the SSR markers ranged from 0.19 to 0.82, with an average value of 0.43, indicating moderate polymorphism in Q. spinosa. The transcriptomic profile and SSR repertoire obtained in the present study will facilitate population genetic studies and the selective breeding of amphibian species.
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Affiliation(s)
- Xiaodong Wang
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Yongguang Xie
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Wei Hu
- School of Animal Science, Yangtze University, Jingzhou 434020, China
| | - Zhaoyu Wei
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Xiuying Wei
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Hong Yuan
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Hongyan Yao
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Chen Dunxue
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China.
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Huang J, Chen W, Wang Q, Zhang Y, Liu Q, Yang D. Iso-Seq assembly and functional annotation of full-length transcriptome of turbot (Scophthalmus maximus) during bacterial infection. Mar Genomics 2022; 63:100954. [DOI: 10.1016/j.margen.2022.100954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/28/2022] [Accepted: 04/19/2022] [Indexed: 10/18/2022]
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Hu F, Zhang Y, Liu Q, Wang Z. PurA facilitates Edwardsiella piscicida to escape NF-κB signaling activation. FISH & SHELLFISH IMMUNOLOGY 2022; 124:254-260. [PMID: 35395412 DOI: 10.1016/j.fsi.2022.04.001] [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: 12/13/2021] [Revised: 03/01/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
The host NF-κB signaling pathway plays critical role in defensing against bacterial infection. However, bacteria also evolve strategies to escape from host clearance. Edwardsiella piscicida is a threatening pathogen in aquaculture, while the molecular mechanism of E. piscicida in inhibiting NF-κB signaling remains largely unknown. Herein, using E. piscicida transposon insertion mutant library combined with a NF-κB luciferase reporter system, we identified forty-six genes of E. piscicida, which were involved in inhibiting the NF-κB signaling activation in vitro. Moreover, we further explored the top 10 significantly changed mutants through zebrafish larvae infection model and validated that six genes were involved in inhibiting NF-κB activation in vivo. Specifically, we identified the adenylosuccinate synthase mutated strain (ΔpurA) infection exhibited a robust activation of NF-κB signaling, along with higher expression of cxcl8a and cxcl8b to mediate the recruitment of neutrophils in vivo. Taken together, these results identified the key factors of E. piscicida in inhibiting NF-κB activation, which will contribute to better understanding the pathogenesis of this important pathogen.
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Affiliation(s)
- Feizi Hu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuanxing Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China
| | - Zhuang Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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Gao D, Lei W, Wang C, Ni P, Cui X, Huang X, Ye S. RNA-Sequencing Analysis of the Spleen and Gill of Takifugu rubripes in Response to Vibrio harveyi Infection. Front Vet Sci 2022; 8:813988. [PMID: 35174239 PMCID: PMC8841829 DOI: 10.3389/fvets.2021.813988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Takifugu rubripes is commonly subjected to the disease-causing bacterium, Vibrio harveyi. However, the mechanism involved in the immune response of T. rubripes to V. harveyi infection is unclear. We conducted a transcriptomic analysis of the spleen and gill from T. rubripes infected with V. harveyi. We obtained 60,981,357 and 60,760,550 clean reads from the control and infected spleens, and 57,407,586 and 57,536,651 clean reads from the control and infected gills, respectively. We also identified 1,560 and 1,213 differentially expressed genes in the spleen and gill, respectively. Gene ontology analysis revealed that the most enriched biological process in both the spleen and gill was "immune response". The most enriched Kyoto Encyclopedia of Genes and Genomes immune response-related pathways were the NOD-like receptor signaling pathway in the spleen and cytokine-cytokine receptor interaction in the gill. We found 10 candidate immune-related genes in the spleen and gill. These putative immune pathways and candidate genes will provide insight into the immune response mechanisms of T. rubripes against V. harveyi.
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Affiliation(s)
- Dongxu Gao
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Wei Lei
- State Environmental Protection Key Laboratory of Marine Ecosystem Restoration, National Marine Environmental Monitoring Center, Dalian, China
| | - Chenshi Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Ping Ni
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Xiaoyu Cui
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Xindi Huang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Shigen Ye
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
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Pereiro P, Lama R, Figueras A, Novoa B. Characterization of the turbot (Scophthalmus maximus) interleukin-18: Identification of splicing variants, phylogeny, synteny and expression analysis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 124:104199. [PMID: 34228995 DOI: 10.1016/j.dci.2021.104199] [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: 06/07/2021] [Revised: 07/02/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
Interleukin-18 (IL-18) is a pro-inflammatory cytokine that belongs to the interleukin-1 (IL-1) family of cytokines. As occurs with IL-1β, it is synthetized as an inactive precursor peptide that is mainly processed by the cysteine protease caspase-1 in the inflammasome complex. In mammals, and in collaboration with IL-12, it has been described as an important cytokine controlling the Th1-mediated immune responses through the induction of IFN-γ. Although its function in mammals is well stablished, the activity of this cytokine in teleost remains to be elucidated. This could be due, among other things, to the absence of this gene in the fish model species zebrafish, but also to its complex regulation. As it was observed for rainbow trout and human, il18 splicing variants were also found in turbot, which could represent a regulatory mechanism of its bioactivity. In the case of turbot, three splicing variants were observed (SV1-3), and one of them showed an insertion of 10 amino acids in the middle of the potential caspase-1 cleavage position, reflecting that this is probably a form resistant to the processing by the inflammasome. Phylogenetic and three-dimensional analyses of turbot Il18 revealed that it is relatively well-conserved in vertebrates, although only a partial conservation of the gene synteny was observed between fish and mammals. As it was expected, turbot il18 splicing variants were mainly expressed in immune tissues under healthy conditions, and their expression was induced by a bacterial challenge, although certain inhibitions were observed after viral and parasitic infections. In the case of the viral challenge, il18 downregulations did not seem to be due to the effect of type I IFNs.
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Affiliation(s)
- Patricia Pereiro
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), C/ Eduardo Cabello 6, 36208, Vigo, Spain
| | - Raquel Lama
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), C/ Eduardo Cabello 6, 36208, Vigo, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), C/ Eduardo Cabello 6, 36208, Vigo, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), C/ Eduardo Cabello 6, 36208, Vigo, Spain.
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Yang H, Yang YL, Li GQ, Yu Q, Yang J. Identifications of immune-responsive genes for adaptative traits by comparative transcriptome analysis of spleen tissue from Kazakh and Suffolk sheep. Sci Rep 2021; 11:3157. [PMID: 33542475 PMCID: PMC7862382 DOI: 10.1038/s41598-021-82878-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 01/25/2021] [Indexed: 12/24/2022] Open
Abstract
Aridity and heat are significant environmental stressors that affect sheep adaptation and adaptability, thus influencing immunity, growth, reproduction, production performance, and profitability. The aim of this study was to profile mRNA expression levels in the spleen of indigenous Kazakh sheep breed for comparative analysis with the exotic Suffolk breed. Spleen histomorphology was observed in indigenous Kazakh sheep and exotic Suffolk sheep raised in Xinjiang China. Transcriptome sequencing of spleen tissue from the two breeds were performed via Illumina high-throughput sequencing technology and validated by RT-qPCR. Blood cytokine and IgG levels differed between the two breeds and IgG and IL-1β were significantly higher in Kazakh sheep than in Suffolk sheep (p < 0.05), though spleen tissue morphology was the same. A total of 52.04 Gb clean reads were obtained and the clean reads were assembled into 67,271 unigenes using bioinformatics analysis. Profiling analysis of differential gene expression showed that 1158 differentially expressed genes were found when comparing Suffolk with Kazakh sheep, including 246 up-regulated genes and 912 down-regulated genes. Utilizing gene ontology annotation and pathway analysis, 21 immune- responsive genes were identified as spleen-specific genes associated with adaptive traits and were significantly enriched in hematopoietic cell lineage, natural killer cell-mediated cytotoxicity, complement and coagulation cascades, and in the intestinal immune network for IgA production. Four pathways and up-regulated genes associated with immune responses in indigenous sheep played indispensable and promoting roles in arid and hot environments. Overall, this study provides valuable transcriptome data on the immunological mechanisms related to adaptive traits in indigenous and exotic sheep and offers a foundation for research into adaptive evolution.
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Affiliation(s)
- Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Shihezi, 832000, China.,Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Yong-Lin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Shihezi, 832000, China.,Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Guo-Qing Li
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Shihezi, 832000, China.,Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Shihezi, 832000, China.,Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Jinzeng Yang
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii, Honolulu, HI, 96822, USA.
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11
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Song J, McDowell JR. Comparative transcriptomics of spotted seatrout ( Cynoscion nebulosus) populations to cold and heat stress. Ecol Evol 2021; 11:1352-1367. [PMID: 33598136 PMCID: PMC7863673 DOI: 10.1002/ece3.7138] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/25/2022] Open
Abstract
Resilience to climate change depends on a species' adaptive potential and phenotypic plasticity. The latter can enhance survival of individual organisms during short periods of extreme environmental perturbations, allowing genetic adaptation to take place over generations. Along the U.S. East Coast, estuarine-dependent spotted seatrout (Cynoscion nebulosus) populations span a steep temperature gradient that provides an ideal opportunity to explore the molecular basis of phenotypic plasticity. Genetically distinct spotted seatrout sampled from a northern and a southern population were exposed to acute cold and heat stress (5 biological replicates in each treatment and control group), and their transcriptomic responses were compared using RNA-sequencing (RNA-seq). The southern population showed a larger transcriptomic response to acute cold stress, whereas the northern population showed a larger transcriptomic response to acute heat stress compared with their respective population controls. Shared transcripts showing significant differences in expression levels were predominantly enriched in pathways that included metabolism, transcriptional regulation, and immune response. In response to heat stress, only the northern population significantly upregulated genes in the apoptosis pathway, which could suggest greater vulnerability to future heat waves in this population as compared to the southern population. Genes showing population-specific patterns of expression, including hpt, acot, hspa5, and hsc71, are candidates for future studies aiming to monitor intraspecific differences in temperature stress responses in spotted seatrout. Our findings contribute to the current understanding of phenotypic plasticity and provide a basis for predicting the response of a eurythermal fish species to future extreme temperatures.
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Affiliation(s)
- Jingwei Song
- Virginia Institute of Marine Science (VIMS)College of William and MaryGloucester PointVAUSA
| | - Jan R. McDowell
- Virginia Institute of Marine Science (VIMS)College of William and MaryGloucester PointVAUSA
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12
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Wu Q, Ning X, Jiang S, Sun L. Transcriptome analysis reveals seven key immune pathways of Japanese flounder (Paralichthys olivaceus) involved in megalocytivirus infection. FISH & SHELLFISH IMMUNOLOGY 2020; 103:150-158. [PMID: 32413472 DOI: 10.1016/j.fsi.2020.05.011] [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: 12/05/2019] [Revised: 04/20/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Megalocytivirus is a serious viral pathogen to many farmed fish including Japanese flounder (Paralichthys olivaceus). In this study, in order to systematically identify host immune genes induced by megalocytivirus infection, we examined the transcription profiles of flounder infected by megalocytivirus for 2, 6, and 8 days. Compared with uninfected fish, virus-infected fish exhibited 1242 differentially expressed genes (DEGs), with 225, 275, and 877 DEGs occurring at 2, 6, and 8 days post infection, respectively. Of these DEGs, 728 were upregulated and 659 were downregulated. The majority of DEGs were time-specific and formed four distinct expression profiles well correlated with the time of infection. The DEGs were classified into diverse Gene Ontology (GO) functional terms and enriched in 27 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, approximately one third of which were related to immunity. Weighted co-expression network analysis (WGCNA) was used to identify 16 key immune DEGs belonging to seven immune pathways (RIG-I-like receptor signaling pathway, JAK-STAT signaling pathway, TLR signaling pathway, cytokine-cytokine receptor interaction, phagosome, apoptosis, and p53 signaling pathway). These pathways interacted extensively and formed complicated networks. This study provided a global picture of megalocytivirus-induced gene expression profiles of flounder at the transcriptome level and uncovered a set of key immune genes and pathways closely linked to megalocytivirus infection. These results provided a set of targets for future delineation of the key factors implicated in the anti-megalocytivirus immunity of flounder.
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Affiliation(s)
- Qian Wu
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xianhui Ning
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Shuai Jiang
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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13
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Cui W, Ma A, Wang X, Huang Z. Myo-inositol enhances the low-salinity tolerance of turbot (Scophthalmus maximus) by modulating cortisol synthesis. Biochem Biophys Res Commun 2020; 526:913-919. [DOI: 10.1016/j.bbrc.2020.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/02/2020] [Indexed: 11/26/2022]
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14
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Wu L, Yang Y, Kong L, Bian X, Guo Z, Fu S, Liang F, Li B, Ye J. Comparative transcriptome analysis of the transcriptional heterogeneity in different IgM + cell subsets from peripheral blood of Nile tilapia (Oreochromis niloticus). FISH & SHELLFISH IMMUNOLOGY 2019; 93:612-622. [PMID: 31408730 DOI: 10.1016/j.fsi.2019.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
In teleost fish, IgM+ B cells play important roles in innate and adaptive immunity. Different IgM+ B cells are detected in teleost, named IgMlo and IgMhi B cell subsets, according to the distinct expression levels of membrane IgM (mIgM). However, the study on the heterogeneity in IgM+ B cell subsets remains poorly understood. In this study, the comparative transcriptomic profiles of IgM-, IgMlo and IgMhi from peripheral blood of Nile tilapia (Oreochromis niloticus) were carried out by using RNA-sequencing technique. A total of 6045 and 5470 differentially expressed genes (DEGs) were detected in IgMlo and IgMhi cells, respectively, as compared with IgM- lymphocytes, whereas 3835 genes were differentially expressed when IgMlo compared to IgMhi cells. Analysis of the KEGG database indicated that the DEGs were enriched in immune system categories and signaling transduction and interaction in IgM- vs IgMhi, IgM- vs IgMlo and IgMlo vs IgMhi. Comparatively, in IgMlo vs IgMhi, GO enrichment analysis indicated that the DEGs enriched in nucleic acid binding transcription factor activity. Analysis of crucial transcription factors for B cell differentiation indicated that IgMlo and IgMhi cell clusters belonged to the different B cell subsets. The data generated in this study may provide insights into understanding the heterogeneity of IgM+ cells in teleost, and suggest that IgM+ B cells play a crucial role in innate immunity.
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Affiliation(s)
- Liting Wu
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research, Center for Environmentally-Friendly Aquaculture, Guangzhou, 510631, PR China
| | - Yanjian Yang
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research, Center for Environmentally-Friendly Aquaculture, Guangzhou, 510631, PR China
| | - Linghe Kong
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research, Center for Environmentally-Friendly Aquaculture, Guangzhou, 510631, PR China
| | - Xia Bian
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research, Center for Environmentally-Friendly Aquaculture, Guangzhou, 510631, PR China
| | - Zheng Guo
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research, Center for Environmentally-Friendly Aquaculture, Guangzhou, 510631, PR China
| | - Shengli Fu
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research, Center for Environmentally-Friendly Aquaculture, Guangzhou, 510631, PR China
| | - Fang Liang
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research, Center for Environmentally-Friendly Aquaculture, Guangzhou, 510631, PR China
| | - Bingxi Li
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research, Center for Environmentally-Friendly Aquaculture, Guangzhou, 510631, PR China
| | - Jianmin Ye
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research, Center for Environmentally-Friendly Aquaculture, Guangzhou, 510631, PR China.
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15
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Ceinos RM, Chivite M, López-Patiño MA, Naderi F, Soengas JL, Foulkes NS, Míguez JM. Differential circadian and light-driven rhythmicity of clock gene expression and behaviour in the turbot, Scophthalmus maximus. PLoS One 2019; 14:e0219153. [PMID: 31276539 PMCID: PMC6611576 DOI: 10.1371/journal.pone.0219153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/17/2019] [Indexed: 12/19/2022] Open
Abstract
In fish, the circadian clock represents a key regulator of many aspects of biology and is controlled by combinations of abiotic and biotic factors. These environmental factors are frequently manipulated in fish farms as part of strategies designed to maximize productivity. The flatfish turbot, Scophthalmus maximus, represents one of the most important species within the aquaculture sector in Asia and Europe. Despite the strategic importance of this species, the function and regulation of the turbot circadian system remains poorly understood. Here, we have characterized the core circadian clock genes, clock1, per1, per2 and cry1 in turbot and have studied their daily expression in various tissues under a range of lighting conditions and feeding regimes. We have also explored the influence of light and feeding time on locomotor activity. Rhythmic expression of the four core clock genes was observed in all tissues studied under light dark (LD) cycle conditions. Rhythmicity of clock gene expression persisted upon transfer to artificial free running, constant conditions confirming their endogenous circadian clock control. Furthermore, turbot showed daily cycles of locomotor activity and food anticipatory activity (FAA) under LD and scheduled-feeding, with the activity phase as well as FAA coinciding with and being dependent upon exposure to light. Thus, while FAA was absent under constant dark (DD) conditions, it was still detected in constant light (LL). In contrast, general locomotor activity was arrhythmic in both constant darkness and constant light, pointing to a major contribution of light, in concert with the circadian clock, in timing locomotor activity in this species. Our data represents an important contribution to our understanding of the circadian timing system in the turbot and thereby the optimization of rearing protocols and the improvement of the well-being of turbot within fish farming environments.
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Affiliation(s)
- Rosa M. Ceinos
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo (Pontevedra), Spain
- * E-mail:
| | - Mauro Chivite
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo (Pontevedra), Spain
| | - Marcos A. López-Patiño
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo (Pontevedra), Spain
| | - Fatemeh Naderi
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo (Pontevedra), Spain
| | - José L. Soengas
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo (Pontevedra), Spain
| | - Nicholas S. Foulkes
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Jesús M. Míguez
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo (Pontevedra), Spain
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16
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Zhao C, Jiang G, Zhou S, Wang G, Sha Z, Sun Y, Xiu Y. Molecular identification and expression analysis of four Lysin motif (LysM) domain-containing proteins from turbot (Scophthalmus maximus). FISH & SHELLFISH IMMUNOLOGY 2019; 89:271-280. [PMID: 30940580 DOI: 10.1016/j.fsi.2019.03.074] [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: 02/12/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
Lysin motif (LysM) is involved in chitin, peptidoglycan and other structurally-related oligosaccharides recognition and binding, and it is important for the biological processes of responsing to bacterial and viral infections and pathogen defense. LysM is also a widely spread protein, ranging from prokaryotes to eukaryotes, including bacteria, plants and mammals. However, research of LysM in teleosts especially in marine fish was rarely scarce. In the present study, four novel LysM domain-containing proteins in turbot (Scophthalmus maximus), named as SmLysMd1, SmLysMd2, SmLysMd3, and SmLysMd4, were cloned and identified firstly. The full-length cDNA of SmLysMd1 was 1235 bp with a 678 bp ORF, capable of encoding a peptide of 225 amino acids. The complete cDNA sequence of SmLysMd2 was 1273 bp, and contained a 675 bp ORF, encoding a predicted protein of 224 amino acids. The full-length of SmLysMd3 cDNA was 2132 bp, containing a ORF of 987 bp, with a ORF of encoding 328 amino acids. The full-length SmLysMd4 cDNA was 1115 bp contained a 888 bp ORF, encoding 295 amino acids. And all the four predicated proteins contained a specific LYSM domain. Moreover, SmLysMd1 and SmLysMd2 belong to the intracellular non-secretory types, and SmLysMd3 and SmLysMd4 belong to the anchored transmembrane types. In addition, the four SmLysMd were ubiquitously expressed in all the examined tissues. Moreover, the SmLysMds levels were up-regulated in muscle and liver, and had a reduce tendency immediately in different degree following Vibrio vulnificus challenge, indicating that the turbot LysM could be participant in the immune responses to bacterial infections. The present result of LysM in turbot for the first time in a marine fish will provide foundation knowledge for the functions studies of LysM in immune responses. Further studies should be carried out to better understand their immune mechanism in turbot and other teleosts.
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Affiliation(s)
- Chunyan Zhao
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, PR China
| | - Guangpeng Jiang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, PR China
| | - Shun Zhou
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, PR China
| | - Guodong Wang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, PR China; Homey Group Co. Ltd, Rongcheng, 264306, PR China
| | - Zhenxia Sha
- College of Life Sciences, Qingdao University, Qingdao, 266071, PR China
| | - Yongjun Sun
- Homey Group Co. Ltd, Rongcheng, 264306, PR China
| | - Yunji Xiu
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, PR China.
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17
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Xiao M, Bao F, Zhao Y, Hu Q. Transcriptome sequencing and de novo analysis of the northern snakehead, Ophiocephalus argus. J Genet 2019; 98:49. [PMID: 31204717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Northern snakehead, Ophiocephalus argus Cantor, is an endemic freshwater fish in China. However, wild stocks of O. argus are dwindling sharply. Further, water conservancy projects, environmental pollution and human activities have caused the decrease of wild stocks, which has attracted much attention. Here, we have investigated the genomic information of O. argus using IlluminaHiseq 4000 sequencing. The transcriptomes of O. argus were sequenced by Illumina technology. A total of 67,564 sequences from 79,500,964 paired-end reads were generated, 33,710 unigenes were annotated based on protein databases (NCBI nonredundant (NR) databases). In total, 7182 unigenes had the clusters of orthologous group (COG) classifications, 33,710 unigenes were assigned to 59 gene ontology (GO) terms. Further, a total of 21,464 simple sequence repeats (SSRs) from 67,564 unigenes and 113,518 single nucleotide polymorphism (SNP) sites among 335 Mclean reads were yielded for O. argus based on a transcriptome-wide search. The new transcriptome data which is presented in this study for O. argus will provide valuable information for gene discovery and downstream applications, such as phylogenetic analysis, gene-expression profiling and identification of genetic markers (SSRs andSNP).
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Affiliation(s)
- Mingsong Xiao
- College of Life and Health Science, Anhui Science and Technology University, Fengyang 233100, Anhui, People's Republic of China.
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18
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19
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Zhou S, Jiang G, Zhu Y, Liu L, Liu D, Diao J, Liu H, Xiu Y. Molecular identification and function analysis of bactericidal permeability-increasing protein/LPS-binding protein 1 (BPI/LBP1) from turbot (Scophthalmus maximus). FISH & SHELLFISH IMMUNOLOGY 2019; 87:499-506. [PMID: 30731212 DOI: 10.1016/j.fsi.2019.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/14/2019] [Accepted: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Bactericidal permeability-increasing protein (BPI) and lipopolysaccharide-binding protein (LBP) play important roles in host antimicrobial defense. In the present study, we identified one isoform of BPI/LBP gene from turbot (Scophthalmus maximus), designated as SmBPI/LBP1. The full-length cDNA sequence of SmBPI/LBP1 was 1826 bp, which encoding one secreted protein with 480 amino acid residues. Structurally, the SmBPI/LBP1 showed high similarity to its homologs from other vertebrates or invertebrates, which all contained a signal peptide, a BPI/LBP/CETP N-terminal with a LPS-binding domain, and a BPI/LBP/CETP C-terminal domain. The deduced amino acid sequences of SmBPI/LBP1 shared significant similarity to BPI/LBP of Seriola lalandi dorsalis (71%) and Paralichthys olivaceus (69%). Phylogentic analysis further supported that SmBPI/LBP1 act as a new member of vertebrate BPI/LBP family. SmBPI/LBP1 was ubiquitously expressed in all tested tissues, with the highest expression level in spleen tissue. The mRNA expression of SmBPI/LBP1 in spleen and kidney were significantly up-regulated after Vibrio vulnificus challenge. Finally, the recombinant SmBPI/LBP1 showed high affinity to lipopolysaccharide, followed by peptidoglycan and lipoteichoic acid, which is the ubiquitous component of Gram-negative or Gram-positive bacteria. These results indicated that SmBPI/LBP1 probably played important roles in immune response against bacteria infection.
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Affiliation(s)
- Shun Zhou
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Guangpeng Jiang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ying Zhu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China
| | - Lanhao Liu
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Danyang Liu
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jing Diao
- Shandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, 266104, Qingdao, PR China
| | - Hongjun Liu
- Shandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, 266104, Qingdao, PR China
| | - Yunji Xiu
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China; Shandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, 266104, Qingdao, PR China.
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20
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Syahputra K, Kania PW, Al-Jubury A, Jafaar RM, Dirks RP, Buchmann K. Transcriptomic analysis of immunity in rainbow trout (Oncorhynchus mykiss) gills infected by Ichthyophthirius multifiliis. FISH & SHELLFISH IMMUNOLOGY 2019; 86:486-496. [PMID: 30513380 DOI: 10.1016/j.fsi.2018.11.075] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/22/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
The parasite Ichthyophthirius multifiliis infecting skin, fins and gills of a wide range of freshwater fish species, including rainbow trout, is known to induce a protective immune response in the host. Although a number of studies have reported activation of several immune genes in infected fish host, the immune response picture is still considered incomplete. In order to address this issue, a comparative transcriptomic analysis was performed on infected versus uninfected rainbow trout gills and it showed that a total of 3352 (7.2%) out of 46,585 identified gene sequences were significantly regulated after parasite infection. Of differentially expressed gene sequences, 1796 genes were up-regulated and 1556 genes were down-regulated. These were classified into 61 Gene Ontology (GO) terms and mapped to 282 reference canonical pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Infection of I. multifiliis induced a clear differential expression of immune genes, related to both innate and adaptive immunity. A total of 268 (6.86%) regulated gene sequences were known to take part in 16 immune-related pathways. These involved pathways related to the innate immunity such as the Chemokine signaling pathway, Platelet activation, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and Leukocyte transendothelial migration. Elevated transcription of genes encoding the TLR 8 gene and chemokines (CCL4, CCL19, CCL28, CXCL8, CXCL11, CXCL13, CXCL14) was recorded indicating their roles in recognition of I. multifiliis and subsequent induction of the inflammatory response, respectively. A number of upregulated genes in infected gills were associated with antigen processing/presentation and T and B cell receptor signaling (including B cell marker CD22 involved in B cell development). Overall the analysis supports the notion that I. multifiliis induces a massive and varied innate response upon which a range of adaptive immune responses are established which may contribute to the long lasting protection of immunized rainbow trout.
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Affiliation(s)
- Khairul Syahputra
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark.
| | - Per W Kania
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Azmi Al-Jubury
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Rzgar M Jafaar
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Ron P Dirks
- Future Genomics Technologies B.V., Leiden, the Netherlands
| | - Kurt Buchmann
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Yang M, Wang Q, Wang S, Wang Y, Zeng Q, Qin Q. Transcriptomics analysis reveals candidate genes and pathways for susceptibility or resistance to Singapore grouper iridovirus in orange-spotted grouper (Epinephelus coioides). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 90:70-79. [PMID: 30195709 PMCID: PMC7102672 DOI: 10.1016/j.dci.2018.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 05/05/2023]
Abstract
In this study, the transcriptional response of grouper to Singapore grouper iridovirus (SGIV) stimulation was characterized using RNA sequencing. Transcriptome sequencing of three test groups in the grouper was performed using the Illumina MiSeq platform. The three test groups were a control group, which was injected with PBS buffer; a high-susceptible (HS) group, which died shortly after the SGIV injection; and a high-resistance (HR) group, which survived the SGIV injection. In total, 38,253 unigenes were generated. When the HS group was compared with the control group, 885 unigenes were upregulated and 487 unigenes were downregulated. When the HR and control groups were compared, 1114 unigenes were upregulated and 420 were downregulated, and when the HR and HS groups were compared, 1010 unigenes were upregulated and 375 were downregulated. In the KEGG analysis, two immune-related pathways, the p53 and peroxisome proliferator-activated receptor pathways, were detected with highly significant enrichment. In addition, 7465 microsatellites and 22,1569 candidate single nucleotide polymorphisms were identified from our transcriptome data. The results suggested several pathways that are associated with traits of disease susceptibility or disease resistance, and provided extensive information about novel gene sequences, gene expression profiles, and genetic markers. This may contribute to vaccine research and a breeding program against SGIV infection in grouper.
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Affiliation(s)
- Min Yang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qing Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shaowen Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yuxing Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Qiwei Qin
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Tang X, Du Y, Sheng X, Xing J, Zhan W. Molecular cloning and expression analyses of immunoglobulin tau heavy chain (IgT) in turbot, Scophthalmus maximus. Vet Immunol Immunopathol 2018; 203:1-12. [DOI: 10.1016/j.vetimm.2018.07.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 07/15/2018] [Accepted: 07/29/2018] [Indexed: 11/25/2022]
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Ye H, Lin Q, Luo H. Applications of transcriptomics and proteomics in understanding fish immunity. FISH & SHELLFISH IMMUNOLOGY 2018; 77:319-327. [PMID: 29631024 DOI: 10.1016/j.fsi.2018.03.046] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 03/22/2018] [Accepted: 03/27/2018] [Indexed: 06/08/2023]
Abstract
With the development of intensive aquaculture, economic losses increasingly result from fish mortality due to pathogen infection. In recent years, a growing number of researchers have used transcriptomic and proteomic analyses to study fish immune responses to exogenous pathogen infection. Integrating transcriptomic and proteomic analyses provides a better understanding of the fish immune system including gene expression, regulation, and the intricate biological processes underlying immune responses against infection. This review focuses on the recent advances in the fields of transcriptomics and proteomics, which have contributed to our understanding of fish immunity to exogenous pathogens.
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Affiliation(s)
- Hua Ye
- College of Animal Science, Southwest University, Chongqing 402460, China; Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Hui Luo
- College of Animal Science, Southwest University, Chongqing 402460, China.
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Zhou H, Xu QZ, Zhang R, Zhuang ZX, Ma YQ, Wang W, Ma TY, Sui Y, Liu Y, Cao X. Gonadal transcriptome analysis of hybrid triploid loaches (Misgurnus anguillicaudatus) and their diploid and tetraploid parents. PLoS One 2018; 13:e0198179. [PMID: 29795681 PMCID: PMC5967825 DOI: 10.1371/journal.pone.0198179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/15/2018] [Indexed: 11/18/2022] Open
Abstract
Hybrid triploid loaches (Misgurnus anguillicaudatus) were generated from natural tetraploid and diploid loaches. We studied the gonads of parents and offspring from direct and reciprocal crosses through histological and transcriptome analyses. The triploid offspring had inferior ability to form sperm and egg cells compared with diploid forms. After sequencing the transcriptomes, 655,109,158 clean reads were obtained, and 62,821 unigenes and 178,962 transcripts were assembled. Of these unigenes, 23,189 were annotated in the GO database, 18,525 in the KEGG database and 24,661 in the KOG database. 36 fertility-related genes were found to be differentially expressed between the direct cross (2n × 4n) progenies and their parents, while 53 fertility-related genes between the reciprocal cross (4n × 2n) progenies and their parents. Following protein-protein interaction network analyses, 54 differentially expressed genes, including PLCB4, cyp17a1 and Pla2g4d, were mined, yielding candidate genes involved in the poor fertility of hybrid triploid loaches. This is the first report of transcriptomes of gonads of hybrid triploid loaches and their parents, offering a substantial contribution to sequence resources for this species and providing a deep insight into the molecular mechanism controlling the fertility of hybrid triploid fish.
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Affiliation(s)
- He Zhou
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Qi-Zheng Xu
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Rui Zhang
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Zi-Xin Zhuang
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | | | - Wei Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Tian-Yu Ma
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Yi Sui
- Ma'anshan Municipal Agriculture Commission, Anhui, China
| | - Yang Liu
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Xiaojuan Cao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
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25
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Whole Genome Sequencing of Greater Amberjack ( Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing. Int J Genomics 2018; 2018:7984292. [PMID: 29785397 PMCID: PMC5896239 DOI: 10.1155/2018/7984292] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/04/2018] [Accepted: 01/14/2018] [Indexed: 01/30/2023] Open
Abstract
Greater amberjack (Seriola dumerili) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish. We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology. The assembled sequences were aligned onto a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map by sequence homology. A total of 215 of the longest amberjack sequences, with a total length of 622.8 Mbp (92% of the total length of the genome scaffolds), were lined up on the yellowtail RH map. We resequenced the whole genomes of 20 greater amberjacks and mapped the resulting sequences onto the reference genome sequence. About 186,000 nonredundant SNPs were successfully ordered on the reference genome. Further, we found differences in the genome structural variations between two greater amberjack populations using BreakDancer. We also analyzed the greater amberjack transcriptome and mapped the annotated sequences onto the reference genome sequence.
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Li Z, Liu X, Cheng J, He Y, Wang X, Wang Z, Qi J, Yu H, Zhang Q. Transcriptome profiling provides gene resources for understanding gill immune responses in Japanese flounder (Paralichthys olivaceus) challenged with Edwardsiella tarda. FISH & SHELLFISH IMMUNOLOGY 2018; 72:593-603. [PMID: 29175442 DOI: 10.1016/j.fsi.2017.11.041] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
Marine organisms are commonly under threats from various pathogens. Edwardsiella tarda is one of the fish pathogens that seriously infect cultured and wild fish species. Bacteremia caused by E. tarda can be a fatal disease in humans. Fish gill is a mucosa-associated lymphoid tissue that directly contacted with sea water. Generating gill transcriptomic resources that challenged by E. tarda is crucial for understanding the molecular mechanisms underlying gill immune responses. In this study, we performed transcriptome profiling of gene expression in Japanese flounder gills (Paralichthys olivaceus) challenged by E. tarda with different stress duration. An average of 40 million clean reads per library were obtained, of which approximately 83.2% were successfully mapped to the reference genome. 456 and 1037 differential expressed genes (DEGs) were identified at 8 h and 48 h post-injection, respectively. Gene annotation analysis and protein-protein interaction networks were conducted to obtain the key interaction relationships of immune-related DEGs during pathogens infection. 24 hub genes with multiple protein-protein interaction relationships or involved in multiple KEGG signaling pathways were discovered and validated by qRT-PCR. These hub genes mainly participated in Leukocyte transendothelial migration signaling pathway, B cell receptor signaling pathway, Wnt signaling pathway and Apoptosis signaling pathway. This study represents the first gill transcriptomic analysis based on protein-protein interaction networks in fish and provides valuable gene resources for understanding the fish gill immunity, which can pave the way to understand the molecular mechanisms of immune responses with E. tarda infection.
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Affiliation(s)
- Zan Li
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Xiumei Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Jie Cheng
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Yan He
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Xubo Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Zhigang Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Jie Qi
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Haiyang Yu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China.
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, China
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27
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Li Z, Liu X, Liu J, Zhang K, Yu H, He Y, Wang X, Qi J, Wang Z, Zhang Q. Transcriptome profiling based on protein-protein interaction networks provides a core set of genes for understanding blood immune response mechanisms against Edwardsiella tarda infection in Japanese flounder (Paralichthys olivaceus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 78:100-113. [PMID: 28923591 DOI: 10.1016/j.dci.2017.09.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 08/30/2017] [Accepted: 09/14/2017] [Indexed: 06/07/2023]
Abstract
Marine organisms are commonly under threat from various pathogens. Edwardsiella tarda is one of the fish pathogens that can infect both cultured and wild fish species. E. tarda can also infect other vertebrates, including amphibians, reptiles, and mammals. Bacteremia caused by E. tarda can be a fatal disease in humans. Blood acts as a pipeline for the fish immune system. Generating blood transcriptomic resources from fish challenged by E. tarda is crucial for understanding molecular mechanisms underlying blood immune response process. In this study, we performed transcriptome-wide gene expression profiling of Japanese flounder (Paralichthys olivaceus) challenged by 8 and 48 h E. tarda stress. An average of 37 million clean reads per library was obtained, and approximately 85.6% of these reads were successfully mapped to the reference genome. In addition, 808 and 1265 differential expression genes (DEGs) were found at 8 and 48 h post-injection, respectively. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to search immune-related DEGs. A protein-protein interaction network was constructed to obtain the interaction relationship of immune genes during pathogens stress. Based on KEGG and protein association networks analysis, 30 hub genes were discovered and validated by quantitative RT-PCR. This study represents the first transcriptome analysis based on protein-protein interaction networks in fish and provides us with valuable gene resources for the research of fish blood immunity, which can significantly assist us to further understand the molecular mechanisms of humans and other vertebrates against E. tarda.
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Affiliation(s)
- Zan Li
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China
| | - Xiumei Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China
| | - Jinxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China
| | - Kai Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China
| | - Haiyang Yu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, PR China
| | - Yan He
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, PR China
| | - Xubo Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, PR China
| | - Jie Qi
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, PR China
| | - Zhigang Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, PR China
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, PR China.
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Temperature-dependent immune response of olive flounder (Paralichthys olivaceus) infected with viral hemorrhagic septicemia virus (VHSV). Genes Genomics 2017; 40:315-320. [DOI: 10.1007/s13258-017-0638-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/23/2017] [Indexed: 01/13/2023]
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29
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Pereiro P, Romero A, Díaz-Rosales P, Estepa A, Figueras A, Novoa B. Nucleated Teleost Erythrocytes Play an Nk-Lysin- and Autophagy-Dependent Role in Antiviral Immunity. Front Immunol 2017; 8:1458. [PMID: 29163526 PMCID: PMC5673852 DOI: 10.3389/fimmu.2017.01458] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/18/2017] [Indexed: 01/27/2023] Open
Abstract
With the exception of mammals, vertebrate erythrocytes are nucleated. Nevertheless, these cells are usually considered as mere carriers of hemoglobin. In this work, however, we describe for the first time an unrecognized role of teleost red blood cells (RBCs). We found that Nk-lysin (Nkl), an antimicrobial peptide produced by NK-cells and cytotoxic T-lymphocytes, was also expressed in flatfish turbot (Scophthalmus maximus) erythrocytes. Although the antiviral role of Nkl remains to be elucidated, we found a positive correlation between the transcription of nkl and the resistance to an infection with Rhabdovirus in a teleost fish. Surprisingly, Nkl was found to be present in the autophagolysosomes of erythrocytes, and therefore this higher resistance provided by Nkl could be related to autophagy. The organelles of RBCs are degraded through autophagy during the maturation process of these cells. In this work, we observed that the blockage of autophagy increased the replication of viral hemorrhagic septicemia virus in nucleated teleost erythrocytes, which suggests that this mechanism may also be a key process in the defense against viruses in these cells. Nkl, which possesses membrane-perturbing ability and was affected by this modulation of RBC autophagy, could also participate in this process. For the first time, autophagy has been described not only as a life cycle event during the maturation of erythrocytes but also as a pivotal antiviral mechanism in nucleated erythrocytes. These results suggest a role of erythrocytes and Nkl in the antiviral immunity of fish and other vertebrates with nucleated RBCs.
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Affiliation(s)
- Patricia Pereiro
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain
| | - Alejandro Romero
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain
| | - Patricia Díaz-Rosales
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain
| | - Amparo Estepa
- Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, Elche, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain
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Zhang J, Sun L. Transcriptome analysis reveals temperature-regulated antiviral response in turbot Scophthalmus maximus. FISH & SHELLFISH IMMUNOLOGY 2017; 68:359-367. [PMID: 28735862 DOI: 10.1016/j.fsi.2017.07.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/19/2017] [Accepted: 07/19/2017] [Indexed: 06/07/2023]
Abstract
Megalocytivirus is a severe pathogen to turbot (Scophthalmus maximus), a popular aquaculture species in many countries. In this study, we investigated the effect of temperature on the antiviral response of turbot at transcriptome level. We found that when turbot were infected with megalocytivirus RBIV-C1 at low temperatures (14 °C, 16 °C, and 18 °C), viral replication was undetectable or moderate and no fish mortality occurred; in contrast, when turbot were infected with RBIV-C1 at high temperatures (20 °C, 22 °C, and 24 °C), viral replication was robust and 100% host mortality was observed. During the course of viral infection, downward temperature shift curbed viral replication and augmented host survival, whereas upward temperature shift promoted viral replication and reduced host survival. Comparative transcriptome analyses were conducted to examine the whole-genome transcription of turbot infected with RBIV-C1 at 16 °C and 22 °C for 4 days (samples S16-4d and S22-4d, respectively) and 8 days (samples S16-8d and S22-8d, respectively). The results showed that compared to S22-4d and S22-8d, 1600 and 5927 upregulated unigenes of various functional categories were identified in S16-4d and S16-8d, respectively. Of these genes, 22 were immune-related, most of which were detected in S16-8d and exhibited more genetic subtypes in S16-8d than in S16-4d. In addition, upregulated genes associated with cell junctions and cell membrane were also identified. These results indicate that temperature had a profound effect on the global transcription of turbot, which consequently affects the immune as well as physical resistance of the fish against viral infection.
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Affiliation(s)
- Jian Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Liu X, Li Z, Wu W, Liu Y, Liu J, He Y, Wang X, Wang Z, Qi J, Yu H, Zhang Q. Sequencing-based network analysis provides a core set of gene resource for understanding kidney immune response against Edwardsiella tarda infection in Japanese flounder. FISH & SHELLFISH IMMUNOLOGY 2017; 67:643-654. [PMID: 28651821 DOI: 10.1016/j.fsi.2017.06.051] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/13/2017] [Accepted: 06/23/2017] [Indexed: 06/07/2023]
Abstract
Marine organisms are under a frequent threat from various pathogens. Edwardsiella tarda is one of the major fish pathogens infecting both cultured and wild fish species. It can also infect a variety of other vertebrates, including amphibians, reptiles, and mammals, and bacteremia caused by E. tarda can be fatal in humans. The kidney is the largest lymphoid organ in fish, and generating kidney transcriptomic information under different stresses is crucial for understanding molecular mechanisms underlying the immune responses in the kidneys. In this study, we performed transcriptome-wide gene expression profiling of the Japanese flounder (Paralichthys olivaceus) challenged by 8 and 48 h of E. tarda infection. An average of 40 million clean reads per library was obtained, and approximately 81.6% of these reads were successfully mapped to the reference genome. In addition, 1319 and 4439 differentially expressed genes (DEGs) were found at 8 and 48 h post-injection, respectively. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to search immune-related DEGs. A protein-protein interaction network was constructed to ascertain the relationship between interacting immune genes during pathogen-induced stress. Based on the KEGG and protein association networks analysis, 24 hub genes were discovered and validated by qRT-PCR. To our knowledge, this study is the first to represent the kidney transcriptome analysis based on protein-protein interaction networks in fish. Our results provide valuable gene resources for further research on kidney immune response in fish, which can significantly improve our understanding of the molecular mechanisms underlying the immune response to E. tarda in humans and other vertebrates.
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Affiliation(s)
- Xiumei Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Zan Li
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Wenzhao Wu
- Department of Information Management, Peking University, Beijing 100871, China
| | - Yuxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Jinxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Yan He
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Xubo Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Zhigang Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Jie Qi
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Haiyang Yu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China.
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, China
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32
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Yang Y, Fu Q, Zhou T, Li Y, Liu S, Zeng Q, Wang X, Jin Y, Tian C, Qin Z, Dunham R, Liu Z. Analysis of apolipoprotein genes and their involvement in disease response of channel catfish after bacterial infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 67:464-470. [PMID: 27640368 DOI: 10.1016/j.dci.2016.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/14/2016] [Accepted: 09/14/2016] [Indexed: 06/06/2023]
Abstract
Apolipoproteins are protein component of plasma lipoproteins. They exert crucial roles in lipoprotein metabolism and serve as enzyme cofactors, receptor ligands, and lipid transfer carriers in mammals. In teleosts, apolipoproteins are also involved in diverse processes including embryonic and ontogenic development, liver and digestive system organogenesis, and innate immunity. In this study, we identified a set of 19 apolipoprotein genes in channel catfish (Ictalurus punctatus). Phylogenetic analysis and syntenic analysis were conducted to determine their identities and evolutionary relationships. The expression signatures of apolipoproteins in channel catfish were determined in healthy tissues and after infections with two major bacterial pathogens, Edwardsiella ictaluri and Flavobacterium columnare. In healthy channel catfish, most apolipoprotein genes exhibited tissue-specific expression patterns in channel catfish. After ESC and columnaris infections, 5 and 7 apolipoprotein genes were differentially expressed respectively, which presented a pathogen-specific and time-dependent pattern of regulation. After ESC infection, three exchangeable apolipoproteins (apoA-IB, apoC-I, and apoE-B) were suppressed in catfish intestine, while two nonexchangeable apolipoproteins (apoB-A and apoB-B) were slightly up-regulated. After columnaris infection, apoB-B, apoD-B, and apoE-A were significantly down-regulated in catfish gill, while apoF, apoL-IV, apoO-like, and apo-14 kDa showed significantly up-regulation. Taken together, these results suggested that apolipoprotein genes may play significant roles in innate immune responses to bacterial pathogens in channel catfish.
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Affiliation(s)
- Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Qiang Fu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Yun Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Qifan Zeng
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Xiaozhu Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Changxu Tian
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Zhenkui Qin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
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Kim JO, Kim JO, Kim WS, Oh MJ. Characterization of the Transcriptome and Gene Expression of Brain Tissue in Sevenband Grouper (Hyporthodus septemfasciatus) in Response to NNV Infection. Genes (Basel) 2017; 8:genes8010031. [PMID: 28098800 PMCID: PMC5295026 DOI: 10.3390/genes8010031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/07/2017] [Accepted: 01/09/2017] [Indexed: 12/21/2022] Open
Abstract
Grouper is one of the favorite sea food resources in Southeast Asia. However, the outbreaks of the viral nervous necrosis (VNN) disease due to nervous necrosis virus (NNV) infection have caused mass mortality of grouper larvae. Many aqua-farms have suffered substantial financial loss due to the occurrence of VNN. To better understand the infection mechanism of NNV, we performed the transcriptome analysis of sevenband grouper brain tissue, the main target of NNV infection. After artificial NNV challenge, transcriptome of brain tissues of sevenband grouper was subjected to next generation sequencing (NGS) using an Illumina Hi-seq 2500 system. Both mRNAs from pooled samples of mock and NNV-infected sevenband grouper brains were sequenced. Clean reads of mock and NNV-infected samples were de novo assembled and obtained 104,348 unigenes. In addition, 628 differentially expressed genes (DEGs) in response to NNV infection were identified. This result could provide critical information not only for the identification of genes involved in NNV infection, but for the understanding of the response of sevenband groupers to NNV infection.
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Affiliation(s)
- Jong-Oh Kim
- Department of Aqualife Medicine, College of Fisheries and Ocean Science, Chonnam National University, Yeosu 550-749, Korea.
| | - Jae-Ok Kim
- Department of Aqualife Medicine, College of Fisheries and Ocean Science, Chonnam National University, Yeosu 550-749, Korea.
| | - Wi-Sik Kim
- Department of Aqualife Medicine, College of Fisheries and Ocean Science, Chonnam National University, Yeosu 550-749, Korea.
| | - Myung-Joo Oh
- Department of Aqualife Medicine, College of Fisheries and Ocean Science, Chonnam National University, Yeosu 550-749, Korea.
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Pereiro P, Forn-Cuni G, Figueras A, Novoa B. Pathogen-dependent role of turbot (Scophthalmus maximus) interferon-gamma. FISH & SHELLFISH IMMUNOLOGY 2016; 59:25-35. [PMID: 27742586 DOI: 10.1016/j.fsi.2016.10.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/03/2016] [Accepted: 10/10/2016] [Indexed: 06/06/2023]
Abstract
Interferon-gamma has been typically described as a pro-inflammatory cytokine playing an important role in the resolution of both viral and bacterial diseases. Nevertheless, some anti-inflammatory functions are also attributed to this molecule. In this work we have characterized for the first time the turbot (Scophthalmus maximus) interferon-gamma gene (ifng) and its expression pattern under basal conditions, after type I IFNs administration, and viral and bacterial infection. The intramuscular injection of an expression plasmid encoding turbot Ifng (pMCV1.4-ifng) was not able to affect the transcription of numerous immune genes directly related to the activity of IFN-gamma, with the exception of macrophage-colony stimulating factor (csf1). It was also unable to reduce the mortality caused by a Viral Hemorrhagic Septicemia Virus (VHSV) or Aeromonas salmonicida challenge. Interestingly, at 24 h post-infection, turbot previously inoculated with pMCV1.4-ifng and infected with VHSV showed an increase in the expression of pro-inflammatory cytokines and type I IFNs compared to those fish not receiving expression plasmid, indicating a synergic effect of Ifng and VHSV. On the other hand, some macrophage markers, such as the macrophage receptor with collagenous structure (marco), were down-regulated by Ifng during the viral infection. Ifng had the opposite effect in those turbot infected with the bacteria, showing a reduction in the transcription of pro-inflammatory and type I IFNs genes, and an increase in the expression of genes related to the activity of macrophages.
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Affiliation(s)
- Patricia Pereiro
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Gabriel Forn-Cuni
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain.
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Gao C, Fu Q, Su B, Zhou S, Liu F, Song L, Zhang M, Ren Y, Dong X, Tan F, Li C. Transcriptomic profiling revealed the signatures of intestinal barrier alteration and pathogen entry in turbot (Scophthalmus maximus) following Vibrio anguillarum challenge. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 65:159-168. [PMID: 27431928 DOI: 10.1016/j.dci.2016.07.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/14/2016] [Accepted: 07/14/2016] [Indexed: 06/06/2023]
Abstract
The mucosal immune system serves as the frontline barriers of host defense against pathogen infection, especially for the fishes, which are living in the pathogen rich aquatic environment. The intestine constitutes the largest surface body area in constantly contact with the external pathogens, and plays a vital role in the immune defense against inflammation and pathogen infection. Previous studies have revealed that fish intestine might serves as the portal of entry for Vibrio anguillarum. To characterize the immune actors and their associated immune activities in turbot intestine barrier during bacterial infection, here we examined the gene expression profiles of turbot intestine at three time points following experimental infection with V. anguillarum utilizing RNA-seq technology. A total of 122 million reads were assembled into 183,101 contigs with an average length of 1151 bp and the N50 size of 2302 bp. Analysis of differential gene expression between control and infected samples at 1 h, 4 h, and 12 h revealed 2079 significantly expressed genes. Enrichment and pathway analysis of the differentially expressed genes showed the centrality of the pathogen attachment and recognition, antioxidant/apoptosis, mucus barrier modification and immune activation/inflammation in the pathogen entry and host immune responses. The present study reported the novel gene expression patterns in turbot mucosal immunity, which were overlooked in previous studies. Our results can help to understand the mechanisms of turbot host defense, and may also provide foundation to identify the biomarkers for future selection of disease-resistant broodstock and evaluation of disease prevention and treatment options.
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Affiliation(s)
- Chengbin Gao
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiang Fu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Baofeng Su
- Ministry of Agriculture Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Shun Zhou
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Fengqiao Liu
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Song
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Zhang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yichao Ren
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaoyu Dong
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Fenghua Tan
- School of International Education and Exchange, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China.
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Identification of genes in the hypothalamus-pituitary-gonad axis in the brain of Amur sturgeons (Acipenser schrenckii) by comparative transcriptome analysis in relation to kisspeptin treatment. Gene 2016; 595:53-61. [DOI: 10.1016/j.gene.2016.09.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/31/2016] [Accepted: 09/16/2016] [Indexed: 11/22/2022]
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37
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Dong X, Su B, Zhou S, Shang M, Yan H, Liu F, Gao C, Tan F, Li C. Identification and expression analysis of toll-like receptor genes (TLR8 and TLR9) in mucosal tissues of turbot (Scophthalmus maximus L.) following bacterial challenge. FISH & SHELLFISH IMMUNOLOGY 2016; 58:309-317. [PMID: 27633670 DOI: 10.1016/j.fsi.2016.09.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/04/2016] [Accepted: 09/11/2016] [Indexed: 06/06/2023]
Abstract
Mucosal immune system is one of the most important components in the innate immunity and constitutes the front line of host defense against infection, especially for teleost, which are living in the pathogen-rich aquatic environment. The pathogen recognition receptors (PRRs), which can recognize the conserved pathogen-associated molecular patterns (PAMPs) of bacteria, are considered as one of the most important component for pathogen recognition and immune signaling pathways activation in mucosal immunity. In this regard, we sought to identify TLR8 and TLR9 in turbot (Scophthalmus maximus), as well as their mucosal expression patterns following different bacterial infection in mucosal tissues for the first time. The full-length TLR8 transcript consists of an open reading frame (ORF) of 3108 bp encoding the putative peptide of 1035 amino acids. While the TLR9 was 6730 bp long, containing a 3168 bp ORF that encodes 1055 amino acids. The phylogenetic analysis revealed both TLR8 and TLR9 showed the closest relationship to large yellow croaker. Moreover, both TLR8 and TLR9 could be detected in all examined healthy turbot tissues, with the lowest expression level in liver and a relatively moderate expression pattern in healthy mucosal tissues. Distinct expression patterns of TLR8 and TLR9 were comparatively observed in the mucosal tissues (intestine, gill and skin) following Vibrio anguillarum and Streptococcus iniae infection, suggesting their different roles for mucosal immunity. Further functional studies are needed to better characterize TLR8 and TLR9 and their family members, to better understand the ligand specificity and to identify their roles in different mucosal tissues in protecting fish from the pathogenically hostile environment.
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Affiliation(s)
- Xiaoyu Dong
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China
| | - Baofeng Su
- Ministry of Agriculture Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; National and Local Joint Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Shun Zhou
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China
| | - Mei Shang
- Ministry of Agriculture Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; National and Local Joint Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Hao Yan
- Ministry of Agriculture Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Fengqiao Liu
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China
| | - Chengbin Gao
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China
| | - Fenghua Tan
- School of International Education and Exchange, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China.
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38
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Zhang L, Gao C, Liu F, Song L, Su B, Li C. Characterization and expression analysis of a peptidoglycan recognition protein gene, SmPGRP2 in mucosal tissues of turbot (Scophthalmus maximus L.) following bacterial challenge. FISH & SHELLFISH IMMUNOLOGY 2016; 56:367-373. [PMID: 27461422 DOI: 10.1016/j.fsi.2016.07.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/21/2016] [Accepted: 07/23/2016] [Indexed: 06/06/2023]
Abstract
Peptidoglycan recognition receptor proteins (PGRPs), a group of pattern recognition receptors (PRRs), can recognize peptidoglycan (PGN) of the bacteria cell wall and play an important role in host immune defense against pathogen infection. They are highly structurally conserved through evolution, but with different function in innate immunity between invertebrates and vertebrates. In teleost fish, several PGRPs have been characterized recently. They have both amidase activity and bactericidal activity and are involved in indirectly killing bacteria and regulating multiple signaling pathways. However, the knowledge of PGRPs in mucosal immunity of teleost fish is still limited. In this study, we identified a PGRPs gene (SmPGRP2) of turbot and investigated its expression patterns in mucosal tissues after challenge with Gram-positive bacteria Streptococcus iniae and Gram-negative bacteria Vibrio anguillarum. Phylogenetic analysis showed the strongest relationship of turbot PGRP to halibut, which was consistent with their phylogenetic relationships. In addition, SmPGRP2 was ubiquitously expressed in turbot tissues, and constitutive expression levels were higher in classical immune tissues (including liver, spleen, and head-kidney) than mucosal tissues (intestine, gill and skin). After bacterial challenge, the expression of SmPGRP2 was induced and showed a general trend of up-regulation in mucosal tissues, except in intestine following V. anguillarum infection. These different expression patterns varied depending on both pathogen and tissue type, suggesting its distinct roles in the host immune response to bacterial pathogen.
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Affiliation(s)
- Linan Zhang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chengbin Gao
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Fengqiao Liu
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Song
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baofeng Su
- Ministry of Agriculture Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Chao Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China.
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Liu F, Su B, Gao C, Zhou S, Song L, Tan F, Dong X, Ren Y, Li C. Identification and expression analysis of TLR2 in mucosal tissues of turbot (Scophthalmus maximus L.) following bacterial challenge. FISH & SHELLFISH IMMUNOLOGY 2016; 55:654-661. [PMID: 27368539 DOI: 10.1016/j.fsi.2016.06.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 06/21/2016] [Accepted: 06/27/2016] [Indexed: 06/06/2023]
Abstract
The pathogen recognition receptors (PRRs), which can recognize the conserved pathogen-associated molecular patterns (PAMPs) of the bacteria, play key roles in the mucosal surfaces for pathogen recognition and activation of immune signaling pathways. However, our understanding of the PRRs and their activities in mucosal surfaces in the critical early time points during pathogen infection is still limited. Towards to this end, here, we sought to identify the Toll-like receptor 2 (TLR2) in turbot as well as its expression profiles in mucosal barriers following bacterial infection in the early time points. The full-length TLR2 transcript consists of open reading frame (ORF) of 2451 bp encoding the putative peptide of 816 amino acids. The phylogenetic analysis revealed the turbot TLR2 showed the closest relationship to Paralichthys olivaceus. The TLR2 mRNA expression could be detected in all examined tissues, with the most abundant expression level in liver, and the lowest expression level in skin. In addition, TLR2 showed different expression patterns following Vibrio anguillarum and Streptococcus iniae infection, but was up-regulated following both challenge, especially post S. iniae challenge. Characterization of TLR2 will probably contribute to understanding of a number of infectious diseases and broaden the knowledge of interactions between host and pathogen, which will eventually help in the development of novel intervention strategies for farming turbot.
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Affiliation(s)
- Fengqiao Liu
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baofeng Su
- Ministry of Agriculture Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; National and Local Joint Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Chengbin Gao
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shun Zhou
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Song
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Fenghua Tan
- School of International Education and Exchange, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaoyu Dong
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yichao Ren
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China.
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40
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Hu Y, Huang M, Wang W, Guan J, Kong J. Characterization of gonadal transcriptomes from the turbot (Scophthalmus maximus). Genome 2016; 59:1-10. [PMID: 26745327 DOI: 10.1139/gen-2014-0190] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mechanisms underlying sexual reproduction and sex ratio determination remains unclear in turbot, a flatfish of great commercial value. And there is limited information in the turbot database regarding genes related to the reproductive system. Here, we conducted high-throughput transcriptome profiling of turbot gonad tissues to better understand their reproductive functions and to supply essential gene sequence information for marker-assisted selection programs in the turbot industry. In this study, two gonad libraries representing sex differences in Scophthalmus maximus yielded 453 818 high-quality reads that were assembled into 24 611 contigs and 33 713 singletons by using 454 pyrosequencing, 13 936 contigs and singletons (CS) of which were annotated using BLASTx. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses revealed that various biological functions and processes were associated with many of the annotated CS. Expression analyses showed that 510 genes were differentially expressed in males versus females; 80% of these genes were annotated. In addition, 6484 and 6036 single nucleotide polymorphisms (SNPs) were identified in male and female libraries, respectively. This transcriptome resource will serve as the foundation for cDNA or SNP microarray construction, gene expression characterization, and sex-specific linkage mapping in turbot.
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Affiliation(s)
- Yulong Hu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Meng Huang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Weiji Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Jiantao Guan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Jie Kong
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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Alves RN, Gomes AS, Stueber K, Tine M, Thorne MAS, Smáradóttir H, Reinhard R, Clark MS, Rønnestad I, Power DM. The transcriptome of metamorphosing flatfish. BMC Genomics 2016; 17:413. [PMID: 27233904 PMCID: PMC4884423 DOI: 10.1186/s12864-016-2699-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/06/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Flatfish metamorphosis denotes the extraordinary transformation of a symmetric pelagic larva into an asymmetric benthic juvenile. Metamorphosis in vertebrates is driven by thyroid hormones (THs), but how they orchestrate the cellular, morphological and functional modifications associated with maturation to juvenile/adult states in flatfish is an enigma. Since THs act via thyroid receptors that are ligand activated transcription factors, we hypothesized that the maturation of tissues during metamorphosis should be preceded by significant modifications in the transcriptome. Targeting the unique metamorphosis of flatfish and taking advantage of the large size of Atlantic halibut (Hippoglossus hippoglossus) larvae, we determined the molecular basis of TH action using RNA sequencing. RESULTS De novo assembly of sequences for larval head, skin and gastrointestinal tract (GI-tract) yielded 90,676, 65,530 and 38,426 contigs, respectively. More than 57 % of the assembled sequences were successfully annotated using a multi-step Blast approach. A unique set of biological processes and candidate genes were identified specifically associated with changes in morphology and function of the head, skin and GI-tract. Transcriptome dynamics during metamorphosis were mapped with SOLiD sequencing of whole larvae and revealed greater than 8,000 differentially expressed (DE) genes significantly (p < 0.05) up- or down-regulated in comparison with the juvenile stage. Candidate transcripts quantified by SOLiD and qPCR analysis were significantly (r = 0.843; p < 0.05) correlated. The majority (98 %) of DE genes during metamorphosis were not TH-responsive. TH-responsive transcripts clustered into 6 groups based on their expression pattern during metamorphosis and the majority of the 145 DE TH-responsive genes were down-regulated. CONCLUSIONS A transcriptome resource has been generated for metamorphosing Atlantic halibut and over 8,000 DE transcripts per stage were identified. Unique sets of biological processes and candidate genes were associated with changes in the head, skin and GI-tract during metamorphosis. A small proportion of DE transcripts were TH-responsive, suggesting that they trigger gene networks, signalling cascades and transcription factors, leading to the overt changes in tissue occurring during metamorphosis.
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Affiliation(s)
- Ricardo N Alves
- Comparative Endocrinology and Integrative Biology Group, Centro de Ciências do Mar - CCMAR, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Ana S Gomes
- Department of Biology, University of Bergen, 5020, Bergen, Norway
| | - Kurt Stueber
- Max Planck-Genome Centre, Max Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829, Köln, Germany
| | - Mbaye Tine
- Max Planck-Genome Centre, Max Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829, Köln, Germany.,Current address: Molecular Zoology Laboratory, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - M A S Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | | | - Richard Reinhard
- Max Planck-Genome Centre, Max Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829, Köln, Germany
| | - M S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Ivar Rønnestad
- Department of Biology, University of Bergen, 5020, Bergen, Norway
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology Group, Centro de Ciências do Mar - CCMAR, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
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Pereiro P, Figueras A, Novoa B. Turbot (Scophthalmus maximus) vs. VHSV (Viral Hemorrhagic Septicemia Virus): A Review. Front Physiol 2016; 7:192. [PMID: 27303308 PMCID: PMC4880558 DOI: 10.3389/fphys.2016.00192] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/12/2016] [Indexed: 12/21/2022] Open
Abstract
Turbot (Scophthalmus maximus) is a very valuable fish species both in Europe and China. The culture of this flatfish is well-established but several bacteria, viruses, and parasites can produce mortality or morbidity episodes in turbot farms. Viral Hemorrhagic Septicemia Virus (VHSV) is one of the most threatening pathogens affecting turbot, because neither vaccines nor treatments are commercially available. Although the mortality in the turbot farms is relatively low, when this virus is detected all the stock have to be destroyed. The main goals that need to be improved in order to reduce the incidence of this disease is to know what are the strategies or molecules the host use to fight the virus and, in consequence, try to potentiate this response using different ways. Certain molecules can be selected as potential antiviral treatments because of their high protective effect against VHSV. On the other hand, the use of resistance markers for selective breeding is one of the most attractive approaches. This review englobes all the investigation concerning the immune interaction between turbot and VHSV, which until the last years was very scarce, and the knowledge about VHSV-resistance markers in turbot. Nowadays, the availability of abundant transcriptomic information and the recent sequencing of the turbot genome open the door to a more exhaustive and profuse investigation in these areas.
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Affiliation(s)
- Patricia Pereiro
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas Vigo, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas Vigo, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas Vigo, Spain
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Zou J, Secombes CJ. The Function of Fish Cytokines. BIOLOGY 2016; 5:biology5020023. [PMID: 27231948 PMCID: PMC4929537 DOI: 10.3390/biology5020023] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/28/2016] [Accepted: 05/17/2016] [Indexed: 12/14/2022]
Abstract
What is known about the biological activity of fish cytokines is reviewed. Most of the functional studies performed to date have been in teleost fish, and have focused on the induced effects of cytokine recombinant proteins, or have used loss- and gain-of-function experiments in zebrafish. Such studies begin to tell us about the role of these molecules in the regulation of fish immune responses and whether they are similar or divergent to the well-characterised functions of mammalian cytokines. This knowledge will aid our ability to determine and modulate the pathways leading to protective immunity, to improve fish health in aquaculture.
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Affiliation(s)
- Jun Zou
- Scottish Fish Immunology Research Centre, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK.
| | - Christopher J Secombes
- Scottish Fish Immunology Research Centre, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK.
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Figueras A, Robledo D, Corvelo A, Hermida M, Pereiro P, Rubiolo JA, Gómez-Garrido J, Carreté L, Bello X, Gut M, Gut IG, Marcet-Houben M, Forn-Cuní G, Galán B, García JL, Abal-Fabeiro JL, Pardo BG, Taboada X, Fernández C, Vlasova A, Hermoso-Pulido A, Guigó R, Álvarez-Dios JA, Gómez-Tato A, Viñas A, Maside X, Gabaldón T, Novoa B, Bouza C, Alioto T, Martínez P. Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life. DNA Res 2016; 23:181-92. [PMID: 26951068 PMCID: PMC4909306 DOI: 10.1093/dnares/dsw007] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/03/2016] [Indexed: 01/25/2023] Open
Abstract
The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish. We compare the turbot genome with model fish genomes to investigate teleost chromosome evolution. We observe a conserved macrosyntenic pattern within Percomorpha and identify large syntenic blocks within the turbot genome related to the teleost genome duplication. We identify gene family expansions and positive selection of genes associated with vision and metabolism of membrane lipids, which suggests adaptation to demersal lifestyle and to cold temperatures, respectively. Our data indicate a quick evolution and diversification of flatfish to adapt to benthic life and provide clues for understanding their controversial origin. Moreover, we investigate the genomic architecture of growth, sex determination and disease resistance, key traits for understanding local adaptation and boosting turbot production, by mapping candidate genes and previously reported quantitative trait loci. The genomic architecture of these productive traits has allowed the identification of candidate genes and enriched pathways that may represent useful information for future marker-assisted selection in turbot.
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Affiliation(s)
- Antonio Figueras
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Diego Robledo
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - André Corvelo
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, USA
| | - Miguel Hermida
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Patricia Pereiro
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Juan A Rubiolo
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Jèssica Gómez-Garrido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Laia Carreté
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Xabier Bello
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain Xenómica Comparada de Parasitos Humanos, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela 15706, Spain
| | - Marta Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Ivo Glynne Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Marina Marcet-Houben
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Gabriel Forn-Cuní
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Beatriz Galán
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - José Luis García
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - José Luis Abal-Fabeiro
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain Xenómica Comparada de Parasitos Humanos, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela 15706, Spain
| | - Belen G Pardo
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Xoana Taboada
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Carlos Fernández
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Anna Vlasova
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Antonio Hermoso-Pulido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Roderic Guigó
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - José Antonio Álvarez-Dios
- Departamento de Matemática Aplicada, Facultade de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Antonio Gómez-Tato
- Departamento de Xeometría e Topoloxía, Facultade de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ana Viñas
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Xulio Maside
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain Xenómica Comparada de Parasitos Humanos, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela 15706, Spain
| | - Toni Gabaldón
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Carmen Bouza
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Tyler Alioto
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Paulino Martínez
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
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Low CF, Mariana NS, Maha A, Chee HY, Fatimah MY. Identification of immune response-related genes and signalling pathways in spleen of Vibrio parahaemolyticus-infected Epinephelus fuscoguttatus (Forskal) by next-generation sequencing. JOURNAL OF FISH DISEASES 2016; 39:389-394. [PMID: 25786532 DOI: 10.1111/jfd.12359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 06/04/2023]
Affiliation(s)
- C-F Low
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - N S Mariana
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - A Maha
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - H-Y Chee
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - M Y Fatimah
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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46
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Ma D, Ma A, Huang Z, Wang G, Wang T, Xia D, Ma B. Transcriptome Analysis for Identification of Genes Related to Gonad Differentiation, Growth, Immune Response and Marker Discovery in The Turbot (Scophthalmus maximus). PLoS One 2016; 11:e0149414. [PMID: 26925843 PMCID: PMC4771204 DOI: 10.1371/journal.pone.0149414] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/01/2016] [Indexed: 11/18/2022] Open
Abstract
Background Turbot Scophthalmus maximus is an economically important species extensively aquacultured in China. The genetic selection program is necessary and urgent for the sustainable development of this industry, requiring more and more genome background knowledge. Transcriptome sequencing is an excellent alternative way to identify transcripts involved in specific biological processes and exploit a considerable quantity of molecular makers when no genome sequences are available. In this study, a comprehensive transcript dataset for major tissues of S. maximus was produced on basis of an Illumina platform. Results Total RNA was isolated from liver, spleen, kidney, cerebrum, gonad (testis and ovary) and muscle. Equal quantities of RNA from each type of tissues were pooled to construct two cDNA libraries (male and female). Using the Illumina paired-end sequencing technology, nearly 44.22 million clean reads in length of 100 bp were generated and then assembled into 106,643 contigs, of which 71,107 were named unigenes with an average length of 892 bp after the elimination of redundancies. Of these, 24,052 unigenes (33.83% of the total) were successfully annotated. GO, KEGG pathway mapping and COG analysis were performed to predict potential genes and their functions. Based on our sequence analysis and published documents, many candidate genes with fundamental roles in sex determination and gonad differentiation (dmrt1), growth (ghrh, myf5, prl/prlr) and immune response (TLR1/TLR21/TLR22, IL-15/IL-34), were identified for the first time in this species. In addition, a large number of credible genetic markers, including 21,192 SSRs and 8,642 SNPs, were identified in the present dataset. Conclusion This informative transcriptome provides valuable new data to increase genomic resources of Scophthalmus maximus. The future studies of corresponding gene functions will be very useful for the management of reproduction, growth and disease control in turbot aquaculture breeding programs. The molecular markers identified in this database will aid in genetic linkage analyses, mapping of quantitative trait loci, and acceleration of marker assisted selection programs.
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Affiliation(s)
- Deyou Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Dalian Ocean University, Dalian, 116023, China
| | - Aijun Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- * E-mail:
| | - Zhihui Huang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Guangning Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Ting Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Dandan Xia
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Benhe Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
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47
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Ribas L, Robledo D, Gómez-Tato A, Viñas A, Martínez P, Piferrer F. Comprehensive transcriptomic analysis of the process of gonadal sex differentiation in the turbot (Scophthalmus maximus). Mol Cell Endocrinol 2016; 422:132-149. [PMID: 26586209 DOI: 10.1016/j.mce.2015.11.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/03/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022]
Abstract
The turbot is a flatfish with a ZW/ZZ sex determination system but with a still unknown sex determining gene(s), and with a marked sexual growth dimorphism in favor of females. To better understand sexual development in turbot we sampled young turbot encompassing the whole process of gonadal differentiation and conducted a comprehensive transcriptomic study on its sex differentiation using a validated custom oligomicroarray. Also, the expression profiles of 18 canonical reproduction-related genes were studied along gonad development. The expression levels of gonadal aromatase cyp19a1a alone at three months of age allowed the accurate and early identification of sex before the first signs of histological differentiation. A total of 56 differentially expressed genes (DEG) that had not previously been related to sex differentiation in fish were identified within the first three months of age, of which 44 were associated with ovarian differentiation (e.g., cd98, gpd1 and cry2), and 12 with testicular differentiation (e.g., ace, capn8 and nxph1). To identify putative sex determining genes, ∼4.000 DEG in juvenile gonads were mapped and their positions compared with that of previously identified sex- and growth-related quantitative trait loci (QTL). Although no genes mapped to the previously identified sex-related QTLs, two genes (foxl2 and 17βhsd) of the canonical reproduction-related genes mapped to growth-QTLs in linkage group (LG) 15 and LG6, respectively, suggesting that these genes are related to the growth dimorphism in this species.
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Affiliation(s)
- L Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), 08003, Barcelona, Spain
| | - D Robledo
- Departamento de Genética. Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - A Gómez-Tato
- Departamento de Matemática Aplicada, Facultad de Matemáticas, Universidad de Santiago de Compostela, 15781, Santiago de Compostela, Spain
| | - A Viñas
- Departamento de Genética. Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - P Martínez
- Departamento de Genética. Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - F Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), 08003, Barcelona, Spain.
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Qi Z, Wu P, Zhang Q, Wei Y, Wang Z, Qiu M, Shao R, Li Y, Gao Q. Transcriptome analysis of soiny mullet (Liza haematocheila) spleen in response to Streptococcus dysgalactiae. FISH & SHELLFISH IMMUNOLOGY 2016; 49:194-204. [PMID: 26707943 DOI: 10.1016/j.fsi.2015.12.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/21/2015] [Accepted: 12/16/2015] [Indexed: 06/05/2023]
Abstract
Soiny mullet (Liza haematocheila) is becoming an economically important aquaculture mugilid species in China and other Asian countries. However, increasing incidences of bacterial pathogenic diseases has greatly hampered the production of the soiny mullet. Deeper understanding of the soiny mullet immune system and its related genes in response to bacterial infections are necessary for disease control in this species. In this study, the transcriptomic profile of spleen from soiny mullet challenged with Streptococcus dysgalactiae was analyzed by Illumina-based paired-end sequencing method. After assembly, 86,884 unique transcript fragments (unigenes) were assembled, with an average length of 991 bp. Approximately 41,795 (48.1%) unigenes were annotated in the nr NCBI database and 57.9% of the unigenes were similar to that of the Nile tilapia. A total of 24,299 unigenes were categorized into three Gene Ontology (GO) categories (molecular function, cellular component and biological process), 13,570 unigenes into 25 functional Clusters of Orthologous Groups of proteins (COG) categories, and 30,547 unigenes were grouped into 258 known pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Following S. dysgalactiae infection, 11,461 differentially expressed unigenes were identified including 4658 up-regulated unigenes and 6803 down-regulated unigenes. Significant enrichment analysis of these differentially expressed unigenes identified major immune related pathways, including the Toll-like receptor, complement and coagulation cascades, T cell receptor signaling pathway and B cell receptor signaling pathway. In addition, 24,813 simple sequence repeats (SSRs) and 127,503 candidate single nucleotide polymorphisms (SNPs) were identified from the mullet spleen transcriptome. To this date, this study has globally analyzed the transcriptome profile from the spleen of L. haematocheila after S. dysgalactiae infection. Therefore, the results of our study contributes to better on the immune system and defense mechanisms of soiny mullet in response to bacterial infection, and provides valuable references for related studies in mugilidae species which currently lack genomic reference.
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Affiliation(s)
- Zhitao Qi
- Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province, Department of Ocean Technology, Yancheng Institute of Technology, Yancheng, Jiangsu, 224051, China.
| | - Ping Wu
- Hubei Province Key Laboratory on Cardiovascular, Cerebrovascular, and Metabolic Disorders, Hubei University of Science and Technology, Xianning, Hubei, 437100, China
| | - Qihuan Zhang
- Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province, Department of Ocean Technology, Yancheng Institute of Technology, Yancheng, Jiangsu, 224051, China
| | - Youchuan Wei
- Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization, Guangxi University, Nanning, Guangxi Autonomous Region, 530004, China
| | - Zisheng Wang
- Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province, Department of Ocean Technology, Yancheng Institute of Technology, Yancheng, Jiangsu, 224051, China
| | - Ming Qiu
- Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province, Department of Ocean Technology, Yancheng Institute of Technology, Yancheng, Jiangsu, 224051, China
| | - Rong Shao
- Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province, Department of Ocean Technology, Yancheng Institute of Technology, Yancheng, Jiangsu, 224051, China
| | - Yao Li
- Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province, Department of Ocean Technology, Yancheng Institute of Technology, Yancheng, Jiangsu, 224051, China
| | - Qian Gao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
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Comparative analysis of the hepatopancreas transcriptome of grass carp (Ctenopharyngodon idellus) fed with lard oil and fish oil diets. Gene 2015; 565:192-200. [DOI: 10.1016/j.gene.2015.04.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 03/31/2015] [Accepted: 04/06/2015] [Indexed: 01/23/2023]
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50
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Tran NT, Gao ZX, Zhao HH, Yi SK, Chen BX, Zhao YH, Lin L, Liu XQ, Wang WM. Transcriptome analysis and microsatellite discovery in the blunt snout bream (Megalobrama amblycephala) after challenge with Aeromonas hydrophila. FISH & SHELLFISH IMMUNOLOGY 2015; 45:72-82. [PMID: 25681750 DOI: 10.1016/j.fsi.2015.01.034] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 06/04/2023]
Abstract
The blunt snout bream, Megalobrama amblycephala, is a herbivorous freshwater fish species native to China and a major aquaculture species in Chinese freshwater polyculture systems. In recent years, the bacterium Aeromonas hydrophila has been reported to be its pathogen causing great losses of farmed fish. To understand the immune response of the blunt snout bream to A. hydrophila infection, we used the Solexa/Illumina technology to analyze the transcriptomic profile after artificial bacterial infection. Two nonnormalized cDNA libraries were synthesized from tissues collected from control blunt snout bream or those injected with A. hydrophila. After assembly, 155,052 unigenes (average length 692.8 bp) were isolated. All unigenes were annotated using BLASTX relative to several public databases: the National Center for Biotechnology Information nonreduntant (Nr) database, SwissProt, Eukaryotic Orthologous Groups of proteins (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO). The sequence similarity (86%) of the assembled unigenes was to zebrafish based on the Nr database. A number of unigenes (n = 30,482) were assigned to three GO categories: biological processes (25,242 unigenes), molecular functions (26,096 unigenes), and cellular components (22,778 unigenes). 20,909 unigenes were classified into 25 KOG categories and 28,744 unigenes were assigned into 315 specific signaling pathways. In total, 238 significantly differentially expressed unigenes (mapped to 125 genes) were identified: 101 upregulated genes and 24 downregulated genes. Another 303 unigenes were mapped to unknown or novel genes. Among the known expressed genes identified, 53 were immune-related genes and were distributed in 71 signaling pathways. The expression patterns of selected up- and downregulated genes from the control and injected groups were determined with reverse transcription-quantitative PCR (RT-qPCR). Microsatellites (n = 10,877), including di-to pentanucleotide repeat motifs, were also identified in the blunt snout bream transcriptome profiles. This study extends our understanding of the immune defense mechanisms of the blunt snout bream against A. hydrophila and provides useful data for further studies of the immunogenetics of this species.
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Affiliation(s)
- Ngoc Tuan Tran
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Ze-Xia Gao
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Hong-Hao Zhao
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Shao-Kui Yi
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Bo-Xiang Chen
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Animal Husbandry and Fisheries Research Center of Haid Group Co., Ltd, Guangzhou 511400, China.
| | - Yu-Hua Zhao
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Li Lin
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Xue-Qin Liu
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Wei-Min Wang
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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