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Li M, Deng A, He C, Yao Z, Zhuo Z, Wang XY, Wang Z. Genome sequencing, comparative analysis, and gene expression responses of cytochrome P450 genes in Oryzias curvinotus provide insights into environmental adaptation. Ecol Evol 2024; 14:e11565. [PMID: 38895576 PMCID: PMC11184212 DOI: 10.1002/ece3.11565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
The mangrove fish (Oryzias curvinotus) serves as a model for researching environmental adaptation and sexual development. To further such research, we sequenced and assembled a high-quality 842 Mb reference genome for O. curvinotus. Comparative genomic analysis revealed 891 expanded gene families, including significantly expanded cytochrome P450 (CYP) detoxification genes known to be involved in xenobiotic defense. We identified 69 O. curvinotus CYPs (OcuCYPs) across 18 families and 10 clans using multiple methods. Extensive RNA-seq and qPCR analysis demonstrated diverse spatiotemporal expression patterns of OcuCYPs by developmental stage, tissue type, sex, and pollutant exposure (17β-estradiol (E2) and testosterone (MT)). Many OcuCYPs exhibited sexual dimorphism in gonads, suggesting reproductive roles in steroidogenesis, while their responsiveness to model toxicants indicates their importance in environmental adaptation through enhanced detoxification. Pathway analysis highlighted expanded CYP genes in arachidonic acid metabolism, drug metabolism, and steroid hormone biosynthesis. This chromosome-level genomic resource provides crucial biological insights to elucidate the functional roles of expanded CYPs in environmental adaptation, sexual development, early life history, and conservation in the anthropogenically impacted mangrove habitats of O. curvinotus. It also enables future ecotoxicology research leveraging O. curvinotus as a pollution sentinel species.
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Affiliation(s)
- Ming Li
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
| | - Aiping Deng
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
| | - Chuanmeng He
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
| | - Zebin Yao
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
| | - Zixuan Zhuo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
| | - Xiu yue Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy CultureFisheries College, Guangdong Ocean UniversityZhanjiangChina
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Abou-Okada M, Rashad MM, Ali GE, Abdel-Radi S, Hassan A. Oxidative stress, gene expression and histopathology of cultured gilthead sea bream (Sparus aurata) naturally co-infected with Ergasilus sieboldi and Vibrio alginolyticus. BMC Vet Res 2023; 19:277. [PMID: 38104092 PMCID: PMC10724927 DOI: 10.1186/s12917-023-03840-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Parasitic and bacterial co-infections have been associated with increasing fish mortalities and severe economic losses in aquaculture through the past three decades. The aim of this study was to evaluate the oxidative stress, histopathology, and immune gene expression profile of gilthead sea bream (Sparus aurata) co-infected with Ergasilus sieboldi and Vibrio alginolyticus. RESULTS Vibrio alginolyticus and Ergasilus sieboldi were identified using 16 S rRNA and 28 S rRNA sequencing, respectively. The collagenase virulence gene was found in all Vibrio alginolyticus isolates, and the multiple antimicrobial resistance index ranged from 0.286 to 0.857. Oxidant-antioxidant parameters in the gills, skin, and muscles of naturally infected fish revealed increased lipid peroxidation levels and a decrease in catalase and glutathione antioxidant activities. Moreover, naturally co-infected gilthead sea bream exhibited substantial up-regulation of il-1β, tnf-α, and cyp1a1. Ergasilus sieboldi encircled gill lamellae with its second antennae, exhibited severe gill architectural deformation with extensive eosinophilic granular cell infiltration. Vibrio alginolyticus infection caused skin and muscle necrosis in gilthead sea bream. CONCLUSION This study described some details about the gill, skin and muscle tissue defense mechanisms of gilthead sea bream against Ergasilus sieboldi and Vibrio alginolyticus co-infections. The prevalence of co-infections was 100%, and no resistant fish were detected. These co-infections imbalance the health status of the fish by hampering the oxidant-antioxidant mechanisms and proinflammatory/inflammatory immune genes to a more detrimental side. Our results suggest that simultaneous screening for bacterial and parasitic pathogens should be considered.
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Affiliation(s)
- Mahmoud Abou-Okada
- Department of Aquatic Animal Medicine and Management, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
| | - Maha M Rashad
- Department of Biochemistry and Chemistry of Nutrition, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Ghada E Ali
- Department of Biochemistry and Chemistry of Nutrition, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Shimaa Abdel-Radi
- Department of Parasitology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Azza Hassan
- Department of Pathology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
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Slattery O, Dahle MK, Sundaram AYM, Nowak BF, Gjessing MC, Solhaug A. Functional and molecular characterization of the Atlantic salmon gill epithelium cell line ASG-10; a tool for in vitro gill research. Front Mol Biosci 2023; 10:1242879. [PMID: 37916189 PMCID: PMC10616884 DOI: 10.3389/fmolb.2023.1242879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/08/2023] [Indexed: 11/03/2023] Open
Abstract
Fish gills are not only the respiratory organ, but also essential for ion-regulation, acid-base control, detoxification, waste excretion and host defense. Multifactorial gill diseases are common in farmed Atlantic salmon, and still poorly understood. Understanding gill pathophysiology is of paramount importance, but the sacrifice of large numbers of experimental animals for this purpose should be avoided. Therefore, in vitro models, such as cell lines, are urgently required to replace fish trials. An Atlantic salmon gill epithelial cell line, ASG-10, was established at the Norwegian Veterinary institute in 2018. This cell line forms a monolayer expressing cytokeratin, e-cadherin and desmosomes, hallmarks of a functional epithelial barrier. To determine the value of ASG-10 for comparative studies of gill functions, the characterization of ASG-10 was taken one step further by performing functional assays and comparing the cell proteome and transcriptome with those of gills from juvenile freshwater Atlantic salmon. The ASG-10 cell line appear to be a homogenous cell line consisting of epithelial cells, which express tight junction proteins. We demonstrated that ASG-10 forms a barrier, both alone and in co-culture with the Atlantic salmon gill fibroblast cell line ASG-13. ASG-10 cells can phagocytose and express several ATP-binding cassette transport proteins. Additionally, ASG-10 expresses genes involved in biotransformation of xenobiotics and immune responses. Taken together, this study provides an overview of functions that can be studied using ASG-10, which will be an important contribution to in vitro gill epithelial research of Atlantic salmon.
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Affiliation(s)
- Orla Slattery
- Marine and Freshwater Research Centre, Atlantic Technological University, Galway, Ireland
| | | | - Arvind Y. M. Sundaram
- Norwegian Veterinary Institute, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Barbara F. Nowak
- Institute of Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
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Liu C, Li J, Qi X, Wang L, Sun D, Zhang J, Zhang K, Li J, Li Y, Wen H. Cytochrome P450 superfamily in spotted sea bass: Genome-wide identification and expression profiles under trichlorfon and environmental stresses. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101078. [PMID: 37121223 DOI: 10.1016/j.cbd.2023.101078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/02/2023]
Abstract
Cytochrome P450s (CYPs), as one of the most diverse enzyme superfamilies in nature, play critical functions in antioxidant reactions against endogenous and exogenous compounds. In this study, we performed genome-wide characterization of CYP superfamily members and analyzed their expression patterns under several abiotic stresses in spotted sea bass, which is known as an economically important fish species in the Chinese aquaculture industry. A total of 55 CYP genes were identified and divided into 17 families within 10 clans. The analysis of phylogeny, gene structure, and syntenic relationships provided evidence for the evolution of CYP genes and confirmed their annotation and orthology. The expression of CYP genes was examined in the liver during trichlorfon stress using quantitative real-time PCR. The results showed that 20 tested CYP genes displayed significant mRNA expression changes, indicating that they may play crucial roles in the metabolism of trichlorfon and can be potential biomarkers for trichlorfon pollution. Moreover, by screening transcriptomic databases, 10, 3 and 19 CYP genes exhibited differential expression patterns in response to hypoxia, alkalinity and heat stress, respectively. Taken together, this study provided insights into the regulation of CYP genes by toxicological and environmental stresses, laid basis for extensive functional studies of the CYP superfamily in spotted sea bass and other teleost species.
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Affiliation(s)
- Cong Liu
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Junjie Li
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Xin Qi
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Lingyu Wang
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Donglei Sun
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Jingru Zhang
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Kaiqiang Zhang
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Jianshuang Li
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Yun Li
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China.
| | - Haishen Wen
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China.
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5
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Nissa MU, Pinto N, Ghosh B, Singh U, Goswami M, Srivastava S. Proteomic analysis of liver tissue reveals Aeromonas hydrophila infection mediated modulation of host metabolic pathways in Labeo rohita. J Proteomics 2023; 279:104870. [PMID: 36906258 DOI: 10.1016/j.jprot.2023.104870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/20/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
Abstract
Aeromonas hydrophila (Ah) is a Gram-negative bacterium and a serious global pathogen causing Motile Aeromonas Septicaemia (MAS) in fish leading to global loss in aquaculture. Investigation of the molecular alterations of host tissues such as liver could be a powerful approach to identify mechanistic and diagnostic immune signatures of disease pathogenesis. We performed a proteomic analysis of Labeo rohita liver tissue to examine the protein dynamics in the host cells during Ah infection. The proteomic data was acquired using two strategies; discovery and targeted proteomics. Label-free quantification was performed between Control and challenged group (AH) to identify the differentially expressed proteins (DEPs). A total of 2525 proteins were identified and 157 were DEPs. DEPs include metabolic enzymes (CS, SUCLG2), antioxidative proteins, cytoskeletal proteins and immune related proteins (TLR3, CLEC4E). Pathways like lysosome pathway, apoptosis, metabolism of xenobiotics by cytochrome P450 were enriched by downregulated proteins. However, upregulated proteins majorly mapped to innate immune system, signaling of B cell receptor, proteosome pathway, ribosome, carbon metabolism and protein processing in ER. Our study would help in exploring the role of Toll-like receptors, C-type lectins and, metabolic intermediates like citrate and succinate in Ah pathogenesis to understand the Ah infection in fish. SIGNIFICANCE: Bacterial diseases such as motile aeromonas septicaemia (MAS) are among the most serious problems in aquaculture industry. Small molecules that target the metabolism of the host have recently emerged as potential treatment possibilities in infectious diseases. However, the ability to develop new therapies is hampered due to lack of knowledge about pathogenesis mechanisms and host-pathogen interactions. We examined alterations in the host proteome during MAS caused by Aeromonas hydrophila (Ah) infection, in Labeo rohita liver tissue to find cellular proteins and processes affected by Ah infection. Upregulated proteins belong to innate immune system, signaling of B cell receptor, proteosome pathway, ribosome, carbon metabolism and protein processing. Our work is an important step towards leveraging host metabolism in targeting the disease by providing a bigger picture on proteome pathology correlation during Ah infection.
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Affiliation(s)
- Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Nevil Pinto
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Versova, Mumbai, Maharashtra 400061, India
| | - Biplab Ghosh
- Regional Centre for Biotechnology, Faridabad 121001, India
| | - Urvi Singh
- Department of Biochemistry, Sri Venkateswara College, University of Delhi, 110034, India
| | - Mukunda Goswami
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Versova, Mumbai, Maharashtra 400061, India.
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Behrens KA, Girasek QL, Sickler A, Hyde J, Buonaccorsi VP. Regions of genetic divergence in depth-separated Sebastes rockfish species pairs: Depth as a potential driver of speciation. Mol Ecol 2021; 30:4259-4275. [PMID: 34181798 DOI: 10.1111/mec.16046] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/20/2022]
Abstract
Depth separation is a proposed driver of speciation in marine fishes, with marine rockfish (genus Sebastes) providing a potentially informative study system. Sebastes rockfishes are commercially and ecologically important. This genus encompasses more than one hundred species and the ecological and morphological variance between these species provides opportunity for identifying speciation-driving adaptations, particularly along a depth gradient. A reduced-representation sequencing method (ddRADseq) was used to compare 95 individuals encompassing six Sebastes species. In this study, we sought to identify regions of divergence between species that were indicative of divergent adaptation and reproductive barriers leading to speciation. A pairwise comparison of S. chrysomelas (black-and-yellow rockfish) and S. carnatus (gopher rockfish) FST values revealed three major regions of elevated genomic divergence, two of which were also present in the S. miniatus (vermilion rockfish) and S. crocotulus (sunset rockfish) comparison. These corresponded with regions of both elevated DXY values and reduced nucleotide diversity in two cases, suggesting a speciation-with-gene-flow evolutionary model followed by post-speciation selective sweeps within each species. Limited whole-genome resequencing was also performed to identify mutations with predicted effects between S. chrysomelas and S. carnatus. Within these islands, we identified important SNPs in genes involved in immune function and vision. This supports their potential role in speciation, as these are adaptive vectors noted in other organisms. Additionally, changes to genes involved in pigment expression and mate recognition shed light on how S. chrysomelas and S. carnatus may have become reproductively isolated.
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Affiliation(s)
- Kristen A Behrens
- Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA
| | - Quinn L Girasek
- Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA
| | - Alex Sickler
- Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - John Hyde
- Fisheries Resources Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, California, USA
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Kushwaha B, Pandey M, Das P, Joshi CG, Nagpure NS, Kumar R, Kumar D, Agarwal S, Srivastava S, Singh M, Sahoo L, Jayasankar P, Meher PK, Shah TM, Hinsu AT, Patel N, Koringa PG, Das SP, Patnaik S, Bit A, Iquebal MA, Jaiswal S, Jena J. The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes. DNA Res 2021; 28:6070145. [PMID: 33416875 PMCID: PMC7934567 DOI: 10.1093/dnares/dsaa031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
The walking catfish Clarias magur (Hamilton, 1822) (magur) is an important catfish species inhabiting the Indian subcontinent. It is considered as a highly nutritious food fish and has the capability to walk to some distance, and survive a considerable period without water. Assembly, scaffolding and several rounds of iterations resulted in 3,484 scaffolds covering ∼94% of estimated genome with 9.88 Mb largest scaffold, and N50 1.31 Mb. The genome possessed 23,748 predicted protein encoding genes with annotation of 19,279 orthologous genes. A total of 166 orthologous groups represented by 222 genes were found to be unique for this species. The Computational Analysis of gene Family Evolution (CAFE) analysis revealed expansion of 207 gene families and 100 gene families have rapidly evolved. Genes specific to important environmental and terrestrial adaptation, viz. urea cycle, vision, locomotion, olfactory and vomeronasal receptors, immune system, anti-microbial properties, mucus, thermoregulation, osmoregulation, air-breathing, detoxification, etc. were identified and critically analysed. The analysis clearly indicated that C. magur genome possessed several unique and duplicate genes similar to that of terrestrial or amphibians’ counterparts in comparison to other teleostean species. The genome information will be useful in conservation genetics, not only for this species but will also be very helpful in such studies in other catfishes.
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Affiliation(s)
- Basdeo Kushwaha
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Manmohan Pandey
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Naresh S Nagpure
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Ravindra Kumar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Suyash Agarwal
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Shreya Srivastava
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Mahender Singh
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Pallipuram Jayasankar
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Prem K Meher
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Tejas M Shah
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Namrata Patel
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Sofia P Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Siddhi Patnaik
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Amrita Bit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Mir A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Joykrushna Jena
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
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8
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Chaube R, Rawat A, Inbaraj RM, Joy KP. Cloning and characterization of estrogen hydroxylase (cyp1a1 and cyp1b1) genes in the stinging catfish Heteropneustes fossilis and induction of mRNA expression during final oocyte maturation. Comp Biochem Physiol A Mol Integr Physiol 2020; 253:110863. [PMID: 33301890 DOI: 10.1016/j.cbpa.2020.110863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
Estrogen hydroxylases (EHs) are cytochrome P450 Family 1 (Cyp1, Clan 2) proteins involved in estrogen hydroxylations at 2-, 4- or 16- carbon positions to form catecholestrogens. EHs are encoded by CYP1A1, CYP1A2 and CYP1B1 in mammals. In the catfish Heteropneustes fossilis, cyp1a1 and cyp1b1 cDNAs were cloned and characterized from liver and ovary. The cyp1a1 cDNA is 2071 bp long and codes for a 518 amino acids (aa) long protein. The cloned cyp1b1 cDNA is 1927 bp long and codes for a 509 residue protein. The deduced proteins clustered distinctly into teleost Cyp1a1 and Cyp1b1 clades, distinct from the tetrapod clusters and featured common function domains and homology with other teleost proteins. In the qPCR assay, the transcripts were the most abundant in the liver, followed by brain and ovary, and moderate in gill, kidney and muscle. Evidence was presented to show the involvement of the genes in reproduction. Expression of brain and ovarian transcripts showed significant seasonal variations with the highest abundance in the spawning phase. In situ hybridization showed the transcripts in the follicular layer (theca and granulosa) of the ovarian follicles. Periovulatory changes in the expression cyp1a1 and cyp1b1 were obtained during final oocyte maturation (FOM) and ovulation induced by human chorionic gonadotropin (hCG), both in vivo and in vitro, and by 2-hydroxyestradiol-17β (catecholestrogen) in vitro. In the brain, the transcript levels increased with time but in the ovary, the increase was maximal at 16 h and decreased at 24 h. The periovulatory activation of the cyp1 genes was reported in this study and discussed on the basis of complex regulation of FOM and ovulation.
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Affiliation(s)
- R Chaube
- Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | - A Rawat
- Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | - R M Inbaraj
- Department of Zoology, Madras Christian College, Chennai 600059, India
| | - K P Joy
- Department of Biotechnology, Cochin University of Science and Technology, Kochi 682022, India.
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Choi BS, Park JC, Kim MS, Han J, Kim DH, Hagiwara A, Sakakura Y, Hwang UK, Lee BY, Lee JS. The reference genome of the selfing fish Kryptolebias hermaphroditus: Identification of phases I and II detoxification genes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100684. [PMID: 32464543 DOI: 10.1016/j.cbd.2020.100684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/18/2020] [Accepted: 04/01/2020] [Indexed: 01/05/2023]
Abstract
The selfing fish Kryptolebias hermaphroditus has unique reproductive system for self-fertilization, making genetically homozygous offsprings. Here, we report on high density genetic map-based genome assembly for the K. hermaphroditus Panama line (PanRS). The numbers of scaffolds were 5212 and the genome was 683,992,224 bp (N50 = 27.45 Mb). The length of anchored scaffold onto 24 linkage groups was 652,231,070 bp (95.3% of genome) with 0.01% of the gap and 39.33% of GC content and complete Benchmarking Universal Single-Copy Orthologs value was 96.6%. The numbers of annotated genes were 36,756 (average gene length 1368 bp) with the GC content of 54.1%. To examine the difference between the two sister species in the genus Kryptolebias, we compared the genomes of K. hermaphroditus PanRS and Kryptolebias marmoratus PAN line on the composition of transposable elements. To demonstrate applications of genome library, phase I and II detoxification related gene families have been analyzed, and compared the syntenies containing loci of CYP and GST genes on linkage groups. This K. hermaphroditus genome information will be helpful for a better understanding on genome-wide mechanistic view of detoxification and antioxidant-related genes over evolution in the view of fish environmental ecotoxicology.
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Affiliation(s)
| | - Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jeonghoon Han
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Atsushi Hagiwara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki 852-8521, Japan; Organization for Marine Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan
| | - Yoshitaka Sakakura
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki 852-8521, Japan; Organization for Marine Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan
| | - Un-Ki Hwang
- Marine Ecological Risk Assessment Center, West Sea Fisheries Research Institute, National Institute of Fisheries Science, Incheon 46083, South Korea
| | - Bo-Young Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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10
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Ponce M, Zuasti E, Anguís V, Fernández-Díaz C. Effects of the sulfated polysaccharide ulvan from Ulva ohnoi on the modulation of the immune response in Senegalese sole (Solea senegalensis). FISH & SHELLFISH IMMUNOLOGY 2020; 100:27-40. [PMID: 32113938 DOI: 10.1016/j.fsi.2020.02.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
Sulfated polysaccharides derived from green seaweeds exhibit many beneficial biological activities and have great potential to be used as nutraceutical in aquaculture. In this work, we evaluated the effects of the sulfated polysaccharide ulvan from Ulva ohnoi on Senegalese sole (Solea senegalensis) juveniles at the transcriptomic level. Cytotoxicity assay performed in liver primary cell cultures from sole determined that the different ulvan concentrations assayed did not impair cell viability. Juveniles were intraperitoneally (IP) injected with ulvan (0.5 mg/fish) followed by a challenge with Photobacterium damselae subsp. piscicida (Phdp) at 7 days. RNASeq analyses at 2 days post injection (dpi) revealed that 402 transcripts were differentially expressed in liver between ulvan IP injected and control groups before the challenge. Genes related to bacterial and antiviral defence, complement system, chemokines, proteasomes and antigen presentation were upregulated in ulvan treated groups. A detailed expression analysis of sixteen genes related to innate and adaptive immune system was performed in two systemic tissues: liver and spleen. Ulvan injection provoked the upregulation of tlr22 and a transient inflammatory response was initiated in both liver and spleen at 2 dpi. As consequence, expression of acute phase proteins, antimicrobial peptides and complement genes was induced. Moreover, expression of mhcI, mhcII, psmb10 and bcl6 was also induced 2 dpi. At 2 dpi with Phdp, inflammatory cytokines and genes related to bacterial and antiviral defense, iron metabolism, complement system and antigen presentation were differentially modulated in survival juveniles previously IP injected with ulvan. Moreover, mortality was retarded in ulvan treated juveniles. These results provide new evidence about the role of ulvan as a bioactive compound with immunomodulatory activity in Senegalese sole as well as its possible use as vaccine adjuvant against Phdp. This is the first published study that evaluates the transcriptomic response of Senegalese sole IP injected with ulvan.
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Affiliation(s)
- Marian Ponce
- IFAPA Centro El Toruño, Camino Tiro Pichón s/n, 11500, El Puerto de Santa María, Cádiz, Spain.
| | - Eugenia Zuasti
- IFAPA Centro El Toruño, Camino Tiro Pichón s/n, 11500, El Puerto de Santa María, Cádiz, Spain
| | - Victoria Anguís
- IFAPA Centro El Toruño, Camino Tiro Pichón s/n, 11500, El Puerto de Santa María, Cádiz, Spain
| | - Catalina Fernández-Díaz
- IFAPA Centro El Toruño, Camino Tiro Pichón s/n, 11500, El Puerto de Santa María, Cádiz, Spain.
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11
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Wang Y, Wang Q, Li Y, Yin J, Ren Y, Shi C, Bergmann SM, Zhu X, Zeng W. Integrated analysis of mRNA-miRNA expression in Tilapia infected with Tilapia lake virus (TiLV) and identifies primarily immuneresponse genes. FISH & SHELLFISH IMMUNOLOGY 2020; 99:208-226. [PMID: 32001353 DOI: 10.1016/j.fsi.2020.01.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/27/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
We investigated differential gene expression in Tilapia infected with the Tilapia Lake virus (TiLV).We used high-throughput sequencing to identify mRNAs and miRNAs involved in TiLV infection progression We identified 25,359 differentially expressed genes that included 863 new genes. We identified 1770, 4142 and 4947 differently expressed genes comparing non-infected controls with 24 and 120 h infections and between the infected groups, respectively. These genes were enriched to 291 GO terms and 62 KEGG pathways and included immune system progress and virion genes. High-throughput miRNA sequencing identified 316 conserved miRNAs, 525 known miRNAs and 592 novel miRNAs. Furthermore, 138, 198 and 153 differently expressed miRNAs were found between the 3 groups listed above, respectively. Target prediction revealed numerous genes including erythropoietin isoform X2, double-stranded RNA-specific adenosine deaminase isoform X1, bone morphogenetic protein 4 and tapasin-related protein that are involved in immune responsiveness. Moreover, these target genes overlapped with differentially expressed mRNAs obtained from RNA-seq. These target genes were significantly enriched to GO terms and KEGG pathways including immune system progress, virion and Wnt signaling pathways. Expression patterns of differentially expressed mRNA and miRNAs were validated in 20 mRNA and 19 miRNAs by qRT-PCR. We also were able to construct a miRNA-mRNA target network that can further understand the molecular mechanisms on the pathogenesis of TiLV and guide future research in developing effective agents and strategies to combat TiLV infections in Tilapia.
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Affiliation(s)
- Yingying Wang
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, PR China.
| | - Qing Wang
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China.
| | - Yingying Li
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China
| | - Jiyuan Yin
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China
| | - Yan Ren
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China
| | - Cunbin Shi
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China
| | - Sven M Bergmann
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Infectology, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Xinping Zhu
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Weiwei Zeng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528231, China.
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12
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Adrian-Kalchhauser I, Blomberg A, Larsson T, Musilova Z, Peart CR, Pippel M, Solbakken MH, Suurväli J, Walser JC, Wilson JY, Alm Rosenblad M, Burguera D, Gutnik S, Michiels N, Töpel M, Pankov K, Schloissnig S, Winkler S. The round goby genome provides insights into mechanisms that may facilitate biological invasions. BMC Biol 2020; 18:11. [PMID: 31992286 PMCID: PMC6988351 DOI: 10.1186/s12915-019-0731-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
Background The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. Results We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby’s capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions. Conclusions The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish. Electronic supplementary material The online version of this article (10.1186/s12915-019-0731-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland. .,University of Bern, Institute for Fish and Wildlife Health, Länggassstrasse 122, 3012, Bern, Austria.
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Tomas Larsson
- Department of Marine Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Zuzana Musilova
- Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Claire R Peart
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152 Planegg-, Martinsried, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Monica Hongroe Solbakken
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371, Oslo, Norway
| | - Jaanus Suurväli
- Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674, Köln, Germany
| | - Jean-Claude Walser
- Genetic Diversity Centre, ETH, Universitätsstrasse 16, 8092, Zurich, Switzerland
| | - Joanna Yvonne Wilson
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Magnus Alm Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden.,NBIS Bioinformatics Infrastructure for Life Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Demian Burguera
- Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Silvia Gutnik
- Biocenter, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Nico Michiels
- Institute of Evolution and Ecology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Mats Töpel
- University of Bern, Institute for Fish and Wildlife Health, Länggassstrasse 122, 3012, Bern, Austria
| | - Kirill Pankov
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Siegfried Schloissnig
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
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13
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Mei X, Liu Y, Huang H, Du F, Huang L, Wu J, Li Y, Zhu S, Yang M. Benzothiazole inhibits the growth of Phytophthora capsici through inducing apoptosis and suppressing stress responses and metabolic detoxification. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 154:7-16. [PMID: 30765059 DOI: 10.1016/j.pestbp.2018.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/21/2018] [Accepted: 12/10/2018] [Indexed: 05/22/2023]
Abstract
Benzothiazole (BZO) is an antimicrobial secondary metabolite volatilized by many plants and microbes. However, the mechanism of BZO against phytopathogens is still unclear. Here, we found that BZO has antimicrobial activity against the oomycete pathogen Phytophthora capsici. Transcriptome and proteome analyses demonstrated that BZO significantly suppressed the expression of genes and proteins involved in morphology, abiotic stress defense and detoxification, but induced the activity of apoptosis. Annexin V-FITC/PI staining confirmed that the process of apoptosis was significantly induced by BZO at concentration of 150 mg L-1. FITC-phalloidin actin-cytoskeleton staining combined with hyphal cell wall staining and hyphal ultrastructure studies further confirmed that BZO disrupted the cell membrane and hyphal morphology through disrupting the cytoskeleton, eventually inhibiting the growth of hyphae. These data demonstrated that BZO has multiple modes of action and may act as potential leading compound for the development of new oomycete fungicides. These results also showed that the combination of transcriptomic and proteomic approaches was a useful method for exploring the novel antifungal mechanisms of natural compounds.
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Affiliation(s)
- Xinyue Mei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; College of Resources and Environment, Yunnan Agricultural University, Kunming, Yunnan Province, China
| | - Yixiang Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Fei Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Lanlin Huang
- College of Resources and Environment, Yunnan Agricultural University, Kunming, Yunnan Province, China
| | - Jiaqing Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yiwen Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.
| | - Min Yang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
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14
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Gao L, Yuan Z, Yu S, Yang Y, Li Y, He C. Genome-wide identification of HSP70/110 genes in sea cucumber Apostichopus japonicus and comparative analysis of their involvement in aestivation. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 28:162-171. [PMID: 30265919 DOI: 10.1016/j.cbd.2018.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 12/18/2022]
Abstract
HSP70/110s are a subgroup of heat shock proteins and play crucial roles in protein homeostasis. HSP70/110s can enhance cell survival in response to a multitude of stressful stimuli, of which the most studied one is heat stress. To perform a systematic study of HSP70/110s in sea cucumber Apostichopus japonicus, 15 HSP70/110 genes, including 13 HSP70s and two HSP110s, were identified and characterized from the transcriptome and genome of sea cucumber. Moderate expansion and conserved structure were found by the phylogenetic and syntenic analysis. Differential expression patterns of HSP70/110s were observed in adult individuals during aestivation, with the comparison of juvenile individuals without aestivation in chronic heat stress. Tissue-specific expression profiles were found both in adult and juvenile individuals, which might indicate that the functional tissues (intestine and respiratory tree) could be restored to normal physiological activity prior to protecting and sporting tissues (body wall and muscle). Differential expression profiles were also observed between the adult and juvenile individuals, which was mainly due to the hypometabolism in aestivation. Taken together, tissue-specific pattern and individual-specific pattern were observed in the HSP70/110 expression profiles in sea cucumber during aestivation. These findings could provide early insight into the involvement of HSP70/110s in the aestivation of marine invertebrate.
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Affiliation(s)
- Lei Gao
- Key Laboratory of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, China.
| | - Zihao Yuan
- The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Simeng Yu
- Key Laboratory of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, China
| | - 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
| | - Yunfeng Li
- Key Laboratory of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, China
| | - Chongbo He
- Key Laboratory of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, China
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15
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Sakalli S, Giang PT, Burkina V, Zamaratskaia G, Rasmussen MK, Bakal T, Tilami SK, Sampels S, Kolarova J, Grabic R, Turek J, Randak T, Zlabek V. The effects of sewage treatment plant effluents on hepatic and intestinal biomarkers in common carp (Cyprinus carpio). THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 635:1160-1169. [PMID: 29710571 DOI: 10.1016/j.scitotenv.2018.04.188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/09/2018] [Accepted: 04/14/2018] [Indexed: 06/08/2023]
Abstract
Sewage treatment plants (STPs) are one of the major source of pharmaceuticals and personal care products in the aquatic environment. Generally, the effects of individual chemicals on fish are studied under laboratory conditions, which leads to results that are potentially not realistic regarding the effects of these chemicals under environmental conditions. Therefore, in this study, common carps were held in exposed pond that receive water from STP effluents for 360 days under natural conditions. Elimination of xenobiotics starts in the fish intestine, in which the microbial community strongly influences its function. Moreover, the fish intestine functions as crucial organ for absorbing lipids and fatty acids (FA), with consequent transport to the liver where their metabolism occurs. The liver is the primary organ performing xenobiotic metabolism in fish, and therefore, the presence of pollutants may interact with the metabolism of FA. The catalytic activity of CYP1A and CYP3A-like enzymes, their gene expression, FA composition and intestinal microbiome consortia were measured. The catalytic activity of enzymes and their gene and protein expression, were induced in hepatic and intestinal tissues of fish from the exposed pond. Also, fish from the exposed pond had different compositions of FA than those from the control pond: concentration of 18:1 n-9 and 18:2 n-6 were significantly elevated and the longer chain n-3 FA 20:5 n-3, 22:5 n-3 and 22:6 n-3 were significantly lowered. There were clear differences among microbiome consortia in fish intestines across control and exposed groups. Microbiome taxa measured in exposed fish were also associated with those found in STP activated sludge. This study reveals that treated STP water, which is assumed to be clean, affected measured biomarkers in common carp.
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Affiliation(s)
- Sidika Sakalli
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
| | - Pham Thai Giang
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic
| | - Viktoriia Burkina
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic
| | - Galia Zamaratskaia
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic; Swedish University of Agricultural Sciences, Department of Molecular Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | | | - Tomas Bakal
- Institute of Microbiology AS CR, Videnska 1083, 142 00 Prague 4, Czech Republic
| | - Sarvenaz Khalili Tilami
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic
| | - Sabine Sampels
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic; Swedish University of Agricultural Sciences, Department of Molecular Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Jitka Kolarova
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic
| | - Roman Grabic
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic
| | - Jan Turek
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic
| | - Tomas Randak
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic
| | - Vladimir Zlabek
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic
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16
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Zhou T, Yuan Z, Tan S, Jin Y, Yang Y, Shi H, Wang W, Niu D, Gao L, Jiang W, Gao D, Liu Z. A Review of Molecular Responses of Catfish to Bacterial Diseases and Abiotic Stresses. Front Physiol 2018; 9:1113. [PMID: 30210354 PMCID: PMC6119772 DOI: 10.3389/fphys.2018.01113] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 07/25/2018] [Indexed: 12/11/2022] Open
Abstract
Catfish is one of the major aquaculture species in the United States. However, the catfish industry is threatened by several bacterial diseases such as enteric septicemia of catfish (ESC), columnaris disease and Aeromonas disease, as well as by abiotic stresses such as high temperature and low oxygen. Research has been conducted for several decades to understand the host responses to these diseases and abiotic stresses. With the development of sequencing technologies, and the application of genome-wide association studies in aquaculture species, significant progress has been made. This review article summarizes recent progress in understanding the molecular responses of catfish after bacterial infection and stress challenges, and in understanding of genomic and genetic basis for disease resistance and stress tolerance.
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Affiliation(s)
- Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Huitong Shi
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Wenwen Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Donghong Niu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Lei Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Wansheng Jiang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Dongya Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Zhanjiang Liu
- Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY, United States
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17
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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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Lee BY, Kim DH, Kim HS, Kim BM, Han J, Lee JS. Identification of 74 cytochrome P450 genes and co-localized cytochrome P450 genes of the CYP2K, CYP5A, and CYP46A subfamilies in the mangrove killifish Kryptolebias marmoratus. BMC Genomics 2018; 19:7. [PMID: 29295707 PMCID: PMC5751882 DOI: 10.1186/s12864-017-4410-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mangrove killifish Kryptolebias marmoratus is the only vertebrate that reproduces by self-fertilizing and is an important model species in genetics and marine ecotoxicology. Using whole-genome and transcriptome sequences, we identified all members of the cytochrome P450 (CYP) family in this model teleost and compared them with those of other teleosts. RESULTS A total of 74 cytochrome P450 genes and one pseudogene were identified in K. marmoratus. Phylogenetic analysis indicated that the CYP genes in clan 2 were most expanded, while synteny analysis with other species showed orthologous relationships of CYP subfamilies among teleosts. In addition to the CYP2K expansions, five tandem duplicated gene copies of CYP5A were observed. These features were unique to K. marmoratus. CONCLUSIONS These results shed a light on CYP gene evolution, particularly the co-localized CYP2K, CYP5A, and CYP46A subfamilies in fish. Future studies of CYP expression could identify specific endogenous and exogenous environmental factors that triggered the evolution of tandem CYP duplication in K. marmoratus.
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Affiliation(s)
- Bo-Young Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Hui-Su Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Bo-Mi Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea.
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19
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Robinson NA, Timmerhaus G, Baranski M, Andersen Ø, Takle H, Krasnov A. Training the salmon's genes: influence of aerobic exercise, swimming performance and selection on gene expression in Atlantic salmon. BMC Genomics 2017; 18:971. [PMID: 29246115 PMCID: PMC5731093 DOI: 10.1186/s12864-017-4361-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/01/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Farmed and wild Atlantic salmon are exposed to many infectious and non-infectious challenges that can cause mortality when they enter the sea. Exercise before transfer promotes growth, health and survival in the sea. Swimming performance in juveniles at the freshwater parr stage is positively associated with resistance to some diseases. Genetic variation is likely to affect response to exercise. In this study we map genetic differences associated with aerobic exercise, swimming performance and genetic origin. Eggs from the selectively bred Bolaks salmon and wild Lærdal River salmon strains were reared until parr in a common environment. Swimming performance was assessed by subjecting the fish to either continuous hard exercise or control conditions for 18 days. Heart was sampled for examination of gene expression using RNA-seq (~60 fish/treatment). RESULTS Lower expression of genes affecting immune function was found in domesticated than wild parr. Among wild parr under control exercise the expression of a large number of genes involved in general metabolism, stress and immune response was lower in superior swimmers suggesting that minimisation of energy expenditure during periods of low activity makes parr better able to sustain bursts of swimming for predator avoidance. A similar set of genes were down-regulated with training among wild parr with inferior swimming performance. These parr react to training in a way that their cardiac expression patterns become like the superior performing wild parr under control exercise conditions. Diversifying selection caused by breeding of domesticated stock, and adaptive pressures in wild stock, has affected the expression and frequency of single nucleotide polymorphisms (SNPs) for multiple functional groups of genes affecting diverse processes. SNPs associated with swimming performance in wild parr map to genes involved in energetic processes, coding for contractile filaments in the muscle and controlling cell proliferation. CONCLUSIONS Domesticated parr have less phenotypic plasticity in response to training and lower expression of genes with functions affecting immune response. The genetic response to training is complex and depends on the background of parr and their swimming ability. Exercise should be tailored to the genetics and swimming performance of fish.
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Affiliation(s)
- Nicholas A. Robinson
- Nofima, Osloveien 1, 1430 Ås, Norway
- Sustainable Aquaculture Laboratory - Temperate and Tropical (SALTT), School of BioSciences, The University of Melbourne, Parkville, Vic 3010 Australia
- Nofima, PO Box 210, 1431 Ås, Norway
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20
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Salinas I, Magadán S. Omics in fish mucosal immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:99-108. [PMID: 28235585 DOI: 10.1016/j.dci.2017.02.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 05/22/2023]
Abstract
The mucosal immune system of fish is a complex network of immune cells and molecules that are constantly surveilling the environment and protecting the host from infection. A number of "omics" tools are now available and utilized to understand the complexity of mucosal immune systems in non-traditional animal models. This review summarizes recent advances in the implementation of "omics" tools pertaining to the four mucosa-associated lymphoid tissues in teleosts. Genomics, transcriptomics, proteomics, and "omics" in microbiome research require interdisciplinary collaboration and careful experimental design. The data-rich datasets generated are proving really useful at discovering new innate immune players in fish mucosal secretions, identifying novel markers of specific mucosal immune responses, unraveling the diversity of the B and T cell repertoires and characterizing the diversity of the microbial communities present in teleost mucosal surfaces. Bioinformatics, data analysis and storage platforms should be developed to facilitate rapid processing of large datasets, especially when mammalian tools such as bioinformatics analysis software are not available in fishes.
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Affiliation(s)
- Irene Salinas
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Susana Magadán
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, University of New Mexico, Albuquerque, NM 87131, USA; Immunology Laboratory, Biomedical Research Center (CINBIO), University of Vigo, Campus Lagoas Marcosende, Vigo, Pontevedra 36310, Spain.
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21
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Siangphoe U, Archer KJ. Estimation of random effects and identifying heterogeneous genes in meta-analysis of gene expression studies. Brief Bioinform 2017; 18:602-618. [PMID: 27345525 DOI: 10.1093/bib/bbw050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/12/2022] Open
Abstract
Combining effect sizes from individual studies using random-effects meta-analysis models are commonly applied in high-dimensional gene expression data. However, unknown study heterogeneity can arise from inconsistencies in sample quality and experimental conditions. High heterogeneity of effect sizes can reduce statistical power of the models. In this study, we describe three hypothesis-testing frameworks for meta-analysis of microarray data, and review several existing meta-analytic techniques that have been used in the genomic setting. These include P-value-based methods, rank-based methods and effect-size-based methods. We then discuss limitations of some of these methods and describe random-effects-based methods in detail. We introduce two methods for estimating the inter-study variance in random-effects meta-analytic models and another method for identifying heterogeneous genes for gene expression data. We compared various methods with the standard and existing meta-analytic techniques in the genomic framework. We demonstrate our results through a series of simulations and application in Alzheimer's gene expression data.
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22
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Hu Q, Xiao H, Tian H, Meng Y. Identification and expression of cytochrome P450 genes in the Chinese giant salamander Andrias davidianus. Theriogenology 2017; 95:62-68. [PMID: 28460681 DOI: 10.1016/j.theriogenology.2017.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 03/01/2017] [Accepted: 03/04/2017] [Indexed: 10/20/2022]
Abstract
Cytochrome P450 (cyp) genes play vital roles in biological processes, including in metabolism of endogenous and exogenous compounds. Exogenous hormone influences on gene expression that leads to disruption of gonad development have been studied in several species, but whether exogenous hormones affect cyp genes that show sexually dimorphic expression remains to be determined. Here, we identified and characterized cyp genes from the widely-cultured Chinese giant salamander Andrias davidianus. We obtained 20 cyp genes including 11 genes with complete sequences. Phylogenetic analyses supported the classification of cyp genes similar to other vertebrates. Expression profile of female and male salamanders showed multiple cyp genes to exhibit higher expression in ovary than in testis, including cyp26a, cyp19a, cyp1a1, cyp4v2, cyp3a24, cyp2c20, cyp2d14, cyp2d15, and cyp4b; while cyp11a, cyp2b11, cyp11b1, cyp4f22, cyp2j6, cyp2k1, cyp2k4, cyp1a5 was higher in testis than in ovary. Seven sex-biased genes were detected after aromatase inhibitor injection and with exposure to high water temperatures. Cyp2k1, cyp11b1, and cyp2j6 expression were increased, while cyp26a, cyp2c20, cyp4b genes were decreased with aromatase inhibition. In ovary, cyp26a and cyp2c20 expression were significantly reduced; whereas cyp2k1, cyp2j6, and cyp2k4 expression were significantly elevated with no changes in cyp11a and cyp11b1 expression after temperature treatment. These findings provide valuable information for further study of sex differentiation mechanisms and cyp gene evolution.
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Affiliation(s)
- Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Hanbing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
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23
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Burkina V, Rasmussen MK, Pilipenko N, Zamaratskaia G. Comparison of xenobiotic-metabolising human, porcine, rodent, and piscine cytochrome P450. Toxicology 2017; 375:10-27. [DOI: 10.1016/j.tox.2016.11.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/16/2016] [Accepted: 11/20/2016] [Indexed: 12/25/2022]
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24
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Martin SAM, Dehler CE, Król E. Transcriptomic responses in the fish intestine. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 64:103-117. [PMID: 26995769 DOI: 10.1016/j.dci.2016.03.014] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/05/2016] [Accepted: 03/13/2016] [Indexed: 06/05/2023]
Abstract
The intestine, being a multifunctional organ central to both nutrient uptake, pathogen recognition and regulating the intestinal microbiome, has been subjected to intense research. This review will focus on the recent studies carried out using high-throughput gene expression approaches, such as microarray and RNA sequencing (RNA-seq). These techniques have advanced greatly in recent years, mainly as a result of the massive changes in sequencing methodologies. At the time of writing, there is a transition between relatively well characterised microarray platforms and the developing RNA-seq, with the prediction that within a few years as costs decrease and computation power increase, RNA-seq related approaches will supersede the microarrays. Comparisons between the approaches are made and specific examples of how the techniques have been used to examine intestinal responses to pathogens, dietary manipulations and osmoregulatory challenges are given.
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Affiliation(s)
- Samuel A M Martin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK.
| | - Carola E Dehler
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
| | - Elżbieta Król
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
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25
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Xiong S, Jing J, Wu J, Ma W, Dawar FU, Mei J, Gui JF. Characterization and sexual dimorphic expression of Cytochrome P450 genes in the hypothalamic-pituitary-gonad axis of yellow catfish. Gen Comp Endocrinol 2015; 216:90-7. [PMID: 25937250 DOI: 10.1016/j.ygcen.2015.04.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 04/18/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
Abstract
Yellow catfish (Pelteobagrus fulvidraco) is an important freshwater fish species in China. In particular, an all-male population has been commercially produced for the males grow faster than females. However, the molecular mechanisms underlying sexual dimorphism of body size and sex differentiation are still unclear in yellow catfish. This study attempts to characterize and analyze the expression of Cytochrome P450 (CYP) family members that have been shown to play an important role in sex differentiation and metabolism in teleosts. A total of 25 CYP genes were identified from our transcriptomes by 454 pyrosequencing and Solexa sequencing, including 17 genes with complete open reading frame (ORF). Phylogenetic analyses were conducted to compare these genes with their counterparts from other teleosts. In the tissues of hypothalamic-pituitary-gonad (HPG) axis, most of the genes were expressed at uniform level in both sexes. However, multiple CYP genes displayed sexual dimorphic expression, such as cyp2AD, cyp4b, cyp8a, cyp11b2, cyp17a and cyp27a expressed at higher level in testis than in ovary, whereas cyp2g, cyp7a, cyp8b, cyp19a1a and cyp26a expressed at higher level in ovary than in testis. The expression response of six CYP genes in ovary was also assessed after 17α-methyltestosterone (MT) treatment. Testis-biased expressed cyp11b2 and cyp17a were significantly up-regulated, while cyp11a and cyp19a1a were reduced in ovary after MT treatment. Our work is helpful for understanding molecular evolution of CYP genes in vertebrates and the mechanism of sexual dimorphism in teleosts.
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Affiliation(s)
- Shuting Xiong
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Jing
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Junjie Wu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenge Ma
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Farman Ullah Dawar
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Mei
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jian-Fang Gui
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China.
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26
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Oh S. How are Bayesian and Non-Parametric Methods Doing a Great Job in RNA-Seq Differential Expression Analysis? : A Review. COMMUNICATIONS FOR STATISTICAL APPLICATIONS AND METHODS 2015. [DOI: 10.5351/csam.2015.22.2.181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sunghee Oh
- Department of Veterinary Medicine, Jeju National University, Korea
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