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Sun Z, Lou F, Zhang Y, Song N. Gill Transcriptome Sequencing and De Novo Annotation of Acanthogobius ommaturus in Response to Salinity Stress. Genes (Basel) 2020; 11:genes11060631. [PMID: 32521805 PMCID: PMC7349121 DOI: 10.3390/genes11060631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/23/2020] [Accepted: 06/04/2020] [Indexed: 01/17/2023] Open
Abstract
Acanthogobius ommaturus is a euryhaline fish widely distributed in coastal, bay and estuarine areas, showing a strong tolerance to salinity. In order to understand the mechanism of adaptation to salinity stress, RNA-seq was used to compare the transcriptome responses of Acanthogobius ommaturus to the changes of salinity. Four salinity gradients, 0 psu, 15 psu (control), 30 psu and 45 psu were set to conduct the experiment. In total, 131,225 unigenes were obtained from the gill tissue of A. ommaturus using the Illumina HiSeq 2000 platform (San Diego, USA). Compared with the gene expression profile of the control group, 572 differentially expressed genes (DEGs) were screened, with 150 at 0 psu, 170 at 30 psu, and 252 at 45 psu. Additionally, among these DEGs, Gene Ontology (GO) analysis indicated that binding, metabolic processes and cellular processes were significantly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis detected 3, 5 and 8 pathways related to signal transduction, metabolism, digestive and endocrine systems at 0 psu, 30 psu and 45 psu, respectively. Based on GO enrichment analysis and manual literature searches, the results of the present study indicated that A. ommaturus mainly responded to energy metabolism, ion transport and signal transduction to resist the damage caused by salinity stress. Eight DEGs were randomly selected for further validation by quantitative real-time PCR (qRT-PCR) and the results were consistent with the RNA-seq data.
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Affiliation(s)
| | | | | | - Na Song
- Correspondence: or ; Tel.: +86-532-820-31658
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2
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Zhang CN, Rahimnejad S, Lu KL, Zhou WH, Zhang JL. Molecular characterization of p38 MAPK from blunt snout bream (Megalobrama amblycephala) and its expression after ammonia stress, and lipopolysaccharide and bacterial challenge. FISH & SHELLFISH IMMUNOLOGY 2019; 84:848-856. [PMID: 30381267 DOI: 10.1016/j.fsi.2018.10.074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/22/2018] [Accepted: 10/26/2018] [Indexed: 06/08/2023]
Abstract
p38 mitogen-activated protein kinase (MAPK) is an important protein which plays a key role in regulating the innate immunity, so exploring its molecular characterization is helpful in understanding the resistance against microbial infections in cultured fish. Here, a full-length cDNA of p38 MAPK was cloned from liver of blunt snout bream (Megalobrama amblycephala) which covered 2419 bp with an open reading frame of 1086 bp encoding 361 amino acids. p38 MAPK contained the characteristic structures of Thr-Gly-Tyr (TGY) motif and substrate binding site Ala-Thr-Arg-Trp (ATRW), which are conserved in MAPK family. To investigate p38 MAPK functions, two in vivo experiments were carried out to examine its expression following ammonia exposure and bacterial challenge. Also, an in vitro experiment was conducted to assess the role of p38 MAPK in inflammation of primary hepatocytes induced by lipopolysaccharide (LPS). The results showed the ubiquitous expression of p38 MAPK in all the tested tissues with varying levels. p38 MAPK mRNA expression was significantly up-regulated by ammonia stress and Aeromonas hydrophila challenge, and altered in a time-dependent manner. Moreover, the results indicated that the inflammatory response induced by LPS in hepatocytes is p38 MAPK dependent as knockdown of p38 MAPK using siRNA technology depressed the expression of IL-1β and IL-6. The findings in this study showed that p38 MAPK has anti-stress property, and plays key role in protection against bacterial infection and inflammation in blunt snout bream.
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Affiliation(s)
- Chun-Nuan Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471003, China
| | - Samad Rahimnejad
- Laboratory of Aquatic Animal Nutrition and Physiology, Fisheries College, Jimei University, Xiamen, 361021, China; University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Aquaculture and Protection of Waters, Na Sádkách 1780, 370 05, České Budějovice, Czech Republic
| | - Kang-Le Lu
- Laboratory of Aquatic Animal Nutrition and Physiology, Fisheries College, Jimei University, Xiamen, 361021, China.
| | - Wen-Hao Zhou
- Laboratory of Aquatic Animal Nutrition and Physiology, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Ji-Liang Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471003, China
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Zhang X, Ding L, Yu Y, Kong W, Yin Y, Huang Z, Zhang X, Xu Z. The Change of Teleost Skin Commensal Microbiota Is Associated With Skin Mucosal Transcriptomic Responses During Parasitic Infection by Ichthyophthirius multifillis. Front Immunol 2018; 9:2972. [PMID: 30619329 PMCID: PMC6305302 DOI: 10.3389/fimmu.2018.02972] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/03/2018] [Indexed: 11/13/2022] Open
Abstract
Teleost skin serves as the first line of defense against invading pathogens, and contain a skin-associated lymphoid tissue (SALT) that elicit gut-like immune responses against antigen stimulation. Moreover, exposed to the water environment and the pathogens therein, teleost skin is also known to be colonized by diverse microbial communities. However, little is known about the interactions between microbiota and the teleost skin mucosal immune system, especially dynamic changes about the interactions under pathogen infection. We hypothesized that dramatic changes of microbial communities and strong mucosal immune response would be present in the skin of aquatic vertebrate under parasite infection. To confirm this hypothesis, we construct an infected model with rainbow trout (Oncorhynchus mykiss), which was experimentally challenged by Ichthyophthirius multifiliis (Ich). H & E staining of trout skin indicates the successful invasion of Ich and shows the morphological changes caused by Ich infection. Critically, increased mRNA expression levels of immune-related genes were detected in trout skin from experimental groups using qRT-PCR, which were further studied by RNA-Seq analysis. Here, through transcriptomics, we detected that complement factors, pro-inflammatory cytokines, and antimicrobial genes were strikingly induced in the skin of infected fish. Moreover, high alpha diversity values of microbiota in trout skin from the experimental groups were discovered. Interestingly, we found that Ich infection led to a decreased abundance of skin commensals and increased colonization of opportunistic bacteria through 16S rRNA pyrosequencing, which were mainly characterized by lose of Proteobacteria and increased intensity of Flavobacteriaceae. To our knowledge, our results suggest for the first time that parasitic infection could inhibit symbionts and offer opportunities for other pathogens' secondary infection in teleost skin.
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Affiliation(s)
- Xiaoting Zhang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Liguo Ding
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Yongyao Yu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Weiguang Kong
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Yaxing Yin
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zhenyu Huang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Xuezhen Zhang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zhen Xu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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4
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Li B, Sun S, Zhu J, Yanli S, Wuxiao Z, Ge X. Transcriptome profiling and histology changes in juvenile blunt snout bream (Megalobrama amblycephala) liver tissue in response to acute thermal stress. Genomics 2018; 111:242-250. [PMID: 30458273 DOI: 10.1016/j.ygeno.2018.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 09/21/2018] [Accepted: 11/11/2018] [Indexed: 10/27/2022]
Abstract
To understand the precise mechanism and the pathways activated by thermal stress in fish, we sampled livers from juvenile Megalobrama amblycephala exposed to control (25 °C) and test (35 °C) conditions, and performed short read (100 bp) next-generation RNA sequencing (RNA-seq). Using reads from different temperature, expression analysis identified a total of 440 differentially-expressed genes. These genes were related to oxidative stress, apoptosis, immune responses and so on. We used quantitative real-time reverse transcriptase PCR to assess the differential mRNA expression of selected genes that encode antioxidant enzymes and heat shock proteins in response to thermal stress. Fish exposed to thermal stress also showed liver damage associated with serum biochemical parameter changes. The set of genes identified showed regulatory modulation at different temperatures, and therefore could be further studied to determine how thermal stress damages M. amblycephala livers and the possible roles of reactive oxygen species in this process.
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Affiliation(s)
- Bing Li
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi 214081, PR China
| | - Shengming Sun
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
| | - Jian Zhu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
| | - Su Yanli
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi 214081, PR China
| | - Zhang Wuxiao
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi 214081, PR China
| | - Xianping Ge
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi 214081, PR China.
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5
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Zhang C, Xue Q, Xu Z, Lu C. MiR-5702 suppresses proliferation and invasion in non-small-cell lung cancer cells via posttranscriptional suppression of ZEB1. J Biochem Mol Toxicol 2018; 32:e22163. [PMID: 29975439 DOI: 10.1002/jbt.22163] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/15/2018] [Accepted: 06/11/2018] [Indexed: 12/27/2022]
Abstract
MiRNAs have emerged as important players in tumorigenesis and progression. MiR-5702 is a newly identified miRNA; the exact role of which has not been reported. Here, we found that miR-5702 was significantly decreased in the carcinoma tissues of non-small cell lung cancer (NSCLC) patients and NSCLC cell lines. Then, our results showed that the miR-5702 mimic induced apoptosis and inhibited proliferation and invasion in A549 cells. In contrast, the miR-5702 inhibitor reduced apoptosis and increased proliferation and invasion in A549 cells. Furthermore, bioinformatics and 3'-UTR luciferase reporter assays identified that oncogene zinc finger E-box-binding homeobox 1 (ZEB1) is a target gene of miR-5702. Western blotting analysis showed that miR-5702 overexpression suppressed, and miR-5702 knockdown promoted the expression of ZEB1 protein. Finally, the ZEB1 siRNA exhibited a similar effect to the miR-5702 mimic on expression of ZEB1 and its downstream genes, cell apoptosis, cell proliferation, and cell invasion, and it could antagonize the alternations in ZEB1 expression and cell behaviors by the miR-5702 inhibitor. In conclusion, miR-5702 may function as a tumor suppressor in NSCLC, which suppresses proliferation and invasion NSCLC cells via posttranscriptional suppression of ZEB1.
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Affiliation(s)
- Cheng Zhang
- The first Department of Oncology, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China
| | - Qidi Xue
- Medical Laboratory Technology, Chongqing Medical University, Chongqing, 400016, China
| | - Zhongling Xu
- The first Department of Oncology, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China
| | - Cuilian Lu
- The first Department of Oncology, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China
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Zhao Y, Zhou H, Ayisi CL, Wang Y, Wang J, Chen X, Zhao J. Suppression of miR-26a attenuates physiological disturbances arising from exposure of Nile tilapia ( Oreochromis niloticus) to ammonia. Biol Open 2018; 7:bio.029082. [PMID: 29615414 PMCID: PMC5936054 DOI: 10.1242/bio.029082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs may affect stress responses because they act as rapid responders at the post-translation level. In this study, we found that miR-26a is abundantly expressed in the brain and gill tissues of tilapia. Expression of miR-26a in the brain decreased significantly with increasing ammonia concentrations using stem-loop qPCR. To analyze the function of miRNA in vivo, miR-26a was stably knocked down with an antagomir in tilapia. Following ammonia challenge, miR-26a antagomir treatment significantly suppressed blood ammonia/[Cl−]/[K+] concentration and the reactive oxygen species production, while it markedly enhanced glutamine accumulation and antioxidant enzyme activity in the brain of tilapia, indicating that miR-26a may be involved in the remission of physiological disturbances resulting from ammonia stress. We strongly conclude that there is a direct link between miR-26a and the responses to ammonia in tilapia. Furthermore, bioinformatics analysis and luciferase assays demonstrated that miR-26a regulates HSP70 (heat shock protein 70) and GS (glutamine synthetase) expression by targeting their 3′-UTR and that the suppression of miR-26a could increase the intracellular level of HSP70 and GS in vivo. Summary: Our work increases the available information about the regulation of miR-26a and indicates that miR-26a may be involved in the remission of physiological disorders upon ammonia stress in tilapia.
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Affiliation(s)
- Yan Zhao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, 201306, Shanghai, China .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, 201306, Shanghai, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, 201306, Shanghai, China
| | - Haotian Zhou
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, 201306, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, 201306, Shanghai, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, 201306, Shanghai, China
| | - Christian Larbi Ayisi
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, 201306, Shanghai, China
| | - Yan Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, 201306, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, 201306, Shanghai, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, 201306, Shanghai, China
| | - Jun Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, 201306, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, 201306, Shanghai, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, 201306, Shanghai, China
| | - Xiaowu Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, 201306, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, 201306, Shanghai, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, 201306, Shanghai, China
| | - Jinling Zhao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, 201306, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, 201306, Shanghai, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, 201306, Shanghai, China
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7
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Huang Y, Gong W, Xiong J, Gao XC, Ren HT. Discovery and characterization of conserved and novel microRNAs from blunt snout bream (Megalobrama amblycephala) by deep sequencing. Gene 2018; 654:57-63. [PMID: 29466763 DOI: 10.1016/j.gene.2018.02.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/27/2018] [Accepted: 02/15/2018] [Indexed: 10/18/2022]
Abstract
MicroRNAs (miRNAs) are short, single stranded RNA molecules with approximately 22 nts in length, which regulate the stability and translation of messenger RNAs in several organisms. To increase the repertoire of miRNAs characterized in M. amblycephala, we used the deep sequencing technology to sequence a small RNA library using pooled RNA sample isolated from the 4 different tissues of M. amblycephala. A total of 309 conserved miRNAs that originated from 131 miRNA families were detected. 15 novel candidates miRNA were identified. Randomly selected 6 miRNAs were analyzed by stem-loop qRT-PCR and differential expression patterns were observed in 6 different tissues of M. amblycephala. Furthermore, the potential targets were predicted. GO analysis showed that most of the targets were involved in a broad range of physiological functions including fish growth, development, metabolism, stress responses and so on. Overall, our results significantly increased the number of novel miRNAs in M. amblycephala, which should be useful for further investigation into the role of miRNAs in regulating diverse biological processes.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.
| | - Wangbao Gong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jianli Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Hong Tao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
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8
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Sun S, Xuan F, Ge X, Zhu J, Zhang W. Dynamic mRNA and miRNA expression analysis in response to hypoxia and reoxygenation in the blunt snout bream (Megalobrama amblycephala). Sci Rep 2017; 7:12846. [PMID: 28993687 PMCID: PMC5634510 DOI: 10.1038/s41598-017-12537-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/12/2017] [Indexed: 12/24/2022] Open
Abstract
Adaptation to hypoxia is a complex process involving various pathways and regulation mechanisms. A better understanding of the genetic influence on these mechanisms could permit selection for hypoxia-sensitive fish. To aid this understanding, an integrated analysis of miRNA and mRNA expression was performed in Megalobrama amblycephala under four acute hypoxia and reoxygenation stages. A number of significantly differentially-expressed miRNAs and genes associated with oxidative stress were identified, and their functional characteristics were revealed by GO function and KEGG pathway analysis. They were found to be involved in HIF-1 pathways known to affect energy metabolism and apoptosis. MiRNA-mRNA interaction pairs were detected from comparison of expression between the four different stages. The function annotation results also showed that many miRNA-mRNA interaction pairs were likely to be involved in regulating hypoxia stress. As a unique resource for gene expression and regulation during hypoxia and reoxygenation, this study could provide a starting point for further studies to better understand the genetic background of hypoxia stress.
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Affiliation(s)
- Shengming Sun
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, Wuxi, 214081, P.R. China
| | - Fujun Xuan
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City, Jiangsu Province, 224002, P.R. China
| | - Xianping Ge
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, Wuxi, 214081, P.R. China.
| | - Jian Zhu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, Wuxi, 214081, P.R. China.
| | - Wuxiao Zhang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, P.R. China
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9
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Petit J, David L, Dirks R, Wiegertjes GF. Genomic and transcriptomic approaches to study immunology in cyprinids: What is next? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:48-62. [PMID: 28257855 DOI: 10.1016/j.dci.2017.02.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 02/24/2017] [Accepted: 02/26/2017] [Indexed: 06/06/2023]
Abstract
Accelerated by the introduction of Next-Generation Sequencing (NGS), a number of genomes of cyprinid fish species have been drafted, leading to a highly valuable collective resource of comparative genome information on cyprinids (Cyprinidae). In addition, NGS-based transcriptome analyses of different developmental stages, organs, or cell types, increasingly contribute to the understanding of complex physiological processes, including immune responses. Cyprinids are a highly interesting family because they comprise one of the most-diversified families of teleosts and because of their variation in ploidy level, with diploid, triploid, tetraploid, hexaploid and sometimes even octoploid species. The wealth of data obtained from NGS technologies provides both challenges and opportunities for immunological research, which will be discussed here. Correct interpretation of ploidy effects on immune responses requires knowledge of the degree of functional divergence between duplicated genes, which can differ even between closely-related cyprinid fish species. We summarize NGS-based progress in analysing immune responses and discuss the importance of respecting the presence of (multiple) duplicated gene sequences when performing transcriptome analyses for detailed understanding of complex physiological processes. Progressively, advances in NGS technology are providing workable methods to further elucidate the implications of gene duplication events and functional divergence of duplicates genes and proteins involved in immune responses in cyprinids. We conclude with discussing how future applications of NGS technologies and analysis methods could enhance immunological research and understanding.
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Affiliation(s)
- Jules Petit
- Cell Biology and Immunology Group, Wageningen Institute of Animal Sciences, Wageningen University, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Lior David
- Department of Animal Sciences, R. H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Ron Dirks
- ZF-screens B.V., J.H, Oortweg 19, 2333 CH, Leiden, The Netherlands
| | - Geert F Wiegertjes
- Cell Biology and Immunology Group, Wageningen Institute of Animal Sciences, Wageningen University, PO Box 338, 6700 AH, Wageningen, The Netherlands.
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10
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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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