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Li Y, Xu Q, Liu H, Dai X. Differential expression of microRNAs in giant freshwater prawn (Macrobrachium rosenbergii) during the infection of Vibrio parahaemolyticus. FISH & SHELLFISH IMMUNOLOGY 2024; 153:109827. [PMID: 39134232 DOI: 10.1016/j.fsi.2024.109827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/26/2024] [Accepted: 08/09/2024] [Indexed: 08/22/2024]
Abstract
MicroRNAs (miRNAs) are a category of small non-coding RNAs regarded as vital regulatory factors in various biological processes, especially immune regulation. The differently expressed miRNAs in Macrobrachium rosenbergii after the challenge of Vibrio parahaemolyticus were identified using high-throughput sequencing. A total of 18 known as well as 12 novel miRNAs were markedly differently expressed during the bacterial infection. The results of the target gene prediction and enrichment analysis indicated that a total of 230 target genes involved in a large variety of signaling pathways and biological processes were mediated by the miRNAs identified in the current research. Additionally, the effects of novel-miR-56, a representative differentially expressed miRNA identified in the previous infection experiment, on the immune-related gene expression in M. rosenbergii were explored. The expression of the immune-related genes including Spätzle1(Spz1), Spz4, Toll-like receptor 1 (TLR1), TLR2, TLR3, immune deficiency (IMD), myeloid differentiation factor 88 (MyD88), anti-lipopolysaccharide factor 1 (ALF1), crustin1, as well as prophenoloxidase (proPO) was significantly repressed in the novel-miR-56-overexpressed prawns. The expression of these genes tested in the novel-miR-56-overexpressed M. rosenbergii was still signally lower than the control in the subsequent V. parahaemolyticus challenge, despite the gene expression in each treatment increased significantly after the infection. Additionally, the cumulative mortality of the agomiR-56-treated prawns was significantly higher than the other treatments post the bacterial challenge. These results suggested that novel-miR-56 might function as a negative regulator of the immune-related gene expression of M. rosenbergii in the innate immune defense against V. parahaemolyticus.
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Affiliation(s)
- Yun Li
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Qi Xu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Hong Liu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Xilin Dai
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.
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SiouNing AS, Seong TS, Kondo H, Bhassu S. MicroRNA Regulation in Infectious Diseases and Its Potential as a Biosensor in Future Aquaculture Industry: A Review. Molecules 2023; 28:molecules28114357. [PMID: 37298833 DOI: 10.3390/molecules28114357] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 06/12/2023] Open
Abstract
An infectious disease is the most apprehensive problem in aquaculture as it can lead to high mortality in aquatic organisms and massive economic loss. Even though significant progress has been accomplished in therapeutic, prevention, and diagnostic using several potential technologies, more robust inventions and breakthroughs should be achieved to control the spread of infectious diseases. MicroRNA (miRNA) is an endogenous small non-coding RNA that post-transcriptionally regulates the protein-coding genes. It involves various biological regulatory mechanisms in organisms such as cell differentiation, proliferation, immune responses, development, apoptosis, and others. Furthermore, an miRNA also acts as a mediator to either regulate host responses or enhance the replication of diseases during infection. Therefore, the emergence of miRNAs could be potential candidates for the establishment of diagnostic tools for numerous infectious diseases. Interestingly, studies have revealed that miRNAs can be used as biomarkers and biosensors to detect diseases, and can also be used to design vaccines to attenuate pathogens. This review provides an overview of miRNA biogenesis and specifically focuses on its regulation during infection in aquatic organisms, especially on the host immune responses and how miRNAs enhance the replication of pathogens in the organism. In addition to that, we explored the potential applications, including diagnostic methods and treatments, that can be employed in the aquaculture industry.
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Affiliation(s)
- Aileen See SiouNing
- Animal Genomic and Genetics Evolutionary Laboratory, Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- Terra Aqua Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), Research Management and Innovation Complex, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Tang Swee Seong
- Terra Aqua Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), Research Management and Innovation Complex, University of Malaya, Kuala Lumpur 50603, Malaysia
- Microbial Biochemistry Laboratory, Division of Microbiology and Molecular Genetic, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Subha Bhassu
- Animal Genomic and Genetics Evolutionary Laboratory, Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- Terra Aqua Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), Research Management and Innovation Complex, University of Malaya, Kuala Lumpur 50603, Malaysia
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Qian H, Ma K, Feng J, Guo Z, Gong J, Chen H, Bai H, Qiu G. Transcriptome analysis of the post-larvae of giant freshwater prawn (Macrobrachium rosenbergii) after IAG gene knockdown with microRNA interference. Gen Comp Endocrinol 2022; 325:114054. [PMID: 35580689 DOI: 10.1016/j.ygcen.2022.114054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/02/2022] [Accepted: 05/12/2022] [Indexed: 11/04/2022]
Abstract
The insulin-like androgenic gland hormone gene (IAG) of crustaceans plays pivotal roles in the regulation of sex differentiation. MicroRNAs (miRNAs) are a class of short, non-coding RNAs that function as post-transcriptional gene regulators. However, little information about the regulatory relationship between miRNA and Macrobrachium rosenbergii IAG (MrIAG) were exposed. In this study, we used the 3' untranslated region (UTR) of MrIAG to predict potential target sites of miRNAs. The results showed that miR-184 has one target site in the 3'UTR of MrIAG. Dual-luciferase report assay in vitro confirmed that miR-184 can significantly down-regulate MrIAG expression. Besides, we constructed mutant plasmids of 3'UTR of MrIAG. The result displayed that after co-transfection of mutant plasmids and miR-184 agomir, the activity of luciferase was not affected compared to the control. These results indicated that miR-184 could directly regulate MrIAG. In addition, we found that overexpression of miR-184 in M. rosenbergii can lead to significant changes in the transcription level of genes. Compared with control group, we identified 1510 differentially expressed genes (DEGs) in the miR-184 injection group. Some DEGs were involved in sex differentiation, gonad development, growth and molting were found. qRT-PCR verification was performed on eight DEGs randomly, and the results showed that the expression level of sex-, growth-, and metabolism-related genes changed significantly after MrIAG gene knockdown. Collectively, findings from this study suggest that miR-184, by mediating IAG expression, may be involved in many physiological processes in M. rosenbergii. The current study lays a basic understanding for short-term silencing of MrIAG with miR-184, and facilitates miRNA function analysis in M. rosenbergii in future.
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Affiliation(s)
- Hongli Qian
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China
| | - Keyi Ma
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China.
| | - Jianbin Feng
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China
| | - Ziqi Guo
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jinhua Gong
- Jiangsu Dinghe Aquatic Technology Development Co., Ltd., Taizhou 225300, PR China
| | - Huangen Chen
- Jiangsu Fishery Technology Extension Center, Nanjing 210036, PR China
| | - Haotian Bai
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China
| | - Gaofeng Qiu
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China.
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Crooke-Rosado JL, Diaz-Mendez SC, Claudio-Roman YE, Rivera NM, Sosa MA. De novo assembly of the freshwater prawn Macrobrachium carcinus brain transcriptome for identification of potential targets for antibody development. PLoS One 2021; 16:e0249801. [PMID: 33836025 PMCID: PMC8049718 DOI: 10.1371/journal.pone.0249801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/24/2021] [Indexed: 11/29/2022] Open
Abstract
Crustaceans are major constituents of aquatic ecosystems and, as such, changes in their behavior and the structure and function of their bodies can serve as indicators of alterations in their immediate environment, such as those associated with climate change and anthropogenic contamination. We have used bioinformatics and a de novo transcriptome assembly approach to identify potential targets for developing specific antibodies to serve as nervous system function markers for freshwater prawns of the Macrobrachium spp. Total RNA was extracted from brain ganglia of Macrobrachium carcinus freshwater prawns and Illumina Next Generation Sequencing was performed using an Eel Pond mRNA Seq Protocol to construct a de novo transcriptome. Sequencing yielded 97,202,662 sequences: 47,630,546 paired and 1,941,570 singletons. Assembly with Trinity resulted in 197,898 assembled contigs from which 30,576 were annotated: 9,600 by orthology, 17,197 by homology, and 3,779 by transcript families. We looked for glutamate receptors contigs, due to their main role in crustacean excitatory neurotransmission, and found 138 contigs related to ionotropic receptors, 32 related to metabotropic receptors, and 18 to unidentified receptors. After performing multiple sequence alignments within different biological organisms and antigenicity analysis, we were able to develop antibodies for prawn AMPA ionotropic glutamate receptor 1, metabotropic glutamate receptor 1 and 4, and ionotropic NMDA glutamate receptor subunit 2B, with the expectation that the availability of these antibodies will help broaden knowledge regarding the underlying structural and functional mechanisms involved in prawn behavioral responses to environmental impacts. The Macrobrachium carcinus brain transcriptome can be an important tool for examining changes in many other nervous system molecules as a function of developmental stages, or in response to particular conditions or treatments.
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Affiliation(s)
- Jonathan L. Crooke-Rosado
- Department of Anatomy & Neurobiology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
- Institute of Neurobiology, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Sara C. Diaz-Mendez
- Department of Biology, Cayey Campus, University of Puerto Rico, Cayey, Puerto Rico
| | | | - Nilsa M. Rivera
- Department of Anatomy & Neurobiology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
- Institute of Neurobiology, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Maria A. Sosa
- Department of Anatomy & Neurobiology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
- Institute of Neurobiology, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
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Yu D, Peng Z, Wu H, Zhang X, Ji C, Peng X. Stress responses in expressions of microRNAs in mussel Mytilus galloprovincialis exposed to cadmium. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 212:111927. [PMID: 33508712 DOI: 10.1016/j.ecoenv.2021.111927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/06/2021] [Accepted: 01/10/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs) are known to have complicated functions in aquatic species, but little is known about the role of miRNAs in mollusk species under environmental stress. In this study, we performed small RNA sequencing to characterize the differentially expressed miRNAs in different tissues (whole tissues, digestive glands, gills, and gonads) of blue mussels (Mytilus galloprovincialis) exposed to cadmium (Cd). In summary, 107 known miRNAs and 32 novel miRNAs were significantly (p < 0.01) differentially expressed after Cd exposure. The peak size of miRNAs was 22 nucleotides. Target genes of these differentially expressions of miRNAs related to immune defense, apoptosis, lipid and xenobiotic metabolism showed significant changes under Cd stress. These findings provide the first characterization of miRNAs in mussel M. galloprovincialis and expressions of many target genes in response to Cd stress.
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Affiliation(s)
- Deliang Yu
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems, Shenzhen University, Shenzhen 518060, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
| | - Zheng Peng
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems, Shenzhen University, Shenzhen 518060, PR China
| | - Huifeng Wu
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), YICCAS, Yantai 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China.
| | - Xiaoying Zhang
- AstraZeneca-Shenzhen University Joint Institute of Nephrology, Department of Physiology, Shenzhen University Health Science Center, Shenzhen University, Shenzhen 518060, PR China
| | - Chenglong Ji
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), YICCAS, Yantai 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Xiao Peng
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems, Shenzhen University, Shenzhen 518060, PR China.
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Abo-Al-Ela HG, Faggio C. MicroRNA-mediated stress response in bivalve species. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111442. [PMID: 33038725 DOI: 10.1016/j.ecoenv.2020.111442] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
Bivalve mollusks are important aquatic organisms, which are used for biological monitoring because of their abundance, ubiquitous nature, and abilities to adapt to different environments. MicroRNAs (miRNAs) are small noncoding RNAs, which typically silence the expression of target genes; however, certain miRNAs directly or indirectly upregulate their target genes. They are rapidly modulated and play an essential role in shaping the response of organisms to stresses. Based on the regulatory function and rapid alteration of miRNAs, they could act as biomarkers for biotic and abiotic stress, including environmental stresses and contaminations. Moreover, mollusk, particularly hemocytes, rapidly respond to environmental changes, such as pollution, salinity changes, and desiccation, which makes them an attractive model for this purpose. Thus, bivalve mollusks could be considered a good animal model to examine a system's response to different environmental conditions and stressors. miRNAs have been reported to adjust the adaptation and physiological functions of bivalves during endogenous and environmental stressors. In this review, we aimed to discuss the potential mechanisms underlying the response of bivalves to stressors and how miRNAs orchestrate this process; however, if necessary, other organisms' response is included to explain specific processes.
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Affiliation(s)
- Haitham G Abo-Al-Ela
- Genetics and Biotechnology, Department of Aquaculture, Faculty of Fish Resources, Suez University, Suez 43518, Egypt.
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres, 31, 98166 Messina, Italy.
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Huang X, Li S, Liu X, Huang S, Li S, Zhuo M. Analysis of conserved miRNAs in cynomolgus macaque genome using small RNA sequencing and homology searching. PeerJ 2020; 8:e9347. [PMID: 32728489 PMCID: PMC7357559 DOI: 10.7717/peerj.9347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 05/21/2020] [Indexed: 11/23/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators that fine-tune diverse cellular activities. Cynomolgus macaques (Macaca fascicularis) are used extensively in biomedical and pharmaceutical research; however, substantially fewer miRNAs have been identified in this species than in humans. Consequently, we investigated conserved miRNA profiles in cynomolgus macaques by homology searching and small RNA sequencing. In total, 1,455 high-confidence miRNA gene loci were identified, 408 of which were also confirmed by RNA sequencing, including 73 new miRNA loci reported in cynomolgus macaques for the first time. Comparing miRNA expression with age, we found a positive correlation between sequence conservation and expression levels during miRNA evolution. Additionally, we found that the miRNA gene locations in cynomolgus macaque genome were very flexible. Most were embedded in intergenic spaces or introns and clustered together. Several miRNAs were found in certain gene locations, including 64 exon-resident miRNAs, six splice-site-overlapping miRNAs (SO-miRNAs), and two pairs of distinct mirror miRNAs. We also identified 78 miRNA clusters, 68 of which were conserved in the human genome, including 10 large miRNA clusters predicted to regulate diverse developmental and cellular processes in cynomolgus macaque. Thus, this study not only expands the number of identified miRNAs in cynomolgus macaques but also provides clues for future research on the differences in miRNA repertoire between macaques and humans.
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Affiliation(s)
- Xia Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Shijia Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Xiaoming Liu
- Guangzhou Tulip Information Technologies Ltd., Guangzhou, Guangdong, China
| | - Shuting Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Min Zhuo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
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Qiao H, Jiang S, Xiong Y, Fu H, Zhang W, Wang Y, Gong Y, Jin S, Wu Y. Integrated analysis of differentially expressed microRNAs and mRNAs to screen miRNAs and genes related to reproduction in Macrobrachium nipponense. 3 Biotech 2019; 9:327. [PMID: 31406649 PMCID: PMC6689314 DOI: 10.1007/s13205-019-1847-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/19/2019] [Indexed: 01/29/2023] Open
Abstract
Female Macrobrachium nipponense has the characteristic of short sexual maturity during the breeding season, which can increase breeding risk and lead to prevalent female individual miniaturization. In this study, we characterized micro (mi)RNA-seq data of the eyestalk (E) and cerebral ganglia (B) of female M. nipponense during breeding and non-breeding seasons. A total of 393 and 189 differentially expressed miRNAs (DE miRNAs) were identified in BSE vs. NBSE and BSB vs. NBSB, respectively. The most abundant up- and down-regulated DE miRNAs were miR-124, miR-14, and miR-7. Enrichment analysis showed that DE miRNA target genes were mainly involved in 'metabolic process' and 'binding', and were associated with 'neurohormonal regulation' and 'photoreceptor activity' signaling pathways. Integrated analysis of miRNA-mRNA expression showed that the most abundant DE miRNAs were miR-14 and miR-278 in BSE vs. NBSE and BSB vs. NBSB, respectively. Four pairs of DE miRNAs and their corresponding target annotated genes were selected from the DE miRNA-mRNA interaction network (bmo-miR-316-5p/opsin protein, ame-miR-125/skeletal muscle actin 8, dmo-miR-278/sugar transporter, and tca-miR-3885-5p/5-HT1 receptor). Gene expression analysis of these four pairs in different ovary development stages showed their potential regulatory roles in ovary maturation.
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Affiliation(s)
- Hui Qiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| | - Sufei Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| | - Yiwei Xiong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| | - Hongtuo Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081 People’s Republic of China
| | - Wenyi Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| | - Yabing Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081 People’s Republic of China
| | - Yongsheng Gong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| | - Shubo Jin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| | - Yan Wu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
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Huang Y, Xiong J, Brown PB, Sun X. Discovery of MicroRNAs from Batrachuperus yenyuanensis Using Deep Sequencing and Prediction of Their Targets. BIOCHEMISTRY (MOSCOW) 2019; 84:380-389. [PMID: 31228929 DOI: 10.1134/s0006297919040059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs), a family of ∼22-nucleotide non-coding single-stranded RNA molecules, are considered as key post-transcriptional regulators of gene expression that regulate various biological processes in living organism. Many miRNAs have been identified in animals; however, few have been reported in Hynobiidae species. The present study is aimed to identify a full repertoire of miRNAs in Batrachuperus yenyuanensis (Yenyuan stream salamander), which would significantly increase our knowledge of miRNAs in amphibians. A small RNA library was constructed from B. yenyuanensis and sequenced using deep sequencing. As a result, 1,717,751 clean reads were obtained, representing 356 known and 80 novel miRNAs. Additionally, expression levels of eight randomly selected miRNAs in B. yenyuanensis were confirmed using the stem-loop quantitative real-time reverse transcription PCR. In addition, 13,972 targets were predicted for these identified miRNAs, although the physiological functions of many of these targets remain unknown. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that the predicted targets are involved in a variety of physiological regulatory functions in B. yenyuanensis. These results provide useful information for further research on the miRNAs involved in the growth and development of B. yenyuanensis, as well as adaptation of this species to its high-altitude habitats.
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Affiliation(s)
- Y Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China.
| | - J Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China.
| | - P B Brown
- Purdue University, Department of Forestry and Natural Resources, West Lafayette, IN 47907, USA
| | - X Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China
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10
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Liu X, Luo BY, Feng JB, Zhou LX, Ma KY, Qiu GF. Identification and profiling of microRNAs during gonadal development in the giant freshwater prawn Macrobrachium rosenbergii. Sci Rep 2019; 9:2406. [PMID: 30787336 PMCID: PMC6382778 DOI: 10.1038/s41598-019-38648-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 01/03/2019] [Indexed: 12/14/2022] Open
Abstract
As post-transcriptional regulators, microRNAs (miRNAs) play an important role in growth and reproductive processes. So far, there is limited information regarding crustacean miRNAs. To explore the potential role of miRNAs in the gonadal development of the prawn Macrobrachium rosenbergii, we constructed seven small RNA libraries from ovarian and testicular tissues at various stages using somatic tissue as the control. A total of 1,954 known and 129 novel miRNAs were retrieved. By comparing differentially expressed miRNAs (DEMs) between testes and ovaries, forty-one miRNAs were identified with sex-biased expression patterns, including 17 ovary-biased and 24 testis-biased patterns. Furthermore, the putative target genes of the sex-biased miRNAs, such as cyclin L1, mitogen-activated protein kinase 7 (MAPK 7), heat shock protein (HSP), and zinc finger protein, were significantly enriched in many reproduction-related pathways including the Gonadotropin-releasing hormone (GnRH) pathway, glycolysis, gluconeogenesis pathway, ovarian steroidogenesis, estrogen signaling pathway, MAPK pathway, Wnt pathway, and insulin signaling pathway, implicating potential regulatory roles of miRNAs in reproduction. These data aid in the further investigation of the mechanism of gonadal development and reproductive regulation mediated by miRNA in M. rosenbergii.
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Affiliation(s)
- Xue Liu
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture (Shanghai Ocean University), Shanghai, China
- Shanghai Engineering Research Center of Aquaculture (Shanghai Ocean University), Shanghai, China
| | - Bi-Yun Luo
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture (Shanghai Ocean University), Shanghai, China
- Shanghai Engineering Research Center of Aquaculture (Shanghai Ocean University), Shanghai, China
| | - Jian-Bin Feng
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture (Shanghai Ocean University), Shanghai, China
- Shanghai Engineering Research Center of Aquaculture (Shanghai Ocean University), Shanghai, China
| | - Ling-Xia Zhou
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture (Shanghai Ocean University), Shanghai, China
- Shanghai Engineering Research Center of Aquaculture (Shanghai Ocean University), Shanghai, China
| | - Ke-Yi Ma
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, China.
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture (Shanghai Ocean University), Shanghai, China.
- Shanghai Engineering Research Center of Aquaculture (Shanghai Ocean University), Shanghai, China.
| | - Gao-Feng Qiu
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, China.
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture (Shanghai Ocean University), Shanghai, China.
- Shanghai Engineering Research Center of Aquaculture (Shanghai Ocean University), Shanghai, China.
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11
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microRNAs in Macrobrachium olfersii embryos: Identification, their biogenesis components and potential targets. Comput Biol Chem 2018; 78:205-216. [PMID: 30576966 DOI: 10.1016/j.compbiolchem.2018.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 11/24/2018] [Accepted: 12/11/2018] [Indexed: 12/21/2022]
Abstract
In embryonic development, microRNAs (miRNAs) regulate the complex gene expression associated with the complexity of embryogenesis. Today, few studies have been conducted on the identification of miRNAs and components of miRNA biogenesis on embryonic development in crustaceans, especially in prawns. In this context, the aim of this study was to identify in silico components of miRNA biogenesis, and miRNAs and potential target genes during embryonic development in the prawn Macrobrachium olfersii through small RNAs and transcriptome analyses. Using the miRDeep2 program, we identified 17 miRNA precursors in M. olfersii, which seven (miR-9, miR-10, miR-92, miR-125, miR-305, miR-1175, and miR-2788) were reported in the miRBase database, indicating high evolutionary conservation of these sequences among animals. The other 10 miRNAs of M. olfersii were novel miRNAs and only similar to Macrobrachium niponnense miRNAs, indicating genus-specific miRNAs. In addition, eight key components of miRNA biogenesis (DROSHA, PASHA/DGCR8, XPO5, RAN, DICER, TRBP2, AGO, and PIWI) were identified in M. olfersii embryos unigenes. In the annotation of miRNA targets, 516 genes were similar to known sequences in the GenBank database. Regarding the conserved miRNAs, we verified that they were differentially expressed during embryonic development in M. olfersii. In conclusion, this is the first study that identifies conserved and novel miRNAs in the prawn M. olfersii with some miRNA target genes involved in embryonic development. Our results will allow further studies on the function of these miRNAs and miRNA biogenesis components during embryonic development in M. olfersii and other prawns of commercial interest.
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12
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Zheng J, Cao J, Mao Y, Su Y, Wang J. Identification of microRNAs with heat stress responsive and immune properties in Marsupenaeus japonicus based on next-generation sequencing and bioinformatics analysis: Essential regulators in the heat stress-host interactions. FISH & SHELLFISH IMMUNOLOGY 2018; 81:390-398. [PMID: 29778844 DOI: 10.1016/j.fsi.2018.05.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 06/08/2023]
Abstract
Summer mortality syndrome is one of the most serious issue for Marsupenaeus japonicus aquaculture in China. Since it causes massive economic loss and threatens sustainability of M. japonicus aquaculture industry, thus, there is an urgent desire to reveal the heat stress-host interactions mechanisms that lead to mass mortalities of M. japonicus in hot summer months. MicroRNAs (miRNAs) are small noncoding RNAs that involved in regulation of diverse biological processes, including stress and immune response, and might serve as potential regulators in the heat stress-host interactions. In the present study, miRNAs with heat stress responsive and immune properties were identified and characterized in M. japonicus by small RNA sequencing and bioinformatics analysis. In total, 79 host miRNAs were identified, among which 15 miRNAs were differentially expressed in response to heat stress. Target genes prediction and function annotation revealed that a variety of host cellular processes, such as signal transduction, transcription, anti-stress response, ribosomal biogenesis, lipid metabolism, cytoskeleton, etc, were potentially subject to miRNA-mediated regulation in response to heat stress. Furthermore, a total of 30 host miRNAs that potentially involved in interaction with white spot syndrome virus (WSSV) were obtained via predicting and analyzing the target genes from WSSV. The results showed that a batch of WSSV genes that code for structural proteins and enzymes that are essential for WSSV infection and proliferation, such as envelope proteins, capsid proteins, immediate-early proteins, collagen-like protein, protein kinase, thymidylate synthetase, TATA-box bind protein, etc, were predicted to be targeted by host miRNAs. Several of the host miRNAs with predicted antiviral capacity were down-regulated under heat stress, indicating a repression of host miRNA-mediated antiviral immune response. This study highlighted the essential roles of host miRNAs in the heat stress-host interactions and provided valuable information for further investigation on the mechanism of miRNA-mediated heat stress and immune response of shrimp.
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Affiliation(s)
- Jinbin Zheng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Jiawen Cao
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Yong Mao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.
| | - Yongquan Su
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Jun Wang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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13
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Guo H, Lu ZC, Zhu XW, Zhu CH, Wang CG, Shen YC, Wang W. Differential expression of microRNAs in hemocytes from white shrimp Litopenaeus vannamei under copper stress. FISH & SHELLFISH IMMUNOLOGY 2018; 74:152-161. [PMID: 29305331 DOI: 10.1016/j.fsi.2017.12.053] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/19/2017] [Accepted: 12/28/2017] [Indexed: 06/07/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate diverse cellular processes, including organismal stress response, through posttranscriptional repression of gene transcripts. They are known to have antiviral functions in aquatic crustacean species, but little is known about the role of miRNAs against environmental stress caused by Cu, a common chemical contaminant in aquatic environment. We performed small RNA sequencing to characterize the differentially expressed microRNAs in Cu exposed shrimp. A total of 4524 known miRNAs and 73 novel miRNAs were significantly (P < .05) differentially expressed after Cu exposure. The peak size of miRNAs was 22 nt. Among them, 218 miRNAs were conserved across 115 species. The validation of 12 miRNAs by stem-loop quantitative RT-PCR were found to be coherent with the expression profile of deep sequencing data as evaluated with Pearson's correlation coefficient (r = 0.707). Target genes of these differentially expressed miRNAs related to immune defense, apoptosis, and xenobiotics metabolism also showed significant changes in expression under Cu stress. The present study provides the first characterization of L. vannamei miRNAs and some target genes expression in response to Cu stress, and the findings support the hypothesis that certain miRNAs along with their target genes might be essential in the intricate adaptive response regulation networks. Our current study will provide valuable information to take an insight into molecular mechanism of L. vannamei against environmental stress.
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Affiliation(s)
- Hui Guo
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China
| | - Zhi-Cheng Lu
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China
| | - Xiao-Wen Zhu
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China
| | - Chun-Hua Zhu
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China
| | - Cheng-Gui Wang
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China
| | - Yu-Chun Shen
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China.
| | - Wei Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China.
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14
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Qiang J, Cui YT, Tao FY, Bao WJ, He J, Li XH, Xu P, Sun LY. Physiological response and microRNA expression profiles in head kidney of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) exposed to acute cold stress. Sci Rep 2018; 8:172. [PMID: 29317697 PMCID: PMC5760732 DOI: 10.1038/s41598-017-18512-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/08/2017] [Indexed: 12/30/2022] Open
Abstract
Cold stress has a serious impact on the overwintering survival and yield of genetically improved farmed tilapia (GIFT, Oreochromis niloticus). Understanding the physiological and molecular regulation mechanisms of low-temperature adaptation is necessary to help breed new tolerant strains. The semi-lethal low temperature of juvenile GIFT at 96 h was determined as 9.4 °C. We constructed and sequenced two small RNA libraries from head kidney tissues, one for the control (CO) group and one for the 9.4 °C-stressed (LTS) group, and identified 1736 and 1481 known microRNAs (miRNAs), and 164 and 152 novel miRNAs in the CO and LTS libraries, respectively. We verify the expression of nine up-regulated miRNAs and eight down-regulation miRNAs by qRT-PCR, and found their expression patterns were consistent with the sequencing results. We found that cold stress may have produced dysregulation of free radical and lipid metabolism, decreased superoxide dismutase activity, reduced respiratory burst and phagocytic activity of macrophages, increased malondialdehyde content, and adversely affected the physiological adaptation of GIFT, eventually leading to death. This study revealed interactions among miRNAs and signal regulated pathways in GIFT under cold stress that may help to understand the pathways involved in cold resistance.
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Affiliation(s)
- Jun Qiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.,Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Yan T Cui
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.,Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Fan Y Tao
- Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Wen J Bao
- Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Jie He
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Xia H Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China. .,Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.
| | - Lan Y Sun
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
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15
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Kumaresan V, Palanisamy R, Pasupuleti M, Arockiaraj J. Impacts of environmental and biological stressors on immune system of Macrobrachium rosenbergii. REVIEWS IN AQUACULTURE 2017; 9:283-307. [DOI: 10.1111/raq.12139] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/14/2015] [Indexed: 10/16/2023]
Abstract
AbstractMacrobrachium rosenbergii commonly called giant freshwater prawn is a widely farmed crustacean in freshwater. Similar to other aquatic organisms, their growth and well‐being is influenced by various physical, chemical and biological factors. We discuss about the critical growth limiting factors as well as disease causing agents and the potential immune molecules of M. rosenbergii that are proved to involve in preventing and/or responding to those limiting factors.
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Affiliation(s)
- Venkatesh Kumaresan
- Division of Fisheries Biotechnology & Molecular Biology Department of Biotechnology Faculty of Science and Humanities SRM University Chennai Tamil Nadu India
| | - Rajesh Palanisamy
- Division of Fisheries Biotechnology & Molecular Biology Department of Biotechnology Faculty of Science and Humanities SRM University Chennai Tamil Nadu India
| | - Mukesh Pasupuleti
- Lab PCN 206 Microbiology Division CSIR‐Central Drug Research Institute Lucknow Uttar Pradesh India
| | - Jesu Arockiaraj
- Division of Fisheries Biotechnology & Molecular Biology Department of Biotechnology Faculty of Science and Humanities SRM University Chennai Tamil Nadu India
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16
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Identification and comparative analysis of the pearl oyster Pinctada fucata hemocytes microRNAs in response to Vibrio alginolyticus infection. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0575-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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17
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Qiang J, Tao F, He J, Sun L, Xu P, Bao W. Effects of exposure to Streptococcus iniae on microRNA expression in the head kidney of genetically improved farmed tilapia (Oreochromis niloticus). BMC Genomics 2017; 18:190. [PMID: 28219342 PMCID: PMC5322787 DOI: 10.1186/s12864-017-3591-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 02/14/2017] [Indexed: 12/20/2022] Open
Abstract
Background Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are susceptible to infection by Streptococcus iniae when maintained in modern intensive culture systems. GIFT are commercially important fishes that are cultured widely in southern China. The role of microRNAs (miRNAs) in the regulatory response of GIFT to S. iniae infection has been underestimated and has not yet been well studied. Head kidney has an important immune function in teleost fishes. The main aim of this study was to determine the possible function of miRNAs in head kidney of S. iniae-infected GIFT. MiRNAs are small, non-coding RNAs that regulate gene expression by binding to the 3’-untranslated regions of their target mRNAs. MiRNAs are known to regulate immune-regulated signaling and inflammatory response pathways. Results High-throughput deep sequencing of two libraries (control group [CO] and infected group [IN]) of RNA extracted from GIFT head kidney tissues generated 12,089,630 (CO) and 12,624,975 (IN) clean reads. Bioinformatics analysis identified 1736 and 1729 conserved miRNAs and 164 and 165 novel miRNAs in the CO and IN libraries, respectively. Three miRNAs (miR-310-3p, miR-92, and miR-127) were found to be up-regulated and four miRNAs (miR-92d-3p, miR-375-5p, miR-146-3p, and miR-694) were found to be down-regulated in the S. iniae-infected GIFT. The expressions of these miRNAs were verified by quantitative real-time PCR. RNAhybrid and TargetScan were used to identify complementary miRNA and mRNA target sites, and the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases were used to annotate and predict potential downstream regulation of biological pathways. Seven target genes, which encode immune-related proteins (complement C3, cytidine deaminase, regulator of G-protein Rgs22, mitogen-activated protein kinase Mapk1, metabotropic glutamate receptorm GluR8, calcium-sensing receptor CaSR, and microtubule-associated protein Map1S) were predicted to play crucial roles in the GIFT response to S. iniae infection. Conclusions S. iniae outbreaks have hindered the development of the tilapia industry in China. Understanding the miRNA transcriptome of S. iniae-infected GIFT is important for exploring the immune responses regulated by miRNAs as well as for studying novel regulated networks to prevent and treat S. iniae infections in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3591-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Qiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.
| | - Fanyi Tao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Jie He
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Lanyi Sun
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.
| | - Wenjin Bao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
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18
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Chen H, Wang H, Jiang S, Xu J, Wang L, Qiu L, Song L. An oyster species-specific miRNA scaffold42648_5080 modulates haemocyte migration by targeting integrin pathway. FISH & SHELLFISH IMMUNOLOGY 2016; 57:160-169. [PMID: 27544269 DOI: 10.1016/j.fsi.2016.08.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/07/2016] [Accepted: 08/13/2016] [Indexed: 06/06/2023]
Abstract
miRNAs are important gene regulators at post-transcriptional level and can modulate diverse biological processes, including immune response. Dozens of species-specific miRNAs have been identified in oyster Crassostrea gigas while their functions remain largely unknown. In the present study, an oyster species-specific miRNA scaffold42648_5080 was found responsive to LPS stimulation and might target a total of 31 oyster genes possibly involved in cell communication, cellular localization and cellular response to stimulus. Besides, in gain-of-function assay of scaffold42648_5080 in vivo, the phagocytosis (30.90% in miRNA group verse 23.20% in miRNA control group), apoptosis (3.10% in miRNA group verse 5.30% in miRNA control group) and migration rate (13.88% in miRNA group verse 21.03% in miRNA control group) of oyster haemocytes were found significantly altered after the injection of scaffold42648_5080 mimics. Among the target genes, integrin-linked kinase (CgILK) was considered crucial in cell migration and its interaction with scaffold42648_5080 was then verified both in vitro and in vivo. Consequently, a significant decrease of relative luciferase ratio was observed in CgILK 3'-UTR luciferase reporter assay after transfection of scaffold42648_5080 mimics (0.70-fold of that in blank group, p < 0.01). Meanwhile, when scaffold42648_5080 was overexpressed in vivo (5.41-fold of miRNA control group, p < 0.01), the expression of CgILK declined significantly to 0.25-fold of miRNA control group (p < 0.01). Comparatively, a significant decrease of the haemocyte migration rate (19.76% verse 34.82% in siEGFP control group, p < 0.01) was observed after knock-down of CgILK in vivo. The present study, as far as we know, for the first time revealed the immunomodulation role of an oyster species-specific miRNA, which might provide new insights into miRNA-mediated adaptation mechanism of oysters.
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Affiliation(s)
- Hao Chen
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Shuai Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jiachao Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingling Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China
| | - Limei Qiu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Linsheng Song
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China.
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Kaewkascholkul N, Somboonviwat K, Asakawa S, Hirono I, Tassanakajon A, Somboonwiwat K. Shrimp miRNAs regulate innate immune response against white spot syndrome virus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 60:191-201. [PMID: 26945623 DOI: 10.1016/j.dci.2016.03.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/01/2016] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
MicroRNAs are short noncoding RNAs of RNA interference pathways that regulate gene expression through partial complementary base-pairing to target mRNAs. In this study, miRNAs that are expressed in white spot syndrome virus (WSSV)-infected Penaeus monodon, were identified using next generation sequencing. Forty-six miRNA homologs were identified from WSSV-infected shrimp hemocyte. Stem-loop real-time RT-PCR analysis showed that 11 out of 16 selected miRNAs were differentially expressed upon WSSV infection. Of those, pmo-miR-315 and pmo-miR-750 were highly responsive miRNAs. miRNA target prediction revealed that the miRNAs were targeted at 5'UTR, ORF, and 3'UTR of several immune-related genes such as genes encoding antimicrobial peptides, signaling transduction proteins, heat shock proteins, oxidative stress proteins, proteinases or proteinase inhibitors, proteins in blood clotting system, apoptosis-related proteins, proteins in prophenoloxidase system, pattern recognition proteins and other immune molecules. The highly conserved miRNA homolog, pmo-bantam, was characterized for its function in shrimp. The pmo-bantam was predicted to target the 3'UTR of Kunitz-type serine protease inhibitor (KuSPI). Binding of pmo-bantam to the target sequence of KuSPI gene was analyzed by luciferase reporter assay. Correlation of pmo-bantam and KuSPI expression was observed in lymphoid organ of WSSV-infected shrimp. These results implied that miRNAs might play roles as immune gene regulators in shrimp antiviral response.
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Affiliation(s)
- Napol Kaewkascholkul
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Kulwadee Somboonviwat
- Software Engineering Program, International College, King Mongkut's Institute of Technology Ladkrabang, Chalongkrung Road, Ladkrabang, Bangkok 10520, Thailand
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Minato-ku, Tokyo, Japan
| | - Anchalee Tassanakajon
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand; Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand; Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand.
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Sun S, Fu H, Ge X, Zhu J, Gu Z, Xuan F. Identification and comparative analysis of the oriental river prawn ( Macrobrachium nipponense ) microRNA expression profile during hypoxia using a deep sequencing approach. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 17:41-7. [DOI: 10.1016/j.cbd.2016.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 12/31/2015] [Accepted: 01/10/2016] [Indexed: 01/12/2023]
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21
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Santos CA, Blanck DV, de Freitas PD. RNA-seq as a powerful tool for penaeid shrimp genetic progress. Front Genet 2014; 5:298. [PMID: 25221571 PMCID: PMC4147233 DOI: 10.3389/fgene.2014.00298] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/11/2014] [Indexed: 11/27/2022] Open
Abstract
The sequences of all different RNA transcripts present in a cell or tissue that are related to the gene expression and its functional control represent what it is called a transcriptome. The transcripts vary between cells, tissues, ontogenetic and environmental conditions, and the knowledge that can be gained through them is of a solid relevance for genetic applications in aquaculture. Some of the techniques used in transcriptome studies, such as microarrays, are being replaced for next-generation sequencing approaches. RNA-seq emerges as a new possibility for the transcriptome complexity analysis as well as for the candidate genes and polymorphisms identification of penaeid species. Thus, it may also help to understand the determination of complex traits mechanisms and genetic improvement of stocks. In this review, it is first introduced an overview of transcriptome analysis by RNA-seq, followed by a discussion of how this approach may be applied in genetic progress within penaeid stocks.
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Affiliation(s)
- Camilla A Santos
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos São Carlos, Brazil
| | - Danielly V Blanck
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos São Carlos, Brazil
| | - Patrícia D de Freitas
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos São Carlos, Brazil
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