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Zhong S, Ye X, Liu H, Ma X, Chen X, Zhao L, Huang G, Huang L, Zhao Y, Qiao Y. MicroRNA sequencing analysis reveals immune responses in hepatopancreas of Fenneropenaeus penicillatus under white spot syndrome virus infection. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109432. [PMID: 38331056 DOI: 10.1016/j.fsi.2024.109432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/20/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
White Spot Disease is one of the most harmful diseases of the red tail shrimp, which can cause devastating economic losses due to the highest mortality up to 100% within a few days. MicroRNAs (miRNAs) are large class of small noncoding RNAs with the ability to post-transcriptionally repress the translation of target mRNAs. MiRNAs are considered to have a significant role in the innate immune response of crustaceans, particularly in relation to antiviral defense mechanisms. Numerous crustacean miRNAs have been verified to be required in host immune defense against viral infection, however, till present, the miRNAs functions of F. penicillatus defense WSSV infection have not been studied yet. Here in this study, for the first time, miRNAs involved in the F. penicillatus immune defense against WSSV infection were identified using high-throughput sequencing platform. A total of 432 miRNAs were obtained including 402 conserved miRNAs and 30 novel predicted miRNAs. Comparative analysis between the WSSV-challenged group and the control group revealed differential expression of 159 microRNAs in response to WSSV infection. Among these, 48 were up-regulated and 111 were down-regulated. Ten candidate MicroRNAs associated with immune activities were randomly selected for qRT-PCR analysis, which confirming the expression profiling observed in the MicroRNA sequencing data. As a result, most differentially expressed miRNAs were down-regulated lead to increase the expression of various target genes that mediated immune reaction defense WSSV infection, including genes related to signal transduction, Complement and coagulation cascade, Phagocytosis, and Apoptosis. Furthermore, the genes expression of the key members in Toll and Imd signaling pathways and apoptotic signaling were mediated by microRNAs to activate host immune responses including apoptosis against WSSV infection. These results will help to understand molecular defense mechanism against WSSV infection in F. penicillatus and to develop an effective WSSV defensive strategy in shrimp farming.
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Affiliation(s)
- Shengping Zhong
- Guangxi Key Laboratory of Marine Drugs, Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, 530200, China; Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou, 570100, China.
| | - Xiaowu Ye
- Beihai People's Hospital, Beihai, 536000, China
| | - Hongtao Liu
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou, 570100, China
| | - Xiaowan Ma
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, 536000, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530200, China
| | - Longyan Zhao
- Guangxi Key Laboratory of Marine Drugs, Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Guoqiang Huang
- Guangxi Key Laboratory of Marine Drugs, Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Lianghua Huang
- Guangxi Key Laboratory of Marine Drugs, Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530200, China
| | - Ying Qiao
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, 536000, China.
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Yang LY, Zhu QH, Chen JY, Lin LB, Liang MZ, Zhang QL. Genome-wide transcriptomics and microRNAomics analyses uncover multi-faceted mechanisms to cope with copper stress in ancient macrobenthos amphioxus. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131594. [PMID: 37330373 DOI: 10.1016/j.jhazmat.2023.131594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/20/2023] [Accepted: 05/05/2023] [Indexed: 06/19/2023]
Abstract
The mechanisms underlying the toxicity of environmental stress are unclear for marine macrobenthos. Copper/Cu has posed the most serious threats to amphioxus, an ancient and model benthic cephalochordate. Herein, a dynamic change in the physiological parameters (GR, SOD, ATP, and MDA) was detected with ROS accumulation in Branchiostoma belcheri exposed to 0.3 mg·L-1 Cu. Transcriptomes and microRNAomes of B. belcheri were generated to investigate the molecular mechanisms by which this amphioxus copes with Cu exposure. Time-specific genes identified at different time points after exposure were involved in the stimulus and immune response, detoxification and ionic homeostasis, aging and the nervous system, sequentially, with prolongation of exposure time, forming a dynamic process of molecular response to Cu stress. In total, 57 differentially expressed miRNAs were identified under Cu stress. Transcriptomics-miRNAomics analyses indicate that these miRNAs targeted genes associated with many key biological processes such as xenobiotics degradation, oxidative stress, and energy metabolism. The constructed miRNA-mRNA-pathway network uncovered a broad post-transcriptional regulatory mechanism in B. belcheri to cope with Cu stress. Overall, this integrated analyses show that enhanced defense response, accelerated ROS elimination, and repressed ATP production constitute a comprehensive strategy to cope with Cu toxicity in the ancient macrobenthos.
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Affiliation(s)
- Lin-Yu Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535011, China
| | - Qian-Hua Zhu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jun-Yuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Ming-Zhong Liang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535011, China.
| | - Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.
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3
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Gao J, Zou Y, Wu XJ, Xu Y, Zhu XQ, Zheng WB. Differential miRNA expression profiles in the bone marrow of Beagle dogs at different stages of Toxocara canis infection. BMC Genomics 2022; 23:847. [PMID: 36544082 PMCID: PMC9773451 DOI: 10.1186/s12864-022-09081-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Toxocara canis is distributed worldwide, posing a serious threat to both human and dog health; however, the pathogenesis of T. canis infection in dogs remains unclear. In this study, the changes in microRNA (miRNA) expression profiles in the bone marrow of Beagle dogs were investigated by RNA-seq and bioinformatics analysis. RESULTS Thirty-nine differentially expressed (DE) miRNAs (DEmiRNAs) were identified in this study. Among these, four DEmiRNAs were identified at 24 h post-infection (hpi) and all were up-regulated; eight DEmiRNAs were identified with two up-regulated miRNAs and six down-regulated miRNAs at 96 hpi; 27 DEmiRNAs were identified with 13 up-regulated miRNAs and 14 down-regulated miRNAs at 36 days post-infection (dpi). Among these DEmiRNAs, cfa-miR-193b participates in the immune response by regulating the target gene cd22 at 24 hpi. The novel_328 could participate in the inflammatory and immune responses through regulating the target genes tgfb1 and tespa1, enhancing the immune response of the host and inhibiting the infection of T. canis at 96 hpi. In addition, cfa-miR-331 and novel_129 were associated with immune response and self-protection mechanisms at 36 dpi. 20 pathways were significantly enriched by KEGG pathway analysis, most of which were related to inflammatory response, immune response and cell differentiation, such as Cell adhesion molecules (CAMs), ECM-receptor interaction and Focal adhesion. CONCLUSIONS These findings suggested that miRNAs of Beagle dog bone marrow play important roles in the pathogenesis of T. canis infection in dogs and provided useful resources to better understand the interaction between T. canis and the hosts.
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Affiliation(s)
- Jin Gao
- grid.412545.30000 0004 1798 1300Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801 Shanxi Province China
| | - Yang Zou
- grid.454892.60000 0001 0018 8988State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046 Gansu Province China
| | - Xiao-Jing Wu
- grid.412545.30000 0004 1798 1300Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801 Shanxi Province China
| | - Yue Xu
- grid.412545.30000 0004 1798 1300Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801 Shanxi Province China
| | - Xing-Quan Zhu
- grid.412545.30000 0004 1798 1300Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801 Shanxi Province China ,grid.410696.c0000 0004 1761 2898Key Laboratory of Veterinary Public Health of Higher Education of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan Province China
| | - Wen-Bin Zheng
- grid.412545.30000 0004 1798 1300Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801 Shanxi Province China
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Li M, Huang Q, Lv X, Small HJ, Li C. Integrative omics analysis highlights the immunomodulatory effects of the parasitic dinoflagellate hhematodinium on crustacean hemocytes. FISH & SHELLFISH IMMUNOLOGY 2022; 125:35-47. [PMID: 35526798 DOI: 10.1016/j.fsi.2022.04.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/24/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
Parasitic dinoflagellates in genus Hematodinium have caused substantial economic losses to multiple commercially valuable marine crustaceans around the world. Recent efforts to better understand the life cycle and biology of the parasite have improved our understanding of the disease ecology. However, studies on the host-parasite interaction, especially how Hematodinium parasites evade the host immune response are lacking. To address this shortfall, we used the comprehensive omics approaches (miRNA transcriptomics, iTRAQ-based proteomics) to get insights into the host-parasite interaction between hemocytes from Portunus trituberculatus and Hematodinium perezi in the present study. The parasitic dinoflagellate H. perezi remodeled the miRNome and proteome of hemocytes from challenged hosts, modulated the host immune response at both post-transcriptional and translational levels and caused post-transcriptional regulation to the host immune response. Multiple important cellular and humoral immune-related pathways (ex. Apoptosis, Endocytosis, ECM-receptor interaction, proPO activation pathway, Toll-like signaling pathway, Jak-STAT signaling pathway) were significantly affected by Hematodinium parasites. Through modulation of the host miRNome, the host immune responses of nodulation, proPO activation and antimicrobial peptides were significantly suppressed. Cellular homeostasis was imbalanced via post-transcriptional dysregulation of the phagosome and peroxisome pathways. Cellular structure and communication was seriously impacted by post-transcriptional downregulation of ECM-receptor interaction and focal adhesion pathways. In conclusion, H. perezi parasites could trigger striking changes in the miRNome and proteome of crustacean hemocytes, and this parasite exhibited multifaceted immunomodulatory effects and potential immune-suppressive mechanisms in crustacean hosts.
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Affiliation(s)
- Meng Li
- CAS Key Lab of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Centre for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Qian Huang
- CAS Key Lab of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyang Lv
- CAS Key Lab of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hamish J Small
- Virginia Institute of Marine Science, William & Mary, P.O. Box 1346, Gloucester Point, VA, 23062, USA.
| | - Caiwen Li
- CAS Key Lab of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Centre for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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5
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Davies CE, Thomas JE, Malkin SH, Batista FM, Rowley AF, Coates CJ. Hematodinium sp. infection does not drive collateral disease contraction in a crustacean host. eLife 2022; 11:70356. [PMID: 35179494 PMCID: PMC8856654 DOI: 10.7554/elife.70356] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 02/08/2022] [Indexed: 01/10/2023] Open
Abstract
Host, pathogen, and environment are determinants of the disease triangle, the latter being a key driver of disease outcomes and persistence within a community. The dinoflagellate genus Hematodinium is detrimental to crustaceans globally - considered to suppress the innate defences of hosts, making them more susceptible to co-infections. Evidence supporting immune suppression is largely anecdotal and sourced from diffuse accounts of compromised decapods. We used a population of shore crabs (Carcinus maenas), where Hematodinium sp. is endemic, to determine the extent of collateral infections across two distinct environments (open-water, semi-closed dock). Using a multi-resource approach (PCR, histology, haematology, population genetics, eDNA), we identified 162 Hematodinium-positive crabs and size/sex-matched these to 162 Hematodinium-free crabs out of 1191 analysed. Crabs were interrogated for known additional disease-causing agents; haplosporidians, microsporidians, mikrocytids, Vibrio spp., fungi, Sacculina, trematodes, and haemolymph bacterial loads. We found no significant differences in occurrence, severity, or composition of collateral infections between Hematodinium-positive and Hematodinium-free crabs at either site, but crucially, we recorded site-restricted blends of pathogens. We found no gross signs of host cell immune reactivity towards Hematodinium in the presence or absence of other pathogens. We contend Hematodinium sp. is not the proximal driver of co-infections in shore crabs, which suggests an evolutionary drive towards latency in this environmentally plastic host.
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Affiliation(s)
- Charlotte E Davies
- Department of Biosciences, College of Science, Swansea University, Swansea, United Kingdom
| | - Jessica E Thomas
- Department of Biosciences, College of Science, Swansea University, Swansea, United Kingdom
| | - Sophie H Malkin
- Department of Biosciences, College of Science, Swansea University, Swansea, United Kingdom
| | - Frederico M Batista
- Department of Biosciences, College of Science, Swansea University, Swansea, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom
| | - Andrew F Rowley
- Department of Biosciences, College of Science, Swansea University, Swansea, United Kingdom
| | - Christopher J Coates
- Department of Biosciences, College of Science, Swansea University, Swansea, United Kingdom
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6
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Guo Y, Dong HY, Zhou HC, Zhang ZS, Zhao Y, Zhang YJ. Mechanism of the Passage of Angiostrongylus cantonensis across the Final Host Blood-Brain Barrier Using the Next-Generation Sequencing. IRANIAN JOURNAL OF PARASITOLOGY 2021; 16:454-463. [PMID: 34630591 PMCID: PMC8476730 DOI: 10.18502/ijpa.v16i3.7099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/09/2021] [Indexed: 11/24/2022]
Abstract
Background: Multicellular parasites Angiostrogylus cantonensis larvae develop in the final host rat brain at the fourth stage (L4) and migrate to the lungs by the adult stage. The potential mechanism of its blood-brain barrier (BBB) passage remains unclear. Methods: By using Illumina Hiseq/Miseq sequencing, we obtained the transcriptomes of 3 groups of adult males and 3 groups of female of A. cantonensis to generate similarly expressed genes (SEGs) between 2 genders at the adult stage. Next 2 groups of L4 expressed genes were used to compared with SEGs to create differentially expressed genes (DEGs) between 2 life stages to unlock potential mechanism of BBB passage. Results: In total, we obtained 381 581 802 clean reads and 56 990 699 010 clean bases. Of these, 331 803 unigenes and 482 056 transcripts were successfully annotated. A total of 3 166 DEGs between L4 and adults SEGs were detected. Annotation of these DEGs showed 167 were down-regulated and 181 were up-regulated. Pathway analysis exhibited that calcium signaling pathway, the ECM−receptor interaction, focal adhesion, and cysteine and methionine metabolism were highly associated with DEGs. The function of these pathways might be related to BBB traversal, as well as neuro-regulation, interactions between parasite and host, environmental adaption. Conclusion: This study expanded the regulatory characteristics of the two important life stages of A. cantonensis. This information may provide a better appreciation of the biological features of the stages of the parasitic A. cantonensis.
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Affiliation(s)
- Yue Guo
- School of Medicine, Huzhou University, Huzhou Cent Hosp, Zhejiang, China.,Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou University, Huzhou, Zhejiang, China
| | - Hai Yan Dong
- School of Medicine, Huzhou University, Huzhou Cent Hosp, Zhejiang, China.,Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou University, Huzhou, Zhejiang, China
| | - Hong Chang Zhou
- School of Medicine, Huzhou University, Huzhou Cent Hosp, Zhejiang, China.,Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou University, Huzhou, Zhejiang, China
| | - Zhong Shan Zhang
- School of Medicine, Huzhou University, Huzhou Cent Hosp, Zhejiang, China.,School of Life Sciences, Huzhou University, Zhejiang, China
| | - Yu Zhao
- School of Medicine, Huzhou University, Huzhou Cent Hosp, Zhejiang, China
| | - Yu Jie Zhang
- School of Medicine, Huzhou University, Huzhou Cent Hosp, Zhejiang, China
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7
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Li C, Li M, Huang Q. The parasitic dinoflagellate Hematodinium infects marine crustaceans. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:313-325. [PMID: 37073297 PMCID: PMC10077234 DOI: 10.1007/s42995-020-00061-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/08/2020] [Indexed: 05/03/2023]
Abstract
Hematodinium is a type of parasitic dinoflagellate that infects marine crustaceans globally. The parasite lives mainly in the hemolymph or hemocoels of affected hosts, and results in mortalities due to malfunction or loss of functions of major organs. In recent years, the parasite had developed into an emerging epidemic pathogen not only affecting wild populations of economically valuable marine crustaceans in western countries but also the sustainable yield of aquaculture of major crabs in China. The epidemics of the parasitic diseases expanded recently in the coastal waters of China, and caused frequent outbreaks in aquaculture of major crab species, especially Portunus trituberculatus and Scylla paramamosain. In addition, the pathogen infected two species of co-cultured shrimps and multiple cohabitating wild crabs, implying it is a significant threat to the sustainable culture of commercially valuable marine crustaceans. In particular, the polyculture system that is widely used along the coast of China may facilitate the spread and transmission of the pathogen. Thus, to provide a better understanding of the biological and ecological characteristics of the parasitic dinoflagellate and highlight important directions for future research, we have reviewed the current knowledge on the taxonomy, life cycle, pathogenesis, transmission and epidemiology of Hematodinium spp. Moreover, ecological countermeasures have been proposed for the prevention and control of the emerging infectious disease.
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Affiliation(s)
- Caiwen Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237 China
- Centre for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Meng Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237 China
| | - Qian Huang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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8
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MicroRNA transcriptome analysis of oriental river prawn Macrobrachium nipponense in responding to starvation stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100820. [PMID: 33676153 DOI: 10.1016/j.cbd.2021.100820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/03/2021] [Accepted: 02/23/2021] [Indexed: 12/15/2022]
Abstract
Food deprivation or fasting is an important environmental factor, and a regular occurrence in both natural aquatic habitats and artificial ponds. However, the potential immunoregulatory mechanisms underlying starvation stress in crustaceans remain unclear. MicroRNAs (miRNAs) are a new class of non-coding RNAs that can regulate various biological processes, such as stress and immune responses. In the present work, miRNAs related to starvation stress responses and immune properties were identified and characterised in oriental river prawn Macrobrachium nipponense using high-throughput sequencing and bioinformatics analyses. Twelve small RNA libraries from hepatopancreas tissue were sequenced across four fasting stages lasting 0, 7, 14 or 21 days. In total, 550 miRNAs were identified including 198 putative novel miRNAs and 352 conserved miRNAs belonging to 57 families. Moreover, compared with expression levels at 0 days, 27, 27 and 43 miRNAs were differentially expressed (DE-miRNAs) at 7, 14 and 21 days, respectively. Among these, four DE-miRNAs (ame-miR-190-5p, dme-miR-307a-3p, hme-miR-2788-3p and novel_68) were co-expressed at all three timepoints. Furthermore, 661 target genes regulated by these DE-miRNAs were identified, and associated functional annotations were derived by GO enrichment and KEGG pathway analyses, which showed that most DE-miRNAs were mainly participated in metabolic processes and immune responses. Furthermore, 26 host DE-miRNAs potentially participated in interactions with white spot syndrome virus (WSSV) were identified by predicting and analysing target genes from WSSV. The further WSSV challenge under starvation stress showed that dme-miR-307a-3p played a part in the antiviral responses against WSSV. Our results demonstrate that dme-miR-307a-3p may play vital regulatory roles in responding to starvation stress and WSSV infection. The findings contribute new insight into the molecular mechanisms associated with immune responses to environmental stress in crustaceans.
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9
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Xing K, Liu Y, Yan C, Zhou Y, Sun Y, Su N, Yang F, Xie S, Zhang J. Transcriptome analysis of Neocaridina denticulate sinensis under copper exposure. Gene 2020; 764:145098. [PMID: 32861881 DOI: 10.1016/j.gene.2020.145098] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/23/2022]
Abstract
Neocaridina denticulate sinensis is a small freshwater economic shrimp, as well as excellent laboratory model for their short life cycle and easy availability. However, the response of N. denticulate sinensis to pervasive copper pollution in aquatic environments has not been deeply investigated yet. Herein, we preformed Illumina sequencing technology to mine the alterations of cephalothorax transcriptome under 2.5 μmol/L of Cu2+ after 48 h. 122,512 unigenes were assembled and 219 unigenes were identified as significantly differentially expressed genes (DEGs) between control and Cu2+ treatment groups. Functional enrichment analysis revealed that DEGs were mostly associated with immune responses and molting, such as endocytosis, Fc gamma R-mediated phagocytosis and chitin metabolic process. Seven genes were chosen for qPCR verification, and the results showed that the transcriptome sequencing data were consistent with the qPCR results. This is the first report of transcriptome information about N. denticulate sinensis. These results provided a direction for the future research of resistance to Cu2+ in this shrimp, and simultaneously enriched gene information of N. denticulate sinensis.
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Affiliation(s)
- Kefan Xing
- College of Life Science, Institute of Life and Green Development, Hebei University, Baoding 071002, China
| | - Yujie Liu
- College of Life Science, Institute of Life and Green Development, Hebei University, Baoding 071002, China
| | - Congcong Yan
- College of Life Science, Institute of Life and Green Development, Hebei University, Baoding 071002, China
| | - Yongzhao Zhou
- College of Life Science, Institute of Life and Green Development, Hebei University, Baoding 071002, China
| | - Yuying Sun
- College of Life Science, Institute of Life and Green Development, Hebei University, Baoding 071002, China
| | - Naike Su
- College of Life Science, Institute of Life and Green Development, Hebei University, Baoding 071002, China
| | - Fusheng Yang
- Xiaoshan Donghai Aquaculture Co., Ltd, Xiaoshan 310012, China
| | - Song Xie
- College of Life Science, Institute of Life and Green Development, Hebei University, Baoding 071002, China.
| | - Jiquan Zhang
- College of Life Science, Institute of Life and Green Development, Hebei University, Baoding 071002, China.
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10
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Xu P, Guo H, Wang H, Xie Y, Lee SC, Liu M, Zheng J, Mao X, Wang H, Liu F, Wan C, Qin S, Liu Y, Zhao M, Wang L. Identification and profiling of microRNAs responsive to cadmium toxicity in hepatopancreas of the freshwater crab Sinopotamon henanense. Hereditas 2019; 156:34. [PMID: 31708719 PMCID: PMC6829971 DOI: 10.1186/s41065-019-0110-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/11/2019] [Indexed: 12/19/2022] Open
Abstract
Background Cadmium (Cd) is a ubiquitous environmental toxicant for aquatic animals. The freshwater crab, Sinopotamon henanense (S. henanense), is a useful model for monitoring Cd exposure since it is widely distributed in sediments whereby it tends to accumulate several toxicants, including Cd. In the recent years, the toxic effects of Cd in the hepatopancreas of S. henanense have been demonstrated by a series of biochemical analysis and ultrastructural observations as well as the deep sequencing approaches and gene expression profile analysis. However, the post-transcriptional regulatory network underlying Cd toxicity in S.henanense is still largely unknown. Results The miRNA transcriptional profile of the hepatopancreas of S. henanense was used to investigate the expression levels of miRNAs in response to Cd toxicity. In total, 464 known miRNAs and 191 novel miRNAs were identified. Among these 656 miRNAs, 126 known miRNAs could be matched with the miRNAs of Portunus trituberculatus, Eriocheir sinensis and Scylla paramamosain. Furthermore, a total of 24 conserved miRNAs were detected in these four crab species. Fifty-one differentially expressed miRNAs were identified in the Cd-exposed group, with 31 up-regulated and 20 down-regulated. Eight of the differentially expressed miRNAs were randomly selected and verified by the quantitative real-time PCR (qRT-PCR), and there was a general consistency (87.25%) between the qRT-PCR and miRNA transcriptome data. A total of 5258 target genes were screened by bioinformatics prediction. GO term analysis showed that, 17 GO terms were significantly enriched, which were mainly related to the regulation of oxidoreductase activity. KEGG pathway analysis showed that 18 pathways were significantly enriched, which were mainly associated with the biosynthesis, modification and degradation of proteins. Conclusion In response to Cd toxicity, in the hepatopancreas of S. henanense, the expressions of significant amount of miRNAs were altered, which may be an adaptation to resist the oxidative stress induced by Cd. These results provide a basis for further studies of miRNA-mediated functional adaptation of the animal to combat Cd toxicity.
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Affiliation(s)
- Peng Xu
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China.,2Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Huiqin Guo
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
| | - Huihui Wang
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
| | - Yuxin Xie
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
| | - Shao Chin Lee
- 3School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 China.,1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
| | - Ming Liu
- 4State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China.,5University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jian Zheng
- Department of Cardiopulmonary Function Examination, Shanxi Provincial Cancer Hospital, Taiyuan, 030013 China
| | - Xiuli Mao
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
| | - Huan Wang
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
| | - Fatao Liu
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092 China
| | - Chunling Wan
- 2Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Shengying Qin
- 2Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Yun Liu
- 8Department of Oncology, Fudan University Pudong Medical Center, Shanghai, 201300 China
| | - Meirong Zhao
- 9Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Lan Wang
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
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11
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Zhang QL, Dong ZX, Xiong Y, Li HW, Guo J, Wang F, Deng XY, Chen JY, Lin LB. Genome-wide transcriptional response of microRNAs to the benzo(a)pyrene stress in amphioxus Branchiostoma belcheri. CHEMOSPHERE 2019; 218:205-210. [PMID: 30471501 DOI: 10.1016/j.chemosphere.2018.11.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 06/09/2023]
Abstract
Amphioxus, a cephalochordate found in sand habitats in shallow in-shore seawaters, has been widely used as a model in comparative immunology of chordates. However, the role of microRNAs (miRNAs) in amphioxus under abiotic stress, particularly xenobiotics with strong toxicity, remains largely unknown. Here, a widespread marine contaminant, benzo(a)pyrene (BaP) is used to evaluate its toxic effects on miRNA expression of amphioxus. Six small RNA libraries were sequenced from Branchiostoma belcheri. A total of 144 known and 157 novel miRNAs were identified using deep sequencing and bioinformatics approaches. A total of 58 differentially expressed miRNAs (DEMs) were screened, including 25 up- and 33 down-regulated DEMs under BaP stress. Target genes possibly regulated by DEMs were predicted, and their functional enrichment analyses were performed. Targets of DEMs are primarily involved in xenobiotic and cellular homeostasis, catabolic and transport process. They could be largely linked to nine immune- and toxin detoxification-related pathways, including metabolism of xenobiotics by cytochrome P450, drug metabolism-other enzymes, and drug metabolism-cytochrome P450, etc. Furthermore, quantitative real-time PCR (qRT-PCR) analysis for 12 key BaP-responsive DEMs validates the accuracy of deep sequencing. Experiments were then conducted to investigate their expression responses to BaP stress at different time intervals in detail to further determine their expression dynamic in responses of B. belcheri towards BaP exposure. This study, to the best of our knowledge, investigates the regulatory roles of miRNAs in the toxicological response of amphioxus for the first time, providing valuable information for the protection of lone existing cephalochordate amphioxus.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Zhi-Xiang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yan Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun-Yuan Chen
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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