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Gao JH, Zhao JL, Yao XL, Tola T, Zheng J, Xue WB, Wang DW, Xing Y. Identification of antimicrobial peptide genes from transcriptomes in Mandarin fish (Siniperca chuatsi) and their response to infection with Aeromonas hydrophila. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109247. [PMID: 38006905 DOI: 10.1016/j.fsi.2023.109247] [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: 10/29/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Mandarin fish (Siniperca chuatsi) is a valuable freshwater fish species widely cultured in China. Its aquaculture production is challenged by bacterial septicaemia, which is one of the most common bacterial diseases. Antimicrobial peptides (AMPs) play a critical role in the innate immune system of fish, exhibiting defensive and inhibitory effects against a wide range of pathogens. This study aimed to identify the antimicrobial peptide genes in mandarin fish using transcriptomes data obtained from 17 tissue in our laboratory. Through nucleotide sequence alignment and protein structural domain analysis, 15 antimicrobial peptide genes (moronecidin, pleurocidin, lysozyme g, thymosin β12, hepcidin, leap 2, β-defensin, galectin 8, galectin 9, apoB, apoD, apoE, apoF, apoM, and nk-lysin) were identified, of which 9 antimicrobial peptide genes were identified for the first time. In addition, 15 AMPs were subjected to sequence characterization and protein structure analysis. After injection with Aeromonas hydrophila, the number of red blood cells, hemoglobin concentration, and platelet counts in mandarin fish showed a decreasing trend, indicating partial hemolysis. The expression change patterns of 15 AMP genes in the intestine after A. hydrophila infection were examined by using qRT-PCR. The results revealed, marked up-regulation (approximately 116.04) of the hepcidin gene, down-regulation of the piscidin family genes expression. Moreover, most AMP genes were responded in the early stages after A. hydrophila challenge. This study provides fundamental information for investigating the role of the different antimicrobial peptide genes in mandarin fish in defense against A. hydrophila infection.
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Affiliation(s)
- Jin-Hua Gao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, PR China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Jin-Liang Zhao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, PR China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China.
| | - Xiao-Li Yao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, PR China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Temesgen Tola
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, PR China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Jia Zheng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, PR China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Wen-Bo Xue
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, PR China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Da-Wei Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, PR China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Ying Xing
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, PR China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China
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Chen L, Pan Y, Cheng J, Zhu X, Chu W, Meng YY, Bin S, Zhang J. Characterization of myosin heavy chain (MYH) genes and their differential expression in white and red muscles of Chinese perch, Siniperca chuatsi. Int J Biol Macromol 2023; 250:125907. [PMID: 37482155 DOI: 10.1016/j.ijbiomac.2023.125907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023]
Abstract
Fish skeletal muscle is composed of two anatomically and functionally different fiber layers, white or fast and red or slow muscles. Myosin, the major structural protein of fish skeletal muscle, contains multiple myosin heavy chain (MYH) isoforms involved in the high plasticity of muscle in response to varying functional demands and/or environmental changes. In this study, we comparatively assayed the cellular and ultrastructural feature of white and red skeletal muscles. Then, a total of 28 class II myosin heavy chain genes were identified in by searching the Chinese perch genome database. Among them, 14 genes code for the fast-muscle-type myosin heavy chain, and 7 genes code for the slow-muscle-type myosin heavy chain. Further, the different isoform gene structures, function domains, phylogenetic relations, and muscle-fiber type-specific expression were characterized. This is the first systematic work on the molecular characterization of class II myosin heavy chain isoforms and the differential analysis of their expression in red and white muscle tissues in Chinese perch Siniperca chuatsi. Our work provided valuable information for a better understanding of myh genes and their molecular characteristics, and the correlations of multiple myosin isoforms with potential functions in response to varying functional demands and/or environmental changes.
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Affiliation(s)
- Lin Chen
- College of Biological and Chemical Engineering, Changsha University, Hunan 410003, China
| | - Yaxong Pan
- College of Biological and Chemical Engineering, Changsha University, Hunan 410003, China
| | - Jia Cheng
- College of Biological and Chemical Engineering, Changsha University, Hunan 410003, China
| | - Xin Zhu
- College of Biological and Chemical Engineering, Changsha University, Hunan 410003, China
| | - Wuying Chu
- College of Biological and Chemical Engineering, Changsha University, Hunan 410003, China
| | - Yang Yang Meng
- College of Biological and Chemical Engineering, Changsha University, Hunan 410003, China
| | - Shiyu Bin
- Department of Biology, Guangxi Normal University, Guilin 419034, Guangxi, China.
| | - Jianshe Zhang
- College of Biological and Chemical Engineering, Changsha University, Hunan 410003, China.
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Zhou Y, Fu HC, Wang YY, Huang HZ, Fu XZ, Li NQ. The dynamic immune responses of Mandarin fish (Siniperca chuatsi) to ISKNV in early infection based on full-length transcriptome analysis and weighted gene co-expression network analysis. FISH & SHELLFISH IMMUNOLOGY 2022; 122:191-205. [PMID: 35158068 DOI: 10.1016/j.fsi.2022.02.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 05/26/2023]
Abstract
Mandarin fish (Siniperca chuatsi) been seriously harmed by infectious spleen and kidney necrosis virus (ISKNV) in recent years, but the early immune response mechanism of infection is still unknown. Here, we performed RNA sequencing on the spleens of mandarin fish infected with ISKNV at 0, 12, 24, 48, and 72 h post-infection (hpi) using short-read Illumina RNA sequencing and long-read Pacific Biosciences isoform sequencing to generate a full-length transcriptome. The immune responses of mandarin fish infected with ISKNV at the molecular level were characterized by RNA-seq analysis and weighted gene co-expression network analysis (WGCNA). A total of 26,528 full-length transcript sequences were obtained. There were 2,729 (1,680 up-regulated and 1,112 down-regulated), 1,874 (1,136 up-regulated and 738 down-regulated), 2,032 (1,158 up-regulated and 847 down-regulated), and 4,176 (2,233 up-regulated and 1,943 down-regulated) differentially expressed genes (DEGs) in mandarin fish at 12, 24, 48, and 72 hpi, compared with uninfected fish, respectively. A total of four modules of co-expressed DEGs identified by WGCNA were significantly positively correlated to the four time points after infection, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the immune-related DEGs in all these modules were mainly enriched in Phagosome, Endocytosis, Herpes simplex infection, and Cytokine-cytokine receptor interaction pathways. Further analysis showed that oher signaling pathways, including CAMs, NOD-like receptor and ER protein processing, Intestinal immune network for IgA production, TLR pathway, and Apoptosis significantly enriched in four modules corresponding to 12, 24, 48, and 72 hpi respectively, had specifically participated in the immune response. Hub genes identified based on the high-degree nodes in the WGCN, including CAM3, IL-8, CCL21, STING, SNX1, PFR and TBK1, and some DEGs such as MHCI, MHCII, TfR, STING, TNF α, TBK1, IRF1, and NF-kB, BCR, IgA and Bcl-XL had involved in dynamic molecular response of mandarin fish to ISKNV infection. In sum, this study provides a set of full-length transcriptome of the spleen tissue of mandarin fish for the first time and revealed a group of immune genes and pathways involved in different temporal responses to ISKNV infection, which has implications for resource conservation and aiding the development of strategies to prevent virus early infection for mandarin fish.
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Affiliation(s)
- Yu Zhou
- School of Basic Medicine and Biological Sciences, Fisheries Research Institute, Soochow University, Suzhou, 215123, China
| | - Huang-Cui Fu
- School of Basic Medicine and Biological Sciences, Fisheries Research Institute, Soochow University, Suzhou, 215123, China
| | - Ying-Ying Wang
- School of Basic Medicine and Biological Sciences, Fisheries Research Institute, Soochow University, Suzhou, 215123, China
| | - He-Zhong Huang
- School of Basic Medicine and Biological Sciences, Fisheries Research Institute, Soochow University, Suzhou, 215123, China.
| | - Xiao-Zhe Fu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Provinces, Guangzhou, 510380, China
| | - Ning-Qiu Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Provinces, Guangzhou, 510380, China
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Shen Y, Li H, Zhao J, Tang S, Zhao Y, Gu Y, Chen X. Genomic and expression characterization of aquaporin genes from Siniperca chuatsi. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100819. [PMID: 33652294 DOI: 10.1016/j.cbd.2021.100819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/13/2021] [Accepted: 02/21/2021] [Indexed: 01/07/2023]
Abstract
Aquaporins (AQPs) are major intrinsic proteins that form pores in the membranes of biological cells. We first cloned the full-length sequences of aqp0, 1, 3, 4, 7, 8, 9, 10, 11, and 12 genes in Siniperca chuatsi. The 10 S. chuatsi aqp (Sc-aqp) genes included complete open reading frames and exhibited different exon-intron organizations. Sc-aqp1, 3, 8, 9, 10, and 11 were mostly expressed in the gallbladder, gills, gastric cecum, liver, ovaries, and spleen, respectively; Sc-aqp0 and 4 were mostly expressed in larvae at 1 day after hatching and in gastrula; Sc-aqp7 and 12 were mostly expressed in 2K-cell embryos. The expression levels of Sc-aqp1, 3, 7, 8, 9, and 10 after 10 part per thousand (ppt) salt treatment had significantly changed compared with those after 0 ppt salt treatment. Real-time quantitative PCR analysis further showed that in the intestines, the mRNA levels of Sc-aqp1 and 10 significantly decreased by approximately 2.07- and 2.85-fold, respectively, whereas those of Sc-aqp8 and 9 significantly increased by approximately 7.08- and 4.14-fold, respectively. Sc-aqp1, 8, 9, and 10 showed no significant differences in the gills. Sc-aqp3 significantly decreased by approximately 1.51- and 1.67-fold in the gills and intestines, respectively. Sc-aqp7 significantly increased by approximately 4.18- and 7.04-fold in the gills and intestines, respectively. This study was the first to investigate the tissue expression profiles and response to salt stress of aqp genes in S. chuatsi. Moreover, altering diet and suffering from immune stress could cause changes in the expression level of aqps. This study provided valuable reference information for AQPs' roles in osmoregulation in freshwater fish.
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Affiliation(s)
- Yawei Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Huiyang Li
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Jinliang Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
| | - Shoujie Tang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yan Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yifeng Gu
- The First Affiliated Hospital, College of Medicine, Zhejiang University, China
| | - Xiaowu Chen
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.
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