1
|
Duan C, Zhou D, Feng R, Li X, Yang L, Li X, Li G, Chen H, Liao Y, Tian C. Long-term thermal acclimation enhances heat resistance of Hong Kong catfish (Clarias fuscus) by modulating gill tissue structure, antioxidant capacity and immune metabolic pathways. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:116930. [PMID: 39205351 DOI: 10.1016/j.ecoenv.2024.116930] [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: 05/27/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
The rapid temperature changes caused by global warming significantly challenge fish survival by affecting various biological processes. Fish generally mitigate stress through physiological plasticity, but when temperature changes exceed their tolerance limits, even adaptable species like Siluriformes can experience internal disruptions. This study investigates the effects of extreme thermal climate on Hong Kong catfish (Clarias fuscus), native to tropical and subtropical regions. C. fuscus were exposed to normal temperature (NT, 26 ℃) or high temperature (HT, 34 ℃) condition for 90 days. Subsequently, histological, biochemical, and transcriptomic changes in gill tissue were observed after exposure to acute high temperatures (34 ℃) and subsequent temperature recovery (26 ℃). Histological analysis revealed that C. fuscus in the HT group exhibited less impact from sudden temperature shifts compared to the NT group, as they adapted by reducing the interlamellar cell mass (ILCM) and lamellae thickness (LT) of gill tissue, thereby mitigating the aftermath of acute heat shock. Biochemical analysis showed that catalase (CAT) activity in the high temperature group continued to increase, while malondialdehyde (MDA) levels decreased, suggesting establishment of a new oxidative balance and enhanced environmental adaptability. Transcriptome analysis identified 520 and 463 differentially expressed genes in the NT and HT groups, respectively, in response to acute temperature changes. Enrichment analysis highlighted that in response to acute temperature changes, the NT group inhibited apoptosis and ferroptosis by regulating the activity of alox12, gclc, and hmox1a, thereby attenuating the adverse effects of heat stress. Conversely, the HT group increased the activity of pfkma and pkma to provide sufficient energy for tissue repair. The higher degree of heat shock protein (Hsp) response in NT group also indicated more severe heat stress injury. These findings demonstrate alterations in gill tissue structure, regulation of oxidative balance, and the response of immune metabolic pathways to acute temperature fluctuations in C. fuscus following thermal exposure, suggesting potential avenues for further exploration into the thermal tolerance plasticity of fish adapting to global warming.
Collapse
Affiliation(s)
- Cunyu Duan
- Fisheries College, Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Lab of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, China
| | - Dayan Zhou
- Guangxi Introduction and Breeding Center of Aquaculture, Nanning 530001, China
| | - Ruiqing Feng
- Fisheries College, Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Lab of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, China
| | - Xiaolong Li
- Fisheries College, Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Lab of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, China
| | - Lei Yang
- Fisheries College, Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Lab of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, China
| | - Xinyi Li
- Fisheries College, Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Lab of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, China
| | - Guangli Li
- Fisheries College, Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Lab of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, China
| | - Huapu Chen
- Fisheries College, Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Lab of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, China
| | - Yu Liao
- Guangxi Introduction and Breeding Center of Aquaculture, Nanning 530001, China
| | - Changxu Tian
- Fisheries College, Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Lab of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, China.
| |
Collapse
|
2
|
Ge K, Fan Z, Huang T, Gu W, Wang G, Liu E, Pan R, Li D, Sun Y, Yao Z, Wang L, Zhao C, Xu G. Influence of increasing acclimation temperature on growth, digestion, antioxidant capacity, liver transcriptome and intestinal microflora of Ussruri whitefish Coregonus ussuriensis Berg. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109667. [PMID: 38830520 DOI: 10.1016/j.fsi.2024.109667] [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: 04/17/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/05/2024]
Abstract
For effective restoration, conservation of Ussruri whitefish Coregonus ussuriensis Berg and coping with global climate change, effects of environmental temperature on Ussruri whitefish urgently need to be explored. In current study, the effects of different acclimation temperatures on the growth, digestive physiology, antioxidant ability, liver transcriptional responses and intestinal microflora patterns of Ussruri whitefish were investigated. Ussruri whitefish (15.20 g ± 1.23 g) were reared for 42 days under different acclimation temperatures, i.e., 10, 13, 16, 19, 22 and 25 °C, respectively. Result first determined 28 °C as the semi-lethal temperature in order to design the temperature gradient test. Highest main gain rate (MGR) and specific growth rate (SGR) were observed in fish group having acclimation temperature of 19 °C. Significantly decrease (P < 0.05) in triglyceride (TG) content appeared at 19 °C as compared to the 10 °C and 13 °C temperature groups. 19 °C notablely increased protease activities of stomach and intestine and intestinal lipase and amylase activities. 19 °C group obtained the highest activities of chloramphnicol acetyltransferase (CAT) and total antioxidant capacity (T-AOC) and higher activities of superoxide dismutase (SOD). The intestinal microflora composition was most conducive to maintaining overall intestinal health when the temperature was 19 °C, compared to 10 °C and 25 °C. Ussruri whitefish exposed to 10 °C and 25 °C possessed the lower Lactobacillus abundance compared to exposure to 19 °C. Temperature down to 10 °C or up to 25 °C, respectively, triggered cold stress and heat stress, which leading to impairment in intestinal digestion, liver antioxidant capacity and intestinal microflora structure. Liver transcriptome response to 10 °C, 19 °C and 25 °C revealed that Ussruri whitefish might require the initiation of endoplasmic reticulum stress to correct protein damage from cold-temperature and high-temperature stress, and it was speculated that DNAJB11 could be regarded as a biomarker of cold stress response.Based on the quadratic regression analysis of MGR and SGR against temperature, the optimal acclamation temperature were, respectively, 18.0 °C and 18.1 °C. Our findings provide valuable theoretical insights for an in-depth understanding of temperature acclimation mechanisms and laid the foundation for conservation and development of Ussruri whitefish germplasm resources.
Collapse
Affiliation(s)
- Kaibo Ge
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China
| | - Ze Fan
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China
| | - Tianqing Huang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China
| | - Wei Gu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China
| | - Gaochao Wang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China
| | - Enhui Liu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China
| | - Runlei Pan
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China
| | - Datian Li
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China
| | - Yunchao Sun
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China
| | - Zuochun Yao
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China
| | - Liwei Wang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Cheng Zhao
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Gefeng Xu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China.
| |
Collapse
|
3
|
Liu J, Liu T, Liu Y, Wang Y, Liu L, Gong L, Liu B, Lü Z. Comparative Transcriptome Analyses Provide New Insights into the Evolution of Divergent Thermal Resistance in Two Eel Gobies. Curr Issues Mol Biol 2023; 46:153-170. [PMID: 38248314 PMCID: PMC10813846 DOI: 10.3390/cimb46010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024] Open
Abstract
Adaptation to thermal conditions in tidal mudflats always involves tolerating frequent fluctuations and often extreme environmental temperatures. Regulation of gene expression plays a fundamental role in the evolution of these thermal adaptations. To identify the key gene regulatory networks associated with the thermal adaptation, we investigated the capability of cold tolerance, as well as the transcriptomic changes under cold stress in two mudflat inhabitants (Odontamblyopus lacepedii and O. rebecca) with contrasting latitude affinity. Our results revealed a remarkable divergent capacity of cold tolerance (CTmin: 0.61 °C vs. 9.57 °C) between the two gobies. Analysis of transcriptomic changes under cold stress unveiled 193 differentially expressed genes exhibiting similar expression profiles across all tissues and species, including several classic metabolic and circadian rhythm molecules such as ACOD and CIART that may represent the core cold response machinery in eel gobies. Meanwhile, some genes show a unique expression spectrum in the more cold-tolerant O. lacepedii suggesting their roles in the enhanced cold tolerance and hence the extreme thermal adaptations. In addition, a weighted gene co-expression network analysis (WGCNA) revealed a subset of metabolic hub genes including MYH11 and LIPT2 showing distinct down-regulation in O. lacepedii when exposed to cold stress which highlights the role of reduced energy consumption in the enhanced cold tolerance of eel gobies. These findings not only provide new insights into how mudflat teleosts could cope with cold stress and their potential evolutionary strategies for adapting to their thermal environment, but also have important implications for sound management and conservation of their fishery resources in a scenario of global climate warming in the marine realm.
Collapse
Affiliation(s)
- Jing Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Tianwei Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Yantao Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Yuzhen Wang
- National Engineering Research Center for Facilitated Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| |
Collapse
|
4
|
Kumar PV, Rasal KD, Acharya A, Dey D, Sonwane AA, Reang D, Rajeshkannan R, Pawar SS, Kurade NP, Bhendarkar MP, Krishnani KK, Nagpure NS, Brahmane MP. Muscle Transcriptome Sequencing Revealed Thermal Stress-Responsive Regulatory Genes in Farmed Rohu, Labeo rohita (Hamilton, 1822). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:1057-1075. [PMID: 37878212 DOI: 10.1007/s10126-023-10259-8] [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: 08/16/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]
Abstract
Rohu, Labeo rohita, is one of the most important aquaculture species in the Indian subcontinent. Understanding the molecular-level physiological responses to thermal stress or climate change is essential. In the present work, transcriptome sequencing was carried out in the muscle tissue of the rohu in response to heat stress (35 °C) in comparison with the control (28 °C). A total of 125 Gb of sequence data was generated, and the raw-reads were filtered and trimmed, which resulted in 484 million quality reads. Reference-based assembly of reads was performed using L. rohita genome, and a total of 90.17% of reads were successfully mapped. A total of 37,462 contigs were assembled with an N50 value of 1854. The differential expression analysis revealed a total of 107 differentially expressed genes (DEGs) (15 up-, 37 down-, and 55 neutrally regulated) as compared to the control group (Log2FC > 2, P < 0.05). Gene enrichment analysis of DEGs indicates that transcripts were associated with molecular, biological, and cellular activities. The randomly selected differentially expressed transcripts were validated by RT-qPCR and found consistent expression patterns in line with the RNA-seq data. Several transcripts such as SERPINE1(HSP47), HSP70, HSP90alpha, Rano class II histocompatibility A beta, PGC-1 and ERR-induced regulator, proto-oncogene c-Fos, myozenin2, alpha-crystallin B chain-like protein, angiopoietin-like protein 8, and acetyl-CoA carboxylases have been identified in muscle tissue of rohu that are associated with stress/immunity. This study identified the key biomarker SERPINE1 (HSP47), which showed significant upregulation (~ 2- to threefold) in muscle tissue of rohu exposed to high temperature. This study can pave a path for the identification of stress-responsive biomarkers linked with thermal adaptations in the farmed carps.
Collapse
Affiliation(s)
- Pokanti Vinay Kumar
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Kiran D Rasal
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Arpit Acharya
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Diganta Dey
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Arvind A Sonwane
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Dhalongsaih Reang
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - R Rajeshkannan
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Sachin S Pawar
- School of Atmospheric Stress Management, ICAR - National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India
| | - Nitin P Kurade
- School of Atmospheric Stress Management, ICAR - National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India
| | - Mukesh P Bhendarkar
- School of Atmospheric Stress Management, ICAR - National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India
| | - Kishore K Krishnani
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
- School of Atmospheric Stress Management, ICAR - National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India
| | - Naresh S Nagpure
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Manoj P Brahmane
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India.
- School of Atmospheric Stress Management, ICAR - National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India.
| |
Collapse
|
5
|
Zhou F, Qi M, Li J, Huang Y, Chen X, Liu W, Yao G, Meng Q, Zheng T, Wang Z, Ding X. Comparative Transcriptomic Analysis of Largemouth Bass ( Micropterus salmoides) Livers Reveals Response Mechanisms to High Temperatures. Genes (Basel) 2023; 14:2096. [PMID: 38003039 PMCID: PMC10671503 DOI: 10.3390/genes14112096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
High temperatures are considered one of the most significant limitations to subtropical fishery production. Largemouth bass (Micropterus salmoides) is an economically important freshwater species grown in subtropical areas, which are extremely sensitive to heat stress (HS). However, comprehensive transcriptomic data for the livers of largemouth bass in response to HS are still lacking. In this study, a comparative transcriptomic analysis was performed to investigate the gene expression profiles of the livers of largemouth bass under HS treatment. As a result, 6114 significantly differentially expressed genes (DEGs), which included 2645 up-regulated and 3469 down-regulated genes, were identified in response to HS. Bioinformatics analyses demonstrated that the 'ECM-receptor interaction' pathway was one of the most dramatically changed pathways in response to HS, and eight DEGs assigned to this pathway were taken as hub genes. Furthermore, the expression of these eight hub genes was determined by quantitative reverse transcription PCR, and all of them showed a significant change at the transcriptional level, suggesting a crucial role of the 'ECM-receptor interaction' pathway in the response of largemouth bass to HS. These findings may improve our understanding of the molecular mechanisms underlying the response of largemouth bass to HS.
Collapse
Affiliation(s)
- Fan Zhou
- Zhejiang Fisheries Technical Extension Center, Hangzhou 310023, China; (F.Z.); (M.Q.); (Y.H.); (X.C.); (W.L.); (G.Y.); (Q.M.); (T.Z.)
| | - Ming Qi
- Zhejiang Fisheries Technical Extension Center, Hangzhou 310023, China; (F.Z.); (M.Q.); (Y.H.); (X.C.); (W.L.); (G.Y.); (Q.M.); (T.Z.)
| | - Jiapeng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China;
| | - Yuanfei Huang
- Zhejiang Fisheries Technical Extension Center, Hangzhou 310023, China; (F.Z.); (M.Q.); (Y.H.); (X.C.); (W.L.); (G.Y.); (Q.M.); (T.Z.)
| | - Xiaoming Chen
- Zhejiang Fisheries Technical Extension Center, Hangzhou 310023, China; (F.Z.); (M.Q.); (Y.H.); (X.C.); (W.L.); (G.Y.); (Q.M.); (T.Z.)
| | - Wei Liu
- Zhejiang Fisheries Technical Extension Center, Hangzhou 310023, China; (F.Z.); (M.Q.); (Y.H.); (X.C.); (W.L.); (G.Y.); (Q.M.); (T.Z.)
| | - Gaohua Yao
- Zhejiang Fisheries Technical Extension Center, Hangzhou 310023, China; (F.Z.); (M.Q.); (Y.H.); (X.C.); (W.L.); (G.Y.); (Q.M.); (T.Z.)
| | - Qinghui Meng
- Zhejiang Fisheries Technical Extension Center, Hangzhou 310023, China; (F.Z.); (M.Q.); (Y.H.); (X.C.); (W.L.); (G.Y.); (Q.M.); (T.Z.)
| | - Tianlun Zheng
- Zhejiang Fisheries Technical Extension Center, Hangzhou 310023, China; (F.Z.); (M.Q.); (Y.H.); (X.C.); (W.L.); (G.Y.); (Q.M.); (T.Z.)
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China;
| | - Xueyan Ding
- Zhejiang Fisheries Technical Extension Center, Hangzhou 310023, China; (F.Z.); (M.Q.); (Y.H.); (X.C.); (W.L.); (G.Y.); (Q.M.); (T.Z.)
| |
Collapse
|
6
|
Moreno P, Gemez-Mata J, Alvarez-Torres D, Garcia-Rosado E, Bejar J, Alonso MC. Genomic characterization and transcription analysis of European sea bass (Dicentrarchus labrax) rtp3 genes. Mol Immunol 2023; 163:243-248. [PMID: 37879238 DOI: 10.1016/j.molimm.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/03/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023]
Abstract
Fish RTP3, belonging to the receptor-transporting protein family, display several functions, including a putative antiviral role as virus-responsive gene. In this work, we have identified and characterized two different European sea bass rtp3 genes. In addition, an in vivo transcription analysis in response to LPS, poly I:C and betanodavirus infection (RGNNV genotype) has been performed. The sequence analysis showed that European sea bass displays two rtp3 genes, X1 and X2, composed of two exons and a single intron (1007-bp and 888-bp long, respectively), located within the ORF sequence. The full-length cDNA is 1969 bp for rtp3 X1, and 1491 bp for rtp3 X2. Several ATTTA motifs have been found in the intron sequence of both genes, whereas rtp3 X1 also contains this motif in both untranslated regions. The transcription analyses revealed significant level of rtp3 X2 mRNA in brain and head kidney after LPS and poly I:C inoculation; however, the induction elicited by RGNNV infection was much higher, suggesting an essential role for this protein in controlling NNV infections.
Collapse
Affiliation(s)
- Patricia Moreno
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul (IBYDA), Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain
| | - Juan Gemez-Mata
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul (IBYDA), Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain
| | - Daniel Alvarez-Torres
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul (IBYDA), 29071 Málaga, Spain
| | - Esther Garcia-Rosado
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul (IBYDA), Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain
| | - Julia Bejar
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul (IBYDA), Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, 29071 Málaga, Spain
| | - M Carmen Alonso
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul (IBYDA), Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain.
| |
Collapse
|
7
|
Li J, Wen J, Hu R, Pei S, Li T, Shan B, Huang H, Zhu C. Transcriptome Responses to Different Environments in Intertidal Zones in the Peanut Worm Sipunculus nudus. BIOLOGY 2023; 12:1182. [PMID: 37759582 PMCID: PMC10525638 DOI: 10.3390/biology12091182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/19/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023]
Abstract
The peanut worm (Sipunculus nudus) is an important intertidal species worldwide. Species living in the same aquaculture area might suffer different environmental impacts. To increase knowledge of the molecular mechanisms underlying the response to environmental fluctuations, we performed a transcriptome analysis of S. nudus from different intertidal zones using a combination of the SMRT platform and the Illumina sequencing platform. (1) A total of 105,259 unigenes were assembled, and 23,063 unigenes were perfectly annotated. The results of the PacBio Iso-Seq and IIIumina RNA-Seq enriched the genetic database of S. nudus. (2) A total of 830 DEGs were detected in S. nudus from the different groups. In particular, 33 DEGs had differential expression in the top nine KEGG pathways related to pathogens, protein synthesis, and cellular immune response and signaling. The results indicate that S. nudus from different zones experience different environmental stresses. (3) Several DEGs (HSPA1, NFKBIA, eEF1A, etc.) in pathways related to pathogens (influenza A, legionellosis, measles, and toxoplasmosis) had higher expression in groups M and L. HSPA1 was clearly enriched in most of the pathways, followed by NFKBIA. The results show that the peanut worms from the M and L tidal flats might have suffered more severe environmental conditions. (4) Some DEGs (MKP, MRAS, and HSPB1) were upregulated in peanut worms from the H tidal flat, and these DEGs were mainly involved in the MAPK signaling pathway. These results indicate that the MAPK pathway may play a vital role in the immune response of the peanut worm to the effects of different intertidal flats. This study provides a valuable starting point for further studies to elucidate the molecular basis of the response to different environmental stresses in S. nudus.
Collapse
Affiliation(s)
- Junwei Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (J.L.); (J.W.); (T.L.); (B.S.); (H.H.)
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Jiufu Wen
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (J.L.); (J.W.); (T.L.); (B.S.); (H.H.)
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Ruiping Hu
- Institute of Biological and Medical Engineering, Guangdong Academy of Science, Guangzhou 510316, China
| | - Surui Pei
- Corregene Biotechnology Co., Ltd., Beijing 102600, China;
| | - Ting Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (J.L.); (J.W.); (T.L.); (B.S.); (H.H.)
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Binbin Shan
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (J.L.); (J.W.); (T.L.); (B.S.); (H.H.)
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Honghui Huang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (J.L.); (J.W.); (T.L.); (B.S.); (H.H.)
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Changbo Zhu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| |
Collapse
|
8
|
Liu MJ, Gao J, Guo HY, Zhu KC, Liu BS, Zhang N, Sun JH, Zhang DC. Transcriptomics Reveal the Effects of Breeding Temperature on Growth and Metabolism in the Early Developmental Stage of Platax teira. BIOLOGY 2023; 12:1161. [PMID: 37759561 PMCID: PMC10525949 DOI: 10.3390/biology12091161] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/16/2023] [Accepted: 08/10/2023] [Indexed: 09/29/2023]
Abstract
The growth, development, and survival of fish, especially in the early stages of development, is influenced by a complex of environmental factors, among which temperature is one of the most important. Although the physiological effects of environmental stress in fish have been extensively studied, the molecular mechanisms are poorly understood. However, recent advances in transcriptomic techniques have facilitated the study of the molecular mechanisms of environmental stress responses in aquatic species. Here, we aimed to elucidate the effects of breeding temperatures (21, 24, 27, and 30 °C) on the growth and nutrient metabolism in the early developmental stage of Platax teira, using transcriptomic techniques. Transcriptomic analysis identified 5492, 6937, and 4246 differentially expressed genes (DEGs) in the 21 vs. 24 °C, 27 vs. 24 °C, and 30 vs. 24 °C comparisons, respectively, most of which were involved in cell processes, single organism, metabolism, catalytic activity, and cell part, based on gene ontology (GO) functional annotations. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the DEGs were mainly enriched in pathways related to metabolism of matter and energy, protein digestion and absorption, and glucose and lipid metabolism. Additionally, the expression of genes related to energy, lipid, and glucose metabolism in the fish liver was upregulated under a low-temperature condition (21 °C), although increasing the temperature within the acceptable threshold improved nutrient metabolism and growth in the fish. Meanwhile, nutrient metabolism and growth were suppressed by an extremely high temperature (30 °C) owing to oxidative stress. Overall, it was shown that nutrient metabolism pathways were involved in thermal stress responses in P. teira, and the optimal breeding temperature range was 24-27 °C. Through transcriptomics, the regulatory mechanism of larval development in P. teira under different growth temperatures was elucidated, with the goal of establishing a theoretical basis for industrial breeding.
Collapse
Affiliation(s)
- Ming-Jian Liu
- College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
| | - Jie Gao
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
| | - Hua-Yang Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Ke-Cheng Zhu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Bao-Suo Liu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Nan Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Jin-Hui Sun
- College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Dian-Chang Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| |
Collapse
|
9
|
Li P, Song Z, Huang L, Sun Y, Sun Y, Wang X, Li L. Effects of Dietary Protein and Lipid Levels in Practical Formulation on Growth, Feed Utilization, Body Composition, and Serum Biochemical Parameters of Growing Rockfish Sebastes schlegeli. AQUACULTURE NUTRITION 2023; 2023:9970252. [PMID: 37589032 PMCID: PMC10427231 DOI: 10.1155/2023/9970252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/07/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023]
Abstract
A 3 × 2 factorial experiment (protein levels, 42%, 46%, 50%; lipid levels, 9%, 12%) with three replicates was conducted in a circulating water system to investigate the effects of dietary protein and lipid levels on growth, feed utilization, body composition, and serum biochemical parameters of growing rockfish Sebastes schlegeli (initial weight, 29.98 ± 0.10 g). After an 8 weeks feeding trial, growth performance in terms of final body weight, percent weight gain, and specific growth rate increased with the increase of dietary protein level when fish fed diets containing a consistent level of dietary lipid. The feed conversion rate and daily feed intake were significantly affected by dietary protein and lipid levels, and decreased as dietary protein level increased from 42% to 46% or dietary lipid level increased from 9% to 12% (P < 0.05). Survival rate, viscerosomatic index, and hepatosomatic index were unaffected by dietary protein level (P > 0.05), but significantly increased with the increase of dietary lipid level (P < 0.05). On the contrary, condition factor was unaffected by dietary lipid level (P > 0.05), but significantly increased with dietary protein level increasing up to 46% (P < 0.05). The moisture contents of muscle and liver significantly decreased, but the whole-body crude lipid content, the crude protein and lipid contents of muscle increased as dietary protein or lipid level increased (P < 0.05). The contents of isoleucine, leucine, histidine, glycine, alanine of muscle, as well as the proportions of C14 : 0, C20 : 1, and C22 : 1n-9 in total fatty acids were higher in fish fed diets containing 12% lipid than those fed 9% lipid (P < 0.05), while C18 : 1n-9 and C18 : 2n-6 followed an opposite trend. The contents of phenylalanine, lysine, and tyrosine as well as the proportions of C18 : 0, C18 : 2n-6, C22 : 1n-9, and C22 : 6n-3 in total fatty acids decreased with the increase of dietary protein level (P < 0.05). Serum cholesterol and low-density lipoproteins increased significantly with dietary protein or lipid levels increasing, but TG concentration was elevated significantly in fish fed diets containing 12% lipid. Considering the present results in terms of growth and feed utilization, the suitable protein and lipid levels in diet for growing rockfish were 46% and 12%, respectively.
Collapse
Affiliation(s)
- Peiyu Li
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Zhidong Song
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Long Huang
- Yantai Zhulin Human Resources Service Co. Ltd, Yantai 264006, China
| | - Yongzhi Sun
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Yuming Sun
- Shandong Shengsuo Feed Technology Co. Ltd, Yantai 265500, China
| | - Xiaoyan Wang
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Lu Li
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| |
Collapse
|
10
|
Liu C, Li J, Qi X, Wang L, Sun D, Zhang J, Zhang K, Li J, Li Y, Wen H. Cytochrome P450 superfamily in spotted sea bass: Genome-wide identification and expression profiles under trichlorfon and environmental stresses. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101078. [PMID: 37121223 DOI: 10.1016/j.cbd.2023.101078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/02/2023]
Abstract
Cytochrome P450s (CYPs), as one of the most diverse enzyme superfamilies in nature, play critical functions in antioxidant reactions against endogenous and exogenous compounds. In this study, we performed genome-wide characterization of CYP superfamily members and analyzed their expression patterns under several abiotic stresses in spotted sea bass, which is known as an economically important fish species in the Chinese aquaculture industry. A total of 55 CYP genes were identified and divided into 17 families within 10 clans. The analysis of phylogeny, gene structure, and syntenic relationships provided evidence for the evolution of CYP genes and confirmed their annotation and orthology. The expression of CYP genes was examined in the liver during trichlorfon stress using quantitative real-time PCR. The results showed that 20 tested CYP genes displayed significant mRNA expression changes, indicating that they may play crucial roles in the metabolism of trichlorfon and can be potential biomarkers for trichlorfon pollution. Moreover, by screening transcriptomic databases, 10, 3 and 19 CYP genes exhibited differential expression patterns in response to hypoxia, alkalinity and heat stress, respectively. Taken together, this study provided insights into the regulation of CYP genes by toxicological and environmental stresses, laid basis for extensive functional studies of the CYP superfamily in spotted sea bass and other teleost species.
Collapse
Affiliation(s)
- Cong Liu
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Junjie Li
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Xin Qi
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Lingyu Wang
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Donglei Sun
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Jingru Zhang
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Kaiqiang Zhang
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Jianshuang Li
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Yun Li
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China.
| | - Haishen Wen
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China.
| |
Collapse
|
11
|
Scharsack JP, Franke F. Temperature effects on teleost immunity in the light of climate change. JOURNAL OF FISH BIOLOGY 2022; 101:780-796. [PMID: 35833710 DOI: 10.1111/jfb.15163] [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: 05/19/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Temperature is an important environmental modulator of teleost immune activity. Susceptibility of teleosts to temperature variation depends on the species-specific adaptive temperature range, and the activity of the teleost immune system is generally temperature-dependent. Similar to many physiological and metabolic traits of ectotherms, temperature modulates the activity of immune traits. At low temperatures, acquired immunity of many teleost species is down-modulated, and their immuno-competence mainly depends on innate immunity. At intermediate temperatures, both innate and acquired immunity are fully active and provide optimal protection, including long-lasting immunological memory. When temperatures increase and reach the upper permissive range, teleost immunity is compromised. Moreover, temperature shifts may have negative effects on teleost immune functions, in particular if shifts occur rapidly with high amplitudes. On the contrary, short-term temperature increase may help teleost immunity to fight against pathogens transiently. A major challenge to teleosts therefore is to maintain immuno-competence throughout the temperature range they are exposed to. Climate change coincides with rising temperatures, and more frequent and more extreme temperature shifts. Both are likely to influence the immuno-competence of teleosts. Nonetheless, teleosts exist in habitats that differ substantially in temperature, ranging from below zero in the Arctic's to above 40°C in warm springs, illustrating their enormous potential to adapt to different temperature regimes. The present review seeks to discuss how changes in temperature variation, induced by climate change, might influence teleost immunity.
Collapse
Affiliation(s)
- Jörn Peter Scharsack
- Department for Fish Diseases, Thuenen-Institute of Fisheries Ecology, Bremerhaven, Germany
| | - Frederik Franke
- Bavarian State Institute of Forestry, Department of Biodiversity, Nature Protection & Wildlife Management, Freising, Germany
| |
Collapse
|
12
|
Kim C, Wang X, Kültz D. Prediction and Experimental Validation of a New Salinity-Responsive Cis-Regulatory Element (CRE) in a Tilapia Cell Line. Life (Basel) 2022; 12:787. [PMID: 35743818 PMCID: PMC9225295 DOI: 10.3390/life12060787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
Transcriptional regulation is a major mechanism by which organisms integrate gene x environment interactions. It can be achieved by coordinated interplay between cis-regulatory elements (CREs) and transcription factors (TFs). Euryhaline tilapia (Oreochromis mossambicus) tolerate a wide range of salinity and thus are an appropriate model to examine transcriptional regulatory mechanisms during salinity stress in fish. Quantitative proteomics in combination with the transcription inhibitor actinomycin D revealed 19 proteins that are transcriptionally upregulated by hyperosmolality in tilapia brain (OmB) cells. We searched the extended proximal promoter up to intron1 of each corresponding gene for common motifs using motif discovery tools. The top-ranked motif identified (STREME1) represents a binding site for the Forkhead box TF L1 (FoxL1). STREME1 function during hyperosmolality was experimentally validated by choosing two of the 19 genes, chloride intracellular channel 2 (clic2) and uridine phosphorylase 1 (upp1), that are enriched in STREME1 in their extended promoters. Transcriptional induction of these genes during hyperosmolality requires STREME1, as evidenced by motif mutagenesis. We conclude that STREME1 represents a new functional CRE that contributes to gene x environment interactions during salinity stress in tilapia. Moreover, our results indicate that FoxL1 family TFs are contribute to hyperosmotic induction of genes in euryhaline fish.
Collapse
Affiliation(s)
- Chanhee Kim
- Stress-Induced Evolution Laboratory, Department of Animal Sciences, University of California, Davis, CA 95616, USA;
| | - Xiaodan Wang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai 200241, China;
| | - Dietmar Kültz
- Stress-Induced Evolution Laboratory, Department of Animal Sciences, University of California, Davis, CA 95616, USA;
| |
Collapse
|
13
|
Reid CH, Patrick PH, Rytwinski T, Taylor JJ, Willmore WG, Reesor B, Cooke SJ. An updated review of cold shock and cold stress in fish. JOURNAL OF FISH BIOLOGY 2022; 100:1102-1137. [PMID: 35285021 DOI: 10.1111/jfb.15037] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/23/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Temperature is critical in regulating virtually all biological functions in fish. Low temperature stress (cold shock/stress) is an often-overlooked challenge that many fish face as a result of both natural events and anthropogenic activities. In this study, we present an updated review of the cold shock literature based on a comprehensive literature search, following an initial review on the subject by M.R. Donaldson and colleagues, published in a 2008 volume of this journal. We focus on how knowledge on cold shock and fish has evolved over the past decade, describing advances in the understanding of the generalized stress response in fish under cold stress, what metrics may be used to quantify cold stress and what knowledge gaps remain to be addressed in future research. We also describe the relevance of cold shock as it pertains to environmental managers, policymakers and industry professionals, including practical applications of cold shock. Although substantial progress has been made in addressing some of the knowledge gaps identified a decade ago, other topics (e.g., population-level effects and interactions between primary, secondary and tertiary stress responses) have received little or no attention despite their significance to fish biology and thermal stress. Approaches using combinations of primary, secondary and tertiary stress responses are crucial as a research priority to better understand the mechanisms underlying cold shock responses, from short-term physiological changes to individual- and population-level effects, thereby providing researchers with better means of quantifying cold shock in laboratory and field settings.
Collapse
Affiliation(s)
- Connor H Reid
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | | | - Trina Rytwinski
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, Ontario, Canada
- Canadian Centre for Evidence-Based Conservation, Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
| | - Jessica J Taylor
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, Ontario, Canada
- Canadian Centre for Evidence-Based Conservation, Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
| | | | | | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, Ontario, Canada
| |
Collapse
|
14
|
Qin C, Xie J, Shi X, Tan J. Cold stress after swimming fatigue decreases immunity-related gene expression in the spleen of the Chinese sucker. FISH & SHELLFISH IMMUNOLOGY 2022; 122:455-464. [PMID: 35217195 DOI: 10.1016/j.fsi.2022.02.040] [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: 09/21/2021] [Revised: 01/19/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
For migratory fish, passing through the cold, fast flowing water of a dam causes stress, leading to disease and even death. To determine the immune response to cold stress in a dam-lake after swimming fatigue in Chinese sucker (Myxocyprinus asiaticus), the spleen mRNA expression profiles in response to cold stress (CS) after fatigue stress (FS) were compared with that of the control (SS). We identified 40,952 differentially expressed genes (DEGs) in the spleen for at least one comparison among 211,397 unigenes. We identified 11,869 DEGs (4,968 upregulated and 6,901 downregulated), 17,803 DEGs (10,610 upregulated and 7,193 downregulated), and 30,579 DEGs (20,652 upregulated and 9,927 downregulated) in the SS vs. FS, SS vs. CS, and FS vs. CS comparisons, respectively. Enrichment analysis indicated the involvement of the immune system and infectious diseases, including the toll-like receptor pathway, the complement and coagulation cascade, and the natural killer cell-mediated cytotoxicity pathway. There were 2,991 DEGs (271 upregulated and 2,720 downregulated), and 2,878 DEGs (873 upregulated and 2,005 downregulated) associated with these pathways in the SS vs. FS and SS vs. CS comparisons, respectively. In the cold stress after fatigue group, the expression levels of heat shock protein (HSP) 70 and HSP90 genes were significantly upregulated; however, more immune response genes showed significantly downregulated expression in SS vs. CS compared with that in SS vs. FS, including those encoding tumor necrosis factor, C-C motif chemokines (3, 8, and 13), complement components (C3, C4, C6, and C7), immunoglobulin, and cathepsins. Overall, cold stress combined with swimming fatigue from passing the dam resulted in the downregulation of many immune genes, suggesting that the Chinese sucker might have experienced serious immune suppression.
Collapse
Affiliation(s)
- Chuanjie Qin
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang, 641000, PR China.
| | - Jiang Xie
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang, 641000, PR China
| | - Xiaotao Shi
- Huibei International Science and Technology Cooperation Base of Fish Passage, China Three Gorges University, Yichang, 443002, PR China.
| | - Junjun Tan
- Huibei International Science and Technology Cooperation Base of Fish Passage, China Three Gorges University, Yichang, 443002, PR China
| |
Collapse
|
15
|
Feugere L, Scott VF, Rodriguez-Barucg Q, Beltran-Alvarez P, Wollenberg Valero KC. Thermal stress induces a positive phenotypic and molecular feedback loop in zebrafish embryos. J Therm Biol 2021; 102:103114. [PMID: 34863478 DOI: 10.1016/j.jtherbio.2021.103114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/28/2021] [Accepted: 10/20/2021] [Indexed: 12/17/2022]
Abstract
Aquatic organisms must cope with both rising and rapidly changing temperatures. These thermal changes can affect numerous traits, from molecular to ecological scales. Biotic stressors are already known to induce the release of chemical cues which trigger behavioural responses in other individuals. In this study, we infer whether fluctuating temperature, as an abiotic stressor, may similarly induce stress-like responses in individuals not directly exposed to the stressor. To test this hypothesis, zebrafish (Danio rerio) embryos were exposed for 24 h to fluctuating thermal stress, to medium in which another embryo was thermally stressed before ("stress medium"), and to a combination of these. Growth, behaviour, expression of molecular markers, and of whole-embryo cortisol were used to characterise the thermal stress response and its propagation between embryos. Both fluctuating high temperature and stress medium significantly accelerated development, by shifting stressed embryos from segmentation to pharyngula stages, and altered embryonic activity. Importantly, we found that the expression of sulfide:quinone oxidoreductase (SQOR), the antioxidant gene SOD1, and of interleukin-1β (IL-1β) were significantly altered by stress medium. This study illustrates the existence of positive thermal stress feedback loops in zebrafish embryos where heat stress can induce stress-like responses in conspecifics, but which might operate via different molecular pathways. If similar effects also occur under less severe heat stress regimes, this mechanism may be relevant in natural settings as well.
Collapse
Affiliation(s)
- Lauric Feugere
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Kingston Upon Hull, HU6 7RX, United Kingdom
| | - Victoria F Scott
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Kingston Upon Hull, HU6 7RX, United Kingdom; Energy and Environment Institute, University of Hull, Cottingham Road, Kingston Upon Hull, HU6 7RX, United Kingdom
| | - Quentin Rodriguez-Barucg
- Department of Biomedical Sciences, University of Hull, Cottingham Road, Kingston Upon Hull, HU6 7RX, United Kingdom
| | - Pedro Beltran-Alvarez
- Department of Biomedical Sciences, University of Hull, Cottingham Road, Kingston Upon Hull, HU6 7RX, United Kingdom
| | - Katharina C Wollenberg Valero
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Kingston Upon Hull, HU6 7RX, United Kingdom.
| |
Collapse
|
16
|
Li J, Lyu L, Wen H, Li Y, Wang X, Zhang Y, Yao Y, Qi X. Comparative transcriptomic analysis of gonadal development and renewal in the ovoviviparous black rockfish (Sebastes schlegelii). BMC Genomics 2021; 22:874. [PMID: 34863110 PMCID: PMC8642938 DOI: 10.1186/s12864-021-08169-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/10/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The black rockfish (Sebastes schlegelii) has an ovoviviparous reproductive pattern and long-term sperm storage, resulting in asynchronous gonadal development between the sexes. However, the comprehensive understanding of gonadal development in black rockfish has not yet been achieved. Here, we studied gonadal development and germ cell renewal using histology and RNA-seq. RESULTS In this study, RNA-seq was performed on testes and ovaries to characterize key pathways and genes that are active during development and gamete maturation in black rockfish. Differentially expressed genes (DEGs) were identified and annotated in 4 comparisons (F_III vs. F_IV, F_IV vs. F_V, M_III vs. M_IV and M_IV vs. M_V). Based on analysis of DEGs enriched in the testis, 11 and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were mapped to the M_III vs. M_IV group and the M_IV vs. M_V group, respectively. DEGs in ovarian development were also classified into 10 groups according to their biological functions. The expression patterns of the selected genes determined by qPCR were significantly correlated with the RNA-Seq results, supporting the reliability and accuracy of the RNA-Seq analysis. E2 levels showed down regulation from previtellogenesis to mature stage in female and T level showed down regulation from spermatogenesis to regressed stage in the male. CONCLUSIONS The categories "intercellular interaction and cytoskeleton", "molecule amplification" and "repair in the cell cycle" were revealed to be crucial in testis development and spermatogenesis, as was the biosynthesis of a series of metabolites. Our results provide comprehensive insight into black rockfish gonadal development and provide a basis for further study of reproductive physiology and molecular biology in ovoviviparity teleosts.
Collapse
Affiliation(s)
- Jianshuang Li
- College of Fishery, Ocean University of China, Qingdao, 266000, P. R. China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, P. R. China
| | - Likang Lyu
- College of Fishery, Ocean University of China, Qingdao, 266000, P. R. China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, P. R. China
| | - Haishen Wen
- College of Fishery, Ocean University of China, Qingdao, 266000, P. R. China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, P. R. China
| | - Yun Li
- College of Fishery, Ocean University of China, Qingdao, 266000, P. R. China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, P. R. China
| | - Xiaojie Wang
- College of Fishery, Ocean University of China, Qingdao, 266000, P. R. China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, P. R. China
| | - Ying Zhang
- College of Fishery, Ocean University of China, Qingdao, 266000, P. R. China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, P. R. China
| | - Yijia Yao
- College of Fishery, Ocean University of China, Qingdao, 266000, P. R. China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, P. R. China
| | - Xin Qi
- College of Fishery, Ocean University of China, Qingdao, 266000, P. R. China.
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, P. R. China.
| |
Collapse
|
17
|
Gou N, Ji H, Wu W, Zhong M, Zhang B. Transcriptional response to cold and fasting acclimation in Onychostoma macrolepis during the overwintering stage. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2021; 40:100901. [PMID: 34418784 DOI: 10.1016/j.cbd.2021.100901] [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: 02/04/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
In this study, we investigated the transcriptome responses of the liver of Onychostoma macrolepis in by RNA sequencing. The sampling process involved three groups: 1G (0 week, 10 °C), 2G (12 weeks, 0 °C) and 3G (24 weeks, 10 °C). The body weight, viscera index, hepatopancreas index and intraperitoneal fat index of O. macrolepis showed a decreasing trend with the prolonging of overwintering time. The crude fat contents of whole fish, muscle and liver in O. macrolepis after overwintering were significantly lower than those of the fish before overwintering (p < 0.05). In 1G versus 2G group, 2G versus 3G group and 1G versus 3G group, the differently expressed genes (DEGs) were 4630, 3976 and 2311, respectively. These results indicated that different stages of overwintering period had significant effects on gene expression of O. macrolepis, and the influence degree gradually decreased with the extension of overwintering period. The results of Gene ontology (GO) enrichment showed that these DEGs were mainly related to metabolism and immunity, and most of them were down-regulated. In this study, the KEGG pathway classification results showed that signal transduction was the most representative. In addition, KOG enrichment results showed that many DEGs associated with lipid transport and metabolism were down-regulated during the overwintering period. These observations suggested that slowing metabolism and delaying immunity may be the strategies for overwintering adaptation of O. macrolepis.
Collapse
Affiliation(s)
- Nina Gou
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Shaanxi Institute of Zoology, Xi'an 710032, China
| | - Hong Ji
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Wenyi Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Mingzhi Zhong
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Binxin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| |
Collapse
|
18
|
Transcriptome analysis provides the first insight into the molecular basis of temperature plasticity in Banggai cardinalfish, Pterapogon kauderni. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2021; 40:100909. [PMID: 34479169 DOI: 10.1016/j.cbd.2021.100909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/22/2021] [Accepted: 08/22/2021] [Indexed: 01/11/2023]
Abstract
Banggai cardinalfish, Pterapogon kauderni, is a tropical fish listed as an endangered species by IUCN. Its distribution and survival condition are extremely limited, and the changes of living environment caused by global warming may seriously threaten its geographical distribution. In order to understand the survival temperature range and the potential mechanism of temperature plasticity of P. kauderni, transcriptome analysis was performed under five temperature conditions (18 °C, 22 °C, 26 °C, 30 °C and 34 °C). A total of 432,444,497 clean reads were obtained from the mix tissues of whole head, viscera (except intestine), and muscle. All clean data were spliced into 194,832 unigenes. Compared with 26 °C, 57, 107, 187 and 174 differentially expressed genes (DEGs) were obtained at 18 °C, 22 °C, 30 °C and 34 °C, respectively. Gene Ontology (GO) analysis showed the most highly enriched in the DEGs were cellular processes, binding, metabolic processes and biological regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated circadian rhythm, protein processing in endoplasmic reticulum, influenza A and prion disease were significantly enriched. 47 genes that may be related to temperature stress were identified, such as Per1, MLP, IGFBP1, HSP70, HSP90α, HSPA4, DNAJB1, CALR. This is the first RNA-Seq study of P. kauderni. This information should be valuable for further targeted studies on temperature tolerance, thereby assisting the protection and development of P. kauderni.
Collapse
|
19
|
Zhang Z, Fu Y, Shen F, Zhang Z, Guo H, Zhang X. Barren environment damages cognitive abilities in fish: Behavioral and transcriptome mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 794:148805. [PMID: 34323774 DOI: 10.1016/j.scitotenv.2021.148805] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/12/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
The surrounding environments that animals inhabit shape their behavioral phenotypes, physiological status and molecular processes. As one of the driving forces for the adaptation and evolution of marine animals, environmental complexity has been shown to affect several behavioral characteristics in fish. However, little is known about the effects of environmental complexity on fish spatial cognition and about the relevant regulatory mechanisms. To address this theoretical gap, black rockfish Sebastes schlegelii, which is a typical rock fish species, were exposed to laboratory-based small-scale contrasting environments (i.e., spatially complex environment vs. spatially barren environment) for seven weeks. Subsequently, the spatial cognitive abilities and behavioral performance during captive period were determined, and transcriptome sequencing and analyses for fish telencephalon were conducted. In general, the fish from barren environment had significantly lower spatial learning and memory abilities compared with the fish from complex environment (i.e., the complex fish exited the maze faster). During the whole captive period, the frequency of aggressive behavior among barren fish was significantly higher than complex fish. And meanwhile, the group dispersion index of barren group was also significantly higher than complex group, which indicated that complex fish tended to distribute in a more homogeneous pattern than barren fish. Through transcriptomic analyses, a series of differentially expressed genes and pathways which may underpin the damaged effects of barren environment on fish spatial cognition were identified, and these genes mainly related to stress response, metabolism, organism systems and neural plasticity. However, no significant differences in growth performance, locomotor activity (indicated by swimming behavior and rotatory behavior) between treatments were detected. Based on these results, mechanisms in the levels of behavior and molecule were proposed to explain the environmental effects on fish cognition. This study may provide fundamental information for deeply understanding the environmental effects on marine animals.
Collapse
Affiliation(s)
- Zonghang Zhang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yiqiu Fu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Fengyuan Shen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Zhen Zhang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Haoyu Guo
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xiumei Zhang
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| |
Collapse
|
20
|
Zhao X, Sun Z, Xu H, Song N, Gao T. Transcriptome and co-expression network analyses reveal the regulatory pathways and key genes associated with temperature adaptability in the yellow drum (Nibea albiflora). J Therm Biol 2021; 100:103071. [PMID: 34503808 DOI: 10.1016/j.jtherbio.2021.103071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/14/2021] [Accepted: 08/03/2021] [Indexed: 12/27/2022]
Abstract
The yellow drum (Nibea albiflora) is an important marine economy fish, that is widely distributed in the coastal waters of the Northwest Pacific. To understand the molecular regulatory mechanism of the yellow drum under temperature stress, transcriptome analysis was performed under five temperature conditions (10 °C, 15 °C, 20 °C, 24 °C, 28 °C) in the present study. Compared with 20 °C, 163, 401, 276, and 372 differentially expressed genes (DEGs) were obtained at 10 °C, 15 °C, 24 °C and 28 °C, respectively. Gene Ontology (GO) analysis indicated that the DEGs were mainly involved in cellular processes, metabolic processes, catalytic activity, membrane and binding. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the temperature adaptive regulation of the yellow drum was mainly involved in signal transduction, metabolism, genetic information and protein processing. Weighted gene co-expression network analysis (WGCNA) showed that HMGB1, STAT4, Noct, C1q and CRT may be the key hub genes in the response of the yellow drum to temperature stress. In addition, 20 genes that may be associated with temperature stress were identified based on comparative analysis between the KEGG enrichment and the WGCNA results. Ten DEGs were selected for further validation using quantitative real-time PCR (qRT-PCR), and the results were consistent with the RNA-seq data. This study explored the transcriptional patterns of the yellow drum under temperature stress and provided fundamental information on the temperature adaptability of this species.
Collapse
Affiliation(s)
- Xiang Zhao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China
| | - Zhicheng Sun
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China
| | - Hao Xu
- Qingdao Marine Hazard Mitigation Service, Qingdao, Shandong, 266003, China
| | - Na Song
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China.
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China.
| |
Collapse
|
21
|
Xuan B, Park J, Choi S, You I, Nam BH, Noh ES, Kim EM, Song MY, Shin Y, Jeon JH, Kim EB. Draft Genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle. G3-GENES GENOMES GENETICS 2021; 11:6263857. [PMID: 33944944 PMCID: PMC8496316 DOI: 10.1093/g3journal/jkab147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022]
Abstract
Pond smelt (Hypomesus nipponensis) is a cold-freshwater fish species and a winter economic aquaculture resource in South Korea. Because of its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summers. Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5°C) vs. warm (HT, 23°C) conditions to identify heat stress–induced genes and gene categories. We observed a total of 1987 contigs with N50 of 0.46 Mbp, with the largest contig (3.03 Mbp) in the assembled genome. A total of 20,644 protein-coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology terms and 11,560 genes for KEGG Orthology. We conducted the lost and gained genes analysis compared with three species that: human, zebrafish, and salmon. In the lost genes analysis, we detected that smelt lost 4461 (22.16%), 2825 (10.62%), and 1499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed that smelt gained 1133 (5.49%), 1670 (8.09%), and 229 (1.11%) genes compared with the above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with a false discovery rate <0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that upregulated genes were significantly enriched for lipid biosynthetic process (GO:0008610, P < 0.001) and regulation of apoptotic process (GO:0042981, P < 0.01), and genes were downregulated by immune responses such as myeloid cell differentiation (GO:0030099, P < 0.001) in the liver under heat stress. In muscle tissue, upregulated genes were enriched for hypoxia (GO:0001666, P < 0.05), transcription regulator activity (GO:0140110, P < 0.001), and calcium-release channel activity (GO:0015278, P < 0.01), and genes were downregulated for a nicotinamide nucleotide biosynthetic process (GO:0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. The draft genome and transcriptomic of H. nipponensis will be a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of molecular mechanisms and heat responses and be useful for predicting survival of the smelt and its closely related species under global warming.
Collapse
Affiliation(s)
- Biao Xuan
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea.,Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| | - Jongbin Park
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea.,Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| | - Sukjung Choi
- Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| | - Inhwan You
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea.,Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea
| | - Eun Soo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea
| | - Eun Mi Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea
| | - Mi-Young Song
- Inland Fisheries Research Institute, National Institute of Fisheries Science, Gapyeong 12453, Korea
| | - Younhee Shin
- Research and Development Center, Insilicogen Inc, Yongin 16954, Republic of Korea
| | - Ji-Hyeon Jeon
- Research and Development Center, Insilicogen Inc, Yongin 16954, Republic of Korea.,Department of Biological Science, Sungkyunkwan University, Suwon 16419, Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea.,Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| |
Collapse
|
22
|
Nonnis S, Angiulli E, Maffioli E, Frabetti F, Negri A, Cioni C, Alleva E, Romeo V, Tedeschi G, Toni M. Acute environmental temperature variation affects brain protein expression, anxiety and explorative behaviour in adult zebrafish. Sci Rep 2021; 11:2521. [PMID: 33510219 PMCID: PMC7843641 DOI: 10.1038/s41598-021-81804-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 01/08/2021] [Indexed: 12/11/2022] Open
Abstract
This study investigated the effect of 4-d acute thermal treatments at 18 °C, 26 °C (control) and 34 °C on the nervous system of adult zebrafish (Danio rerio) using a multidisciplinary approach based on behavioural tests and brain proteomic analysis. The behavioural variations induced by thermal treatment were investigated using five different tests, the novel tank diving, light and dark preference, social preference, mirror biting, and Y-Maze tests, which are standard paradigms specifically tailored for zebrafish to assess their anxiety-like behaviour, boldness, social preference, aggressiveness, and explorative behaviour, respectively. Proteomic data revealed that several proteins involved in energy metabolism, messenger RNA translation, protein synthesis, folding and degradation, cytoskeleton organisation and synaptic vesiculation are regulated differently at extreme temperatures. The results showed that anxiety-like behaviours increase in zebrafish at 18 °C compared to those at 26 °C or 34 °C, whereas anxiety-related protein signalling pathways are downregulated. Moreover, treatments at both 18 °C and 34 °C affect the exploratory behaviour that appears not to be modulated by past experiences, suggesting the impairment of fish cognitive abilities. This study is the continuation of our previous work on the effect of 21-d chronic treatment at the same constant temperature level and will enable the comparison of acute and chronic treatment effects on the nervous system function in adult zebrafish.
Collapse
Affiliation(s)
- S Nonnis
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy.,CRC "Innovation for Well-Beeing and Environment" (I-WE), Università degli Studi di Milano, Milano, Italy
| | - E Angiulli
- Department of Biology and Biotechnology ''Charles Darwin", Sapienza University, Via Alfonso Borelli 50, 00161, Rome, Italy
| | - E Maffioli
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy. .,CIMAINA, Università degli Studi di Milano, Milano, Italy.
| | - F Frabetti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - A Negri
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy.,CIMAINA, Università degli Studi di Milano, Milano, Italy
| | - C Cioni
- Department of Biology and Biotechnology ''Charles Darwin", Sapienza University, Via Alfonso Borelli 50, 00161, Rome, Italy
| | - E Alleva
- Center for Behavioural Sciences and Mental Health, IstitutoSuperiore di Sanità, Rome, Italy
| | - V Romeo
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy
| | - G Tedeschi
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy.,CRC "Innovation for Well-Beeing and Environment" (I-WE), Università degli Studi di Milano, Milano, Italy.,CIMAINA, Università degli Studi di Milano, Milano, Italy
| | - M Toni
- Department of Biology and Biotechnology ''Charles Darwin", Sapienza University, Via Alfonso Borelli 50, 00161, Rome, Italy.
| |
Collapse
|
23
|
Li P, Liu Q, Li J, Wang F, Wen S, Li N. Transcriptomic responses to heat stress in gill and liver of endangered Brachymystax lenok tsinlingensis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100791. [PMID: 33465733 DOI: 10.1016/j.cbd.2021.100791] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/21/2022]
Abstract
Global warming significantly affects fish, particularly cold-water fish, because increased temperature adversely impacts their abilities to grow or reproduce, and eventually influences their fitness or even causes death. To survive, fish may alter their distribution or behavior to avoid the stress, and perhaps acclimate or evolve resistance to the elevated temperature. Brachymystax lenok tsinlingensis is an endangered cold-water species in China, and it has been found to alter the altitudinal distribution, decrease swimming efficiency and develop resistance under heat exposure, which badly impact the continuing conservation work. To better protect them, it is essential to understand how they respond to thermal stress behaviorally and physiologically. Therefore, the fish were exposed to 24.5 °C and based on the time taken for them to lose equilibrium, they were separately sampled as sensitive and tolerant groups. Both gill and liver tissues were collected from both groups for transcriptome sequencing. Sequencing results demonstrated that control and tolerant groups were similar in transcriptomic patterns and sensitive groups differentially expressed more genes than tolerant ones, suggesting the gene expression of tolerant groups may return to base levels as exposure time increased. Tissue differences were the major factor affecting gene expression, and they also displayed different physiological responses to heat stress. Consistent with other studies, heat shock response, immune response, metabolic adjustment and ion transport were found to be triggered after exposed to elevated temperature. The findings would contribute to a better understanding of responding mechanisms of fish to thermal stress and provide guidance for future conservation programs.
Collapse
Affiliation(s)
- Ping Li
- Center for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Qigen Liu
- Center for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Feng Wang
- Yellow River Fisheries Research Institute, Chinese Academy of Fishery Science, Xi'an 710086, China
| | - Sien Wen
- Yellow River Fisheries Research Institute, Chinese Academy of Fishery Science, Xi'an 710086, China
| | - Ning Li
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
24
|
Cao M, Zhang M, Yang N, Fu Q, Su B, Zhang X, Li Q, Yan X, Thongda W, Li C. Full length transcriptome profiling reveals novel immune-related genes in black rockfish (Sebastes schlegelii). FISH & SHELLFISH IMMUNOLOGY 2020; 106:1078-1086. [PMID: 32947030 DOI: 10.1016/j.fsi.2020.09.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Lacking full-length transcriptome for black rockfish (Sebastes schlegelii) limits novel gene discoveries and gene structures analysis. Therefore, we constructed the full-length transcriptome of black rockfish using Single-Molecule Real-Time Sequencing technology. Totally, we produced 21.73 Gb raw reads containing 298,904 circular consensus sequence (CCS) reads. Full-length (FL) and Non-full-length (NFL) isoforms were obtained based on the presence of 5' and 3' primers as well as poly (A) tails. The results showed 70.71% reads were identified as FL isoforms. Moreover, the average length of these PacBio isoforms is 2,632 bp, which is much longer than the length of the unigenes with the average length of 589 bp which generated from Illumina platform. Meanwhile, we identified 43,068 non-redundant transcripts, 12,485 alternative splicing (AS), 6,320 polyadenylation (APA) and 499 gene fusions as well as numerous long non-coding RNAs based on mapped FL isoforms. In addition, we identified 147 and 528 immune-related genes from novel genes and unmapped transcripts. The provided dataset can be utilized to discover novel genes and construct a comprehensive transcript dataset for black rockfish.
Collapse
Affiliation(s)
- Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xiaoyan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qi Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xu Yan
- College of Marine Science and Biological Engineering, Qingdao University of Science & Technology, Qingdao, 266011, China
| | - Wilawan Thongda
- Center of Excellence for Shrimp Molecular Biology and Biology (CENTEX Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
25
|
Hou ZS, Wen HS, Li JF, He F, Li Y, Qi X. Environmental hypoxia causes growth retardation, osteoclast differentiation and calcium dyshomeostasis in juvenile rainbow trout (Oncorhynchus mykiss). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135272. [PMID: 31841926 DOI: 10.1016/j.scitotenv.2019.135272] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/08/2019] [Accepted: 10/27/2019] [Indexed: 06/10/2023]
Abstract
Hypoxia generally refers to a dissolved oxygen (DO) level that is less than 2-3 mg/L. With ongoing global warming and environment pollution, environmental or geological studies showed hypoxia frequently occurs in global aquatic systems including ocean, river, estuaries and coasts. A preliminary study was performed to evaluate hypoxia tolerant of rainbow trout (Oncorhynchus mykiss) with parameters of mortality, behavior, endocrine and metabolite, identifying three DO levels including normoxia (Ctrl, 7.0 mg/L), non-lethal hypoxia (NH, 4.5 mg/L) and lethal hypoxia (LH, 3.0 mg/L). Furthermore, trout was treated by Ctrl, NH and LH for six hours to mimic the acute hypoxia in wild and/or farming conditions. A significantly higher mortality was observed in LH group. Trout of NH and LH showed stressful responses with unnormal swimming, increased serum cortisol and up-regulated gill hif1α transcription. Despite trout of NH and LH increased the oxygen delivery abilities by increasing the serum hemoglobin levels, the anerobic metabolism were inevitably observed with increased lactate. This study also showed a prolonged influence of NH and LH on growth after 30-days' recovery. Based on RNA-Seq data, different expression genes (DEGs) associated with stress, apoptosis, antioxidant, chaperone, growth, calcium and vitamin D metabolism were identified. Enrichment analysis showed DEGs were clustered in osteoclast differentiation, apoptosis and intracellular signaling transduction pathways. Results further showed NH and LH significantly decreased bone calcium content and disrupted the growth hormone-insulin-like growth factor (GH-IGF) axis. Our study might contribute to a better understanding of the effects of hypoxia on rainbow trout.
Collapse
Affiliation(s)
- Zhi-Shuai Hou
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, PR China
| | - Hai-Shen Wen
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, PR China.
| | - Ji-Fang Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, PR China
| | - Feng He
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, PR China
| | - Yun Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, PR China
| | - Xin Qi
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, PR China
| |
Collapse
|
26
|
Tian Y, Wen H, Qi X, Zhang X, Liu S, Li B, Sun Y, Li J, He F, Yang W, Li Y. Characterization of Full-Length Transcriptome Sequences and Splice Variants of Lateolabrax maculatus by Single-Molecule Long-Read Sequencing and Their Involvement in Salinity Regulation. Front Genet 2019; 10:1126. [PMID: 31803231 PMCID: PMC6873903 DOI: 10.3389/fgene.2019.01126] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022] Open
Abstract
Transcriptome complexity plays crucial roles in regulating the biological functions of eukaryotes. Except for functional genes, alternative splicing and fusion transcripts produce a vast expansion of transcriptome diversity. In this study, we applied PacBio single-molecule long-read sequencing technology to unveil the whole transcriptome landscape of Lateolabrax maculatus. We obtained 28,809 high-quality non-redundant transcripts, including 18,280 novel isoforms covering 8,961 annotated gene loci within the current reference genome and 3,172 novel isoforms. A total of 10,249 AS events were detected, and intron retention was the predominant AS event. In addition, 1,359 alternative polyadenylation events, 3,112 lncRNAs, 29,609 SSRs, 365 fusion transcripts, and 1,194 transcription factors were identified in this study. Furthermore, we performed RNA-Seq analysis combined with Iso-Seq results to investigate salinity regulation mechanism at the transcripts level. A total of 518 transcripts were differentially expressed, which were further divided into 8 functional groups. Notably, transcripts from the same genes exhibited similar or opposite expression patterns. Our study provides a comprehensive view of the transcriptome complexity in L. maculatus, which significantly improves current gene models. Moreover, the diversity of the expression patterns of transcripts may enhance the understanding of salinity regulatory mechanism in L. maculatus and other euryhaline teleosts.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Yun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| |
Collapse
|
27
|
Xu S, Zhao L, Xiao S, Gao T. Whole genome resequencing data for three rockfish species of Sebastes. Sci Data 2019; 6:97. [PMID: 31222011 PMCID: PMC6586840 DOI: 10.1038/s41597-019-0100-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/21/2019] [Indexed: 01/10/2023] Open
Abstract
Here we report Illumina-based whole genome sequencing of three rockfish species of Sebastes in northwest Pacific. The whole genomic DNA was used to prepare 350-bp pair-end libraries and the high-throughput sequencing yielded 128.5, 137.5, and 124.8 million mapped reads corresponding to 38.54, 41.26, and 37.43 Gb sequence data for S. schlegelii, S. koreanus, and S. nudus, respectively. The k-mer analyses revealed genome sizes were 846.4, 832.5, and 813.1 Mb and the sequencing coverages were 45×, 49×, and 46× for three rockfish, respectively. Comparative genomic analyses identified 46,624 genome-wide single nucleotide polymorphisms (SNPs). Phylogenetic analysis revealed closer relationships of the three species, compared to other six rockfish species. Demographic analysis identified contrasting changes between S. schlegelii and other two species, suggesting drastically different response to climate changes. The reported genome data in this study are valuable for further studies on comparative genomics and evolutionary biology of rockfish species. Design Type(s) | species comparison design • sequence analysis objective | Measurement Type(s) | whole genome sequencing assay | Technology Type(s) | DNA sequencing | Factor Type(s) | | Sample Characteristic(s) | Sebastes schlegelii • Sebastes koreanus • Sebastes nudus |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
Collapse
Affiliation(s)
- Shengyong Xu
- Fishery College, Zhejiang Ocean University, 1st Haidanan Road, Zhoushan, 316022, P.R. China
| | - Linlin Zhao
- The First Institute of Oceanography, Ministry of Natural Resources, 6th Xianxialing Road, Qingdao, 266061, P.R. China
| | - Shijun Xiao
- School of Computer Science and Technology, Wuhan University of Technology, 122th Luoshi Road, Wuhan, 430070, P.R. China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, 1st Haidanan Road, Zhoushan, 316022, P.R. China.
| |
Collapse
|
28
|
Zhang Z, Yu YX, Jiang Y, Wang YG, Liao MJ, Rong XJ, Wang K, Zhang H, Chen J. First report of isolation and complete genome of Vibrio rotiferianus strain SSVR1601 from cage-cultured black rockfish (Sebastes schlegelii) associated with skin ulcer. JOURNAL OF FISH DISEASES 2019; 42:623-630. [PMID: 30851004 DOI: 10.1111/jfd.12963] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Vibrio rotiferianus is an important marine pathogen of various aquatic organisms and can be found widely distributed in the marine environment. To further characterize this pathogen, the pathogenic properties and genome of V. rotiferianus SSVR1601 isolated from Sebastes schlegelii with skin ulcer were analysed. SSVR1601 was shown to be short rod-shaped cell with a single polar flagellum. Different degrees of pathological changes in fish kidney, intestine, gills and liver were observed after SSVR1601 challenge. The SSVR1601 genome consists of two chromosomes and two plasmids with a total of 5,717,113 bp, 42.04%-44.93% GC content, 5,269 predicted CDSs, 134 tRNAs and 40 rRNAs. The common virulence factors including OMPs, haemolysin, flagellin, DNase, entF, algU, tcpI, acfB and rfaD were found in strain SSVR1601. Furthermore, factors responsible for iron uptake (fur, fepC and ccmC) and types II, IV and VI secretion systems were detected, which are likely responsible for the pathogenicity of SSVR1601. The antimicrobial resistance genes, bacA, tet34 and norM, were detected based on Antibiotic Resistance Genes Database. The phylogenetic analysis revealed SSVR1601 to be most closely related to V. rotiferianus strains CAIM577 and B64D1.
Collapse
Affiliation(s)
- Zheng Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yong-Xiang Yu
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, China
| | - Yong Jiang
- National Oceanographic Center, Qingdao, China
| | - Yin-Geng Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Mei-Jie Liao
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao-Jun Rong
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Kai Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, China
| | - Hao Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, China
| | - Jing Chen
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, China
| |
Collapse
|