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Zou X, Liu Q, Guan Q, Zhao M, Zhu X, Pan Y, Liu L, Gao Z. Muscle Fiber Characteristics and Transcriptome Analysis in Slow- and Fast-Growing Megalobrama amblycephala. Genes (Basel) 2024; 15:179. [PMID: 38397169 PMCID: PMC10888202 DOI: 10.3390/genes15020179] [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: 12/25/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Growth is an important trait in aquaculture that is influenced by various factors, among which genetic regulation plays a crucial role. Megalobrama amblycephala, one of the most important freshwater species in China, exhibits wide variations in body mass among individuals of the same age within the same pool. But the molecular mechanisms underlying wide variation in body mass remain unclear. Here, we performed muscle histological and transcriptome analysis of muscle tissues from Fast-Growing (FG) and Slow-Growing (SG) M. amblycephala at the age of 4 months old (4 mo) and 10 months old (10 mo) to elucidate its muscle development and growth mechanism. The muscle histological analysis showed smaller diameter and higher total number of muscle fibers in FG compared to SG at 4 mo, while larger diameter and total number of muscle fibers were detected in FG at 10 mo. The transcriptome analysis of muscle tissue detected 1171 differentially expressed genes (DEGs) between FG and SG at 4 mo, and 718 DEGs between FG and SG at 10 mo. Furthermore, 44 DEGs were consistently up-regulated in FG at both 4 mo and 10 mo. Up-regulated DEGs in FG at 4 mo were mainly enriched in the pathways related to cell proliferation, while down-regulated DEGs were significantly enriched in cell fusion and muscle contraction. Up-regulated DEGs in FG at 10 mo were mainly enriched in the pathways related to cell proliferation and protein synthesis. Therefore, these results provide novel insights into the molecular mechanism of M. amblycephala muscle growth at different stages, and will be of great guiding significance to promote the fast growth of M. amblycephala.
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Affiliation(s)
- Xue Zou
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (X.Z.); (Q.L.); (Q.G.); (M.Z.); (Z.G.)
| | - Qi Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (X.Z.); (Q.L.); (Q.G.); (M.Z.); (Z.G.)
| | - Qianqian Guan
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (X.Z.); (Q.L.); (Q.G.); (M.Z.); (Z.G.)
| | - Ming Zhao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (X.Z.); (Q.L.); (Q.G.); (M.Z.); (Z.G.)
| | - Xin Zhu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha 410003, China; (X.Z.)
| | - Yaxiong Pan
- Department of Bioengineering and Environmental Science, Changsha University, Changsha 410003, China; (X.Z.)
| | - Lusha Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (X.Z.); (Q.L.); (Q.G.); (M.Z.); (Z.G.)
| | - Zexia Gao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (X.Z.); (Q.L.); (Q.G.); (M.Z.); (Z.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan 430070, China
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Huang L, Deng X, Yang X, Tang Z, Fan S, Zhou Z, Tao M, Liu S. Cloning, distribution, and effects of growth regulation of MC3R and MC4R in red crucian carp ( Carassius auratus red var.). Front Endocrinol (Lausanne) 2024; 14:1310000. [PMID: 38322156 PMCID: PMC10846643 DOI: 10.3389/fendo.2023.1310000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/27/2023] [Indexed: 02/08/2024] Open
Abstract
Background Melanocortin-3 and -4 receptors (MC3R and MC4R), G protein-coupled receptors, play vital roles in the regulation of energy homeostasis. To understand the functions of mc3r and mc4r in the energy homeostasis of red crucian carp (Carassius auratus red var., RCC), we cloned mc3r and mc4r, analyzed the tissue expression and localization of the genes, and investigated the effects of knockout of mc3r (mc3r +/-) and mc4r (mc4r +/-) in RCC. Results The full-length cDNAs of RCC mc3r and mc4r were 1459 base pairs (bp) and 1894 bp, respectively. qRT-PCR indicated that mc3r and mc4r were profusely expressed in the brain, but lower expressed in the periphery tissues. ISH revealed that mc3r and mc4r were located in NPP, NPO, NAPv, NSC, NAT, NRL, NLTl, and NLTp of the brain, suggesting that mc3r and mc4r might regulate many physiological and behavioral aspects in RCC. To further verify the roles of mc3r and mc4r in energy homeostasis, the mc3r+/- and mc4r+/- fish were obtained by the CRISPR/Cas9 system. The average body weights, total lengths, body depths, and food intake of mc4r+/- fish were significantly higher than those of mc3r+/- and the normal wild-type (WT) fish, but there was no difference between the mc3r+/- and WT fish, indicating that the RCC phenotype and food intake were mainly influenced by mc4r but not mc3r. Interestingly, mc4r+/- fish displayed more visceral fat mass than mc3r+/- and WT fish, and mc3r+/- fish also exhibited slightly more visceral fat mass compared to WT. RNA-seq of the liver and muscle revealed that a large number of differentially expressed genes (DEGs) differed in WT vs. mc3r+/-, WT vs. mc4r+/-, and mc3r+/- vs. mc4r+/-, mainly related to lipid, glucose, and energy metabolism. The KEGG enrichment analysis revealed that DEGs were mainly enriched in pathways such as steroid biosynthesis, fatty acid metabolism, fatty acid biosynthesis, glycolysis/gluconeogenesis, wnt signaling pathway, PPAR signaling pathway, and MAPK signaling pathway, thereby affecting lipid accumulation and growth. Conclusion In conclusion, these results will assist in the further investigation of the molecular mechanisms in which MC3R and MC4R were involved in the regulation of energy homeostasis in fish.
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Affiliation(s)
| | | | | | | | | | | | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
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Wu X, Lai J, Chen Y, Liu Y, Song M, Li F, Li P, Li Q, Gong Q. Combination of metabolome and proteome analyses provides insights into the mechanism underlying growth differences in Acipenser dabryanus. iScience 2023; 26:107413. [PMID: 37559901 PMCID: PMC10407750 DOI: 10.1016/j.isci.2023.107413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/26/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023] Open
Abstract
To analyze the differences between different-sized Acipenser dabryanus, we randomly selected 600 3-month-old A. dabryanus juveniles. Four months later, the blood and white muscle of these fish were analyzed. The results showed no significant difference in the length-weight relationship (LWR) b value between the large and small A. dabryanus. The levels of serum growth hormone (gh) and insulin-like growth factor 1 (igf1) in the large A. dabryanus were significantly lower than those in the small, whereas the activity levels of Total superoxide dismutase (T-sod) and catalase (cat) were opposite to the results of gh and igf1. A total of 212 and 245 metabolites showed significant changes in the positive and negative polarity mode, respectively. Among 3,308 proteins identified, 69 proteins showed upregulated expression, and 185 proteins showed downregulated expression. These results indicated that the growth advantage of A. dabryanus was closely related to glycolysis, protein synthesis, and antioxidant function.
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Affiliation(s)
- Xiaoyun Wu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Jiansheng Lai
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Yeyu Chen
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Ya Liu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Mingjiang Song
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Feiyang Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Pengcheng Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Qingzhi Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Quan Gong
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
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Jiang G, Li Y, Cheng G, Jiang K, Zhou J, Xu C, Kong L, Yu H, Liu S, Li Q. Transcriptome Analysis of Reciprocal Hybrids Between Crassostrea gigas and C. angulata Reveals the Potential Mechanisms Underlying Thermo-Resistant Heterosis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:235-246. [PMID: 36653591 DOI: 10.1007/s10126-023-10197-5] [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: 11/10/2022] [Accepted: 01/11/2023] [Indexed: 05/06/2023]
Abstract
Heterosis, also known as hybrid vigor, is widely used in aquaculture, but the molecular causes for this phenomenon remain obscure. Here, we conducted a transcriptome analysis to unveil the gene expression patterns and molecular bases underlying thermo-resistant heterosis in Crassostrea gigas ♀ × Crassostrea angulata ♂ (GA) and C. angulata ♀ × C. gigas ♂ (AG). About 505 million clean reads were obtained, and 38,210 genes were identified, of which 3779 genes were differentially expressed between the reciprocal hybrids and purebreds. The global gene expression levels were toward the C. gigas genome in the reciprocal hybrids. In GA and AG, 95.69% and 92.00% of the differentially expressed genes (DEGs) exhibited a non-additive expression pattern, respectively. We observed all gene expression modes, including additive, partial dominance, high and low dominance, and under- and over-dominance. Of these, 77.52% and 50.00% of the DEGs exhibited under- or over-dominance in GA and AG, respectively. The over-dominance DEGs common to reciprocal hybrids were significantly enriched in protein folding, protein refolding, and intrinsic apoptotic signaling pathway, while the under-dominance DEGs were significantly enriched in cell cycle. As possible candidate genes for thermo-resistant heterosis, GRP78, major egg antigen, BAG, Hsp70, and Hsp27 were over-dominantly expressed, while MCM6 and ANAPC4 were under-dominantly expressed. This study extends our understanding of the thermo-resistant heterosis in oysters.
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Affiliation(s)
- Gaowei Jiang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yin Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Geng Cheng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Kunyin Jiang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Jianmin Zhou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Mwaura JG, Wekesa C, Ogutu PA, Okoth P. Whole Transcriptome Analysis of Differentially Expressed Genes in Cultured Nile Tilapia (O. niloticus) Subjected to Chronic Stress Reveals Signaling Pathways Associated with Depressed Growth. Genes (Basel) 2023; 14:genes14040795. [PMID: 37107553 PMCID: PMC10137778 DOI: 10.3390/genes14040795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/11/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Chronic stress is a serious threat to aquaculture as it lowers fish growth performance and compromises fish welfare. The exact mechanism by which growth is retarded is, however, not clearly understood. This study sought to elucidate the gene expression profiles associated with chronic stress in cultured Nile tilapia (Oreochromis niloticus) reared for 70 days at different ammonia concentrations and stocking densities. Fish in the treatment groups showed negative growth, while the controls showed positive allometric growth. The specific condition factor (Kn) ranged from 1.17 for the controls to 0.93 for the ammonia and 0.91 for the stocking density treatments. RNA was extracted from muscle tissue using TRIzol followed by library construction and Illumina sequencing. Comparative transcriptome analysis revealed 209 differentially expressed genes (DEGs) (156 up- and 53 down-regulated) in the ammonia and 252 DEGs (175 up- and 77 down-regulated) in the stocking density treatment. In both treatments, 24 and 17 common DEGs were up- and down-regulated, respectively. DEGs were significantly enriched in six pathways associated with muscle activity, energy mobilization and immunity. The heightened muscular activity consumes energy which would otherwise have been utilized for growth. These results bring to fore the molecular mechanisms underlying chronic stress’ suppression of growth in cultured Nile tilapia.
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Effects of Five Prebiotics on Growth, Antioxidant Capacity, Non-Specific Immunity, Stress Resistance, and Disease Resistance of Juvenile Hybrid Grouper ( Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂). Animals (Basel) 2023; 13:ani13040754. [PMID: 36830542 PMCID: PMC9952795 DOI: 10.3390/ani13040754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
To explore the short-term health benefits of five prebiotics on hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂), six experimental groups fed with different diets (basal diet, diet control (CON); basal diet + 0.2% fructooligosaccharide (FOS), diet FOS; basal diet + 0.5% chitosan, diet chitosan (CTS); basal diet + 0.2% mannan-oligosaccharide (MOS), diet MOS; basal diet + 0.1% β-glucan (GLU), Diet GLU; basal diet + 0.05% xylooligosaccharide (XOS), diet XOS) were set up, and a 4-week feeding trial was conducted. MOS and XOS significantly improved the growth of hybrid grouper compared to the CON group (p < 0.05). Antioxidant enzyme assay showed that the activity of glutathione peroxidase (GPx) was significantly enhanced in the MOS group, and the content of malondialdehyde (MDA) in the XOS group was significantly lower than in the CON group (p < 0.05). The catalase (CAT) activities were significantly enhanced in all prebiotic-supplemented groups compared with the CON group (p < 0.05). Non-specific immunity assay showed that the activities of alkaline phosphatase (AKP) and lysozyme (LZM) were significantly increased in all prebiotic-supplemented groups compared with the CON group (p < 0.05). The total protein content in the XOS group was significantly increased (p < 0.05), and the albumin (ALB) activity in the MOS group was more significantly increased than that in the CON group. Histological examination of the intestine revealed that muscle thickness was significantly increased in all prebiotic-supplemented groups compared to the CON group (p < 0.05). Villi length, villi width, muscle thickness all increased significantly in the MOS group (p < 0.05). In addition, the crowding stress and ammonia nitrogen stress experiments revealed that the survival rates of the MOS and XOS groups after stresses were significantly higher than those of the CON group (p < 0.05). Though MOS and XOS exhibited similar anti-stress effects, the antioxidant and non-specific immunity parameters they regulated were not the same, indicating that the specific mechanisms of MOS and XOS's anti-stress effects were probably different. After being challenged with Vibrio harvey, MOS and GLU groups showed significantly higher post-challenge survival rates than the CON group (p < 0.05). These findings indicated that among the five prebiotics, MOS and XOS showed the best overall short-term beneficial effects and could be considered promising short-term feed additives to improve the stress resistance of juvenile hybrid grouper.
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Kanakachari M, Ashwini R, Chatterjee RN, Bhattacharya TK. Embryonic transcriptome unravels mechanisms and pathways underlying embryonic development with respect to muscle growth, egg production, and plumage formation in native and broiler chickens. Front Genet 2022; 13:990849. [PMID: 36313432 PMCID: PMC9616467 DOI: 10.3389/fgene.2022.990849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Muscle development, egg production, and plumage colors are different between native and broiler chickens. The study was designed to investigate why improved Aseel (PD4) is colorful, stronger, and grew slowly compared with the control broiler (CB). Methods: A microarray was conducted using the 7th-day embryo (7EB) and 18th-day thigh muscle (18TM) of improved Aseel and broiler, respectively. Also, we have selected 24 Gallus gallus candidate reference genes from NCBI, and total RNA was isolated from the broiler, improved Aseel embryo tissues, and their expression profiles were studied by real-time quantitative PCR (qPCR). Furthermore, microarray data were validated with qPCR using improved Aseel and broiler embryo tissues. Results: In the differential transcripts screening, all the transcripts obtained by microarray of slow and fast growth groups were screened by fold change ≥ 1 and false discovery rate (FDR) ≤ 0.05. In total, 8,069 transcripts were differentially expressed between the 7EB and 18TM of PD4 compared to the CB. A further analysis showed that a high number of transcripts are differentially regulated in the 7EB of PD4 (6,896) and fewer transcripts are differentially regulated (1,173) in the 18TM of PD4 compared to the CB. On the 7th- and 18th-day PD4 embryos, 3,890, 3,006, 745, and 428 transcripts were up- and downregulated, respectively. The commonly up- and downregulated transcripts are 91 and 44 between the 7th- and 18th-day of embryos. In addition, the best housekeeping gene was identified. Furthermore, we validated the differentially expressed genes (DEGs) related to muscle growth, myostatin signaling and development, and fatty acid metabolism genes in PD4 and CB embryo tissues by qPCR, and the results correlated with microarray expression data. Conclusion: Our study identified DEGs that regulate the myostatin signaling and differentiation pathway; glycolysis and gluconeogenesis; fatty acid metabolism; Jak-STAT, mTOR, and TGF-β signaling pathways; tryptophan metabolism; and PI3K-Akt signaling pathways in PD4. The results revealed that the gene expression architecture is present in the improved Aseel exhibiting embryo growth that will help improve muscle development, differentiation, egg production, protein synthesis, and plumage formation in PD4 native chickens. Our findings may be used as a model for improving the growth in Aseel as well as optimizing the growth in the broiler.
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Affiliation(s)
- M. Kanakachari
- ICAR-Directorate of Poultry Research, Hyderabad, India
- EVA.4 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - R. Ashwini
- ICAR-Directorate of Poultry Research, Hyderabad, India
| | | | - T. K. Bhattacharya
- ICAR-Directorate of Poultry Research, Hyderabad, India
- *Correspondence: T. K. Bhattacharya,
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Xiao W, Chen B, Wang J, Zou Z, Wang C, Li D, Zhu J, Yu J, Yang H. Integration of mRNA and miRNA Profiling Reveals Heterosis in Oreochromis niloticus × O. aureus Hybrid Tilapia. Animals (Basel) 2022; 12:640. [PMID: 35268207 PMCID: PMC8909811 DOI: 10.3390/ani12050640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 02/08/2023] Open
Abstract
Heterosis is a widespread biological phenomenon in fishes, in which hybrids have superior traits to parents. However, the underlying molecular basis for heterosis remains uncertain. Heterosis in growth and survival rates is apparent in hybrid tilapia (Oreochromis niloticus ♀ × O. aureus ♂). Comparisons of growth and hematological biochemical characteristics and mRNA and miRNA transcriptional analyses were performed in hybrid and parents tilapia stocks to investigate the underlying molecular basis for heterosis. Growth characteristics and hematological glucose and cholesterol parameters were significantly improved in hybrids. Of 3097 differentially expressed genes (DEGs) and 120 differentially expressed miRNAs (DEMs) identified among three stocks (O. niloticus, O. aureus, and hybrids), 1598 DEGs and 62 DEMs were non-additively expressed in hybrids. Both expression level dominance and overdominance patterns occurred for DEGs and DEMs, indicating that dominance and overdominance models are widespread in the transcriptional and post-transcriptional regulation of genes involved in growth, metabolism, immunity, and antioxidant capacity in hybrid tilapia. Moreover, potential negative regulation networks between DEMs and predicted target DEGs revealed that most DEGs from miRNA-mRNA pairs are up-regulated. Dominance and overdominance models in levels of transcriptome and miRNAome facilitate the integration of advantageous parental alleles into hybrids, contributing to heterosis of growth and improved survival. The present study provides new insights into molecular heterosis in hybrid tilapia, advancing our understanding of the complex mechanisms involved in this phenomenon in aquatic animals.
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Affiliation(s)
- Wei Xiao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; (W.X.); (J.W.)
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
| | - Binglin Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
| | - Jun Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; (W.X.); (J.W.)
| | - Zhiying Zou
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
| | - Chenghui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; (W.X.); (J.W.)
| | - Dayu Li
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
| | - Jinglin Zhu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
| | - Jie Yu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
| | - Hong Yang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
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Transcriptome Profiling Revealed Basis for Growth Heterosis in Hybrid Tilapia (Oreochromis niloticus ♀ × O. aureus ♂). FISHES 2022. [DOI: 10.3390/fishes7010043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Hybrid tilapia were produced from hybridization of Nile tilapia (Oreochromis niloticus) and blue tilapia (O. aureus). Comparative transcriptome analysis was carried out on the liver of hybrid tilapia and their parents by RNA sequencing. A total of 2319 differentially expressed genes (DEGs) were identified. Trend co-expression analysis showed that non-additive gene expression accounted for 67.1% of all DEGs. Gene Ontology and KEGG enrichment analyses classified the respective DEGs. Gene functional enrichment analysis indicated that most up-regulated genes, such as FASN, ACSL1, ACSL3, ACSL6, ACACA, ELOVL6, G6PD, ENO1, GATM, and ME3, were involved in metabolism, including fatty acid biosynthesis, unsaturated fatty acid biosynthesis, glycolysis, pentose phosphate pathway, amino acid metabolism, pyruvate metabolism, and the tricarboxylic acid cycle. The expression levels of a gene related to ribosomal biosynthesis in eukaryotes, GSH-Px, and those associated with heat shock proteins (HSPs), such as HSPA5 and HSP70, were significantly down-regulated compared with the parent tilapia lineages. The results revealed that the metabolic pathway in hybrid tilapia was up-regulated, with significantly improved fatty acid metabolism and carbon metabolism, whereas ribosome biosynthesis in eukaryotes and basal defense response were significantly down-regulated. These findings provide new insights into our understanding of growth heterosis in hybrid tilapia.
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Diversity of MHC IIB genes and parasitism in hybrids of evolutionarily divergent cyprinoid species indicate heterosis advantage. Sci Rep 2021; 11:16860. [PMID: 34413384 PMCID: PMC8376869 DOI: 10.1038/s41598-021-96205-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/02/2021] [Indexed: 02/07/2023] Open
Abstract
The genes of the major histocompatibility complex (MHC) are an essential component of the vertebrate immune system and MHC genotypes may determine individual susceptibility to parasite infection. In the wild, selection that favors MHC variability can create situations in which interspecies hybrids experience a survival advantage. In a wild system of two naturally hybridizing leuciscid fish, we assessed MHC IIB genetic variability and its potential relationships to hosts' ectoparasite communities. High proportions of MHC alleles and parasites were species-specific. Strong positive selection at specific MHC codons was detected in both species and hybrids. MHC allele expression in hybrids was slightly biased towards the maternal species. Controlling for a strong seasonal effect on parasite communities, we found no clear associations between host-specific parasites and MHC alleles or MHC supertypes. Hybrids shared more MHC alleles with the more MHC-diverse parental species, but expressed intermediate numbers of MHC alleles and positively selected sites. Hybrids carried significantly fewer ectoparasites than either parent species, suggesting a hybrid advantage via potential heterosis.
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Zhao J, He Z, Chen X, Huang Y, Xie J, Qin X, Ni Z, Sun C. Growth trait gene analysis of kuruma shrimp (Marsupenaeus japonicus) by transcriptome study. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100874. [PMID: 34243027 DOI: 10.1016/j.cbd.2021.100874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/16/2021] [Accepted: 06/28/2021] [Indexed: 10/21/2022]
Abstract
Growth traits are a vital standard for the animal culture industry. The molecular mechanism of growth traits remains poorly understood, especially in aquaculture, which hinders the development of the selective breeding industry. Genomic resources discovered by next-generation sequencing (NGS) have been widely applied in certain species. However, accurate assembly and downstream analysis by NGS are still major challenges for species without reference genomes. In this study, a comparative transcriptome analysis of an economic crustacean species (Marsupenaeus japonicus) between a fast growth group and slow growth group at different stages was performed by SMRT (single molecule real time) and NGS. A high-quality full-length transcriptome (e.g., mean length of unigenes was longer than those unigenes assembled by Illumina clean reads from previous reports, and annotation rate was higher than Illumina sequencing in the same studies) was generated and analyzed. Several differentially expressed genes (DEGs) related to growth were identified and validated by quantitative real-time PCR (qPCR). The results showed that compared with the late stage, more DEGs were identified at the early stage, indicating that the growth-related physiological activity differences between different individuals at the early stage were higher than at the late stage. Moreover, 215 DEGs were shared between the early stage and late stage, and 109 had divergent functions during development. These 109 genes may play an important role in regulating the specific growth rate (SGR) of kuruma shrimp. In addition, twelve growth-related pathways were shared between the two comparative groups. Among these pathways, the fly Hippo signaling pathway and its key gene Mj14-3-3-like were identified for the first time to be involved in growth traits in crustaceans. Further analysis showed that Mj14-3-3-like was significantly downregulated in the fast growth group at the early stage and late stage; its expression level was reduced to its lowest level at the intermolt stage (C), the most important growth stage in shrimp, suggesting that Mj14-3-3-like may inhibit the growth of kuruma shrimp. Our study helps to elucidate the genes involved in the molecular mechanisms governing growth traits in kuruma shrimp, which is valuable for future shrimp developmental research.
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Affiliation(s)
- Jichen Zhao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China
| | - Zihao He
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China
| | - Xieyan Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China
| | - Yiyi Huang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China
| | - Jingjing Xie
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China
| | - Xuan Qin
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China
| | - Zuotao Ni
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China.
| | - Chengbo Sun
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China; Guangdong Provincial Laboratory of Southern Marine Science and Engineering, Zhanjiang, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, PR China.
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Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper ( Epinephelus tukula). BIOLOGY 2021; 10:biology10010036. [PMID: 33430356 PMCID: PMC7825770 DOI: 10.3390/biology10010036] [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: 12/15/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022]
Abstract
Simple Summary The potato grouper is a novel aquaculture species in Taiwan. Due to the lack of genetic information concerning this species, we have developed molecular markers based on transcriptome sequencing and further characterized their association with gene diversity and growth traits of this species. Ultimately, these markers could be utilized as accurate and efficient tools for genetic management and marker-assisted selection of potato grouper with distinct growth traits. Abstract The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.
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Chen Y, Liu W, Ma J, Wang Y, Huang H. Comprehensive physiological and transcriptomic analysis revealing the responses of hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) to the replacement of fish meal with soy protein concentrate. FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:2037-2053. [PMID: 32767005 DOI: 10.1007/s10695-020-00851-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
Plant proteins are suitable and alternative to fish meals (FMs), with less cost compared with that of all other types of fish feeds. In recent years, soy protein concentrate (SPC) has emerged as a cost-effective alternative to FM; however, little is known regarding the effects of dietary SPC on general fish physiology and well-being. This study aimed to perform comprehensive physiological and transcriptomic analysis for testing the applicability of SPC as fish feeds in hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) [SPC replaced 0% (CK), 30% (SPC30), and 75% (SPC75) of FM protein]. Generally, SPC30 promoted fish survival and had less effects on the phenotype, while SPC75 reduced fish survival, promoted inflammation, and regulated multiple physiological responses. Thousands of differentially expressed genes (DEGs) by SPC were identified in the intestine, liver, and muscle, which were enriched in biological regulation, cellular process, metabolic process, single-organism process, cell, cell part, membrane, binding, and catalytic activity based on RNA-seq. Notably, some DEGs involved in amino acid and lipid metabolism in the digestive system highlighted the modulatory effect of SPC on these metabolic processes, consistent with the physiological responses including enzyme activities. The enriched aspects of these predominant DEGs might be directly related to the different effects of SPC30 and SPC75 on fish growth, digestibility, and underlying enzyme activities and histology. In conclusion, the comprehensive physiological and transcriptomic comparative analysis of CK, SPC30, and SPC75 was also effective in testing the applicability of SPC as fish feeds and in designing a proper diet with the best impact on the growth performance and health of fish in hybrid grouper.
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Affiliation(s)
- Yan Chen
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, Hainan province, People's Republic of China
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, Hainan Province, People's Republic of China
| | - Wenkan Liu
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, Hainan province, People's Republic of China
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, Hainan Province, People's Republic of China
| | - Jun Ma
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, Hainan province, People's Republic of China.
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, Hainan Province, People's Republic of China.
| | - Yaorong Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, Guangdong Province, People's Republic of China
| | - Hai Huang
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, Hainan province, People's Republic of China
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, Hainan Province, People's Republic of China
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Zhang J, Shen Y, Xu X, Dai Y, Li J. Transcriptome Analysis of the Liver and Muscle Tissues of Black Carp (Mylopharyngodon piceus) of Different Growth Rates. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:706-716. [PMID: 32914204 DOI: 10.1007/s10126-020-09994-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
In this study, we used RNA-seq to analyze the muscle and liver tissues of black carps (Mylopharyngodon piceus) of different growth rates from the same batch to evaluate their growth traits. We have two groups; they are the black carp group with fast-growth rate and the slow-growth rate. A total of 23,132 genes were enriched in the Gene Ontology analysis, and 285 related pathways were found in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The KEGG pathway analysis showed significant differences in the expression of some genes involved in growth- and development-related metabolic pathways such as the FoxO signaling pathway, p53 signaling pathway, PI3K-Akt signaling pathway, apoptosis, TGF-β signaling pathway, and insulin signaling pathway. The numbers of differentially expressed genes in muscle and liver are 1913 and 1775. Nine of the differently expressed genes involved in the different growth traits and accuracy of the transcriptome data were validated using quantitative real-time PCR. We found that the expression levels of some growth-related genes were significantly higher in the fast-growth rate black carps than in the slow-growth rate black carps. The large number of transcriptome sequences obtained in this study has enriched the black carp gene resources, and the obtained differentially expressed genes and related pathway analysis provide valuable information for understanding the growth traits of the black carp.
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Affiliation(s)
- Jiahua Zhang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rual Affairs, Shanghai Ocean University, Shanghai, China
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rual Affairs, Shanghai Ocean University, Shanghai, China.
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
- College of Aquaculture and Life science, Shanghai Ocean University, Shanghai, 201306, China.
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rual Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yafan Dai
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rual Affairs, Shanghai Ocean University, Shanghai, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rual Affairs, Shanghai Ocean University, Shanghai, China.
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
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Distant hybrids of Heliocidaris crassispina (♀) and Strongylocentrotus intermedius (♂): identification and mtDNA heteroplasmy analysis. BMC Evol Biol 2020; 20:101. [PMID: 32781979 PMCID: PMC7422570 DOI: 10.1186/s12862-020-01667-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/30/2020] [Indexed: 11/27/2022] Open
Abstract
Background Distant hybridization between the sea urchin Heliocidaris crassispina (♀) and the sea urchin Strongylocentrotus intermedius (♂) was successfully performed under laboratory conditions. A new variety of hybrid sea urchin (HS hybrid) was obtained. However, the early-development success rates for the HS hybrids were significantly lower than those of purebred H. crassispina or S. intermedius offspring. In addition, it was difficult to distinguish the HS-hybrid adults from the pure H. crassispina adults, which might lead to confusion in subsequent breeding attempts. In this study, we attempted to develop a method to quickly and effectively identify HS hybrids, and to preliminarily investigate the molecular mechanisms underlying the poor early-development success rates in the HS hybrids. Results The hybrid sea urchins (HS hybrids) were identified both morphologically and molecularly. There were no significant differences in the test height to test diameter ratios between the HS hybrids and the parents. The number and arrangement of ambulacral pore pairs in the HS hybrids differed from those of the parental lines, which might serve as a useful morphological character for the identification of the HS hybrids. A primer pair that identified the HS hybrids was screened by comparing the mitochondrial genomes of the parental lines. Moreover, paternal leakage induced mitochondrial DNA heteroplasmy in the HS hybrids, which might explain the low rates of early development success in these hybrids. Conclusions The distant-hybrid sea urchins were accurately identified using comparative morphological and molecular genetic methods. The first evidence of mtDNA heteroplasmy after the distant hybridization of an echinoderm was also provided.
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Prevalence of Infectious Spleen and Kidney Necrosis Virus (ISKNV), Nervous Necrosis Virus (NNV) and Ectoparasites in Juvenile Epinephelus spp. Farmed in Aceh, Indonesia. Pathogens 2020; 9:pathogens9070578. [PMID: 32708765 PMCID: PMC7400217 DOI: 10.3390/pathogens9070578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 11/26/2022] Open
Abstract
A cross-sectional survey was used to estimate the prevalence of infections with the Infectious spleen and kidney necrosis virus (ISKNV, Megalocytivirus), nervous necrosis virus (NNV, Betanodavirus), and infestations with ectoparasites during the rainy season in juvenile grouper (Epinephelus spp.) farmed in Aceh, Indonesia. The survey was intended to detect aquatic pathogens present at 10% prevalence with 95% confidence, assuming 100% sensitivity and specificity using a sample size of 30 for each diagnostic test. Eight populations of grouper from seven farms were sampled. Additional targeted sampling was conducted for populations experiencing high mortality. Infection with NNV was detected at all farms with seven of the eight populations being positive. The apparent prevalence for NNV ranged from 0% (95% CI: 0–12) to 73% (95% CI: 54–88). All of the fish tested from the targeted samples (Populations 9 and 10) were positive for NNV and all had vacuolation of the brain and retina consistent with viral nervous necrosis (VNN). Coinfections with ISKNV were detected in five populations, with the highest apparent prevalence being 13% (95% CI: 4–31%). Trichodina sp., Cryptocaryonirritans and Gyrodactylus sp. were detected at three farms, with 66% to 100% of fish being infested. Hybrid grouper sourced from a hatchery were 5.4 and 24.9 times more likely to have a NNV infection and a higher parasite load compared to orange-spotted grouper collected from the wild (p < 0.001). This study found that VNN remains a high-impact disease in grouper nurseries in Aceh, Indonesia.
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Lu X, Chen HM, Qian XQ, Gui JF. Transcriptome analysis of grass carp (Ctenopharyngodon idella) between fast- and slow-growing fish. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100688. [PMID: 32454298 DOI: 10.1016/j.cbd.2020.100688] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/11/2020] [Accepted: 04/30/2020] [Indexed: 12/15/2022]
Abstract
Grass carp is one of the most important freshwater aquaculture species in China. However, the mechanisms underlying the growth of muscle tissue in the fish are unclear. High-throughput RNA-Seq was used to analyze the transcriptome of grass carp muscle tissue between fast- and slow-growing fish family groups. Twenty-four individuals each from 4 fast-growing families and 4 slow-growing families were used to reduce background noise. 71 up-regulated and 35 down-regulated genes were identified in the differentially expressed genes (DEGs). GO and KEGG enrichment analyses revealed the DEGs were involved in the GH/IGF axis, calcium metabolism, protein and glycogen synthesis, oxygen transport, cytoskeletal and myofibrillar components. IGFBP1 was up-regulated in big fish while GHR2 was down-regulated. Glutamic pyruvate transaminase 2, an indicator of liver tissue damage, was down-regulated in big grass carp, which indicates that the fish was better adapted to an artificially formulated diet. GAPDH, the rate-limiting enzyme in glycolytic flux was highly expressed in fast-growing grass carp, reflecting enhanced carbohydrate metabolism. Higher expression of ALAS2 and myoglobin 1 in big grass carp, related to oxygen transport might promote aerobic exercise along with food intake and muscle growth. Genes for cytoskeletal and myofibrillar components such as tropomyosin, meromyosin, and troponin I were also up-regulated in big grass carp. These results provide valuable information about the key genes for use as biomarkers of growth in selective breeding programs for grass carp and contribute to our understanding of the molecular mechanisms and regulative pathways regulating growth in fish.
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Affiliation(s)
- Xue Lu
- Key Laboratory of Utilization for Microbiological Resources in Breeding Industries, Ministry of Agriculture and Rural Affairs, Haid Central Research Institute, Animal Husbandry and Fisheries Research Center of Guangdong Haid Group Co., Ltd., Guangzhou 511400, China
| | - Hui-Min Chen
- Key Laboratory of Utilization for Microbiological Resources in Breeding Industries, Ministry of Agriculture and Rural Affairs, Haid Central Research Institute, Animal Husbandry and Fisheries Research Center of Guangdong Haid Group Co., Ltd., Guangzhou 511400, China
| | - Xue-Qiao Qian
- Key Laboratory of Utilization for Microbiological Resources in Breeding Industries, Ministry of Agriculture and Rural Affairs, Haid Central Research Institute, Animal Husbandry and Fisheries Research Center of Guangdong Haid Group Co., Ltd., Guangzhou 511400, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
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Wang D, Chen X, Zhang X, Li J, Yi Y, Bian C, Shi Q, Lin H, Li S, Zhang Y, You X. Whole Genome Sequencing of the Giant Grouper ( Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes. Mar Drugs 2019; 17:md17090503. [PMID: 31466296 PMCID: PMC6780625 DOI: 10.3390/md17090503] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/20/2019] [Accepted: 08/26/2019] [Indexed: 12/25/2022] Open
Abstract
Giant groupers, the largest grouper type in the world, are of economic importance in marine aquaculture for their rapid growth. At the same time, bacterial and viral diseases have become the main threats to the grouper industry. Here, we report a high-quality genome of a giant grouper sequenced by an Illumina HiSeq X-Ten and PacBio Bioscience Sequel platform. A total of 254 putative antimicrobial peptide (AMP) genes were identified, which can be divided into 34 classes according to the annotation of the Antimicrobial Peptides Database (APD3). Their locations in pseudochromosomes were also determined. Thrombin-, lectin-, and scolopendin-derived putative AMPs were the three largest parts. In addition, expressions of putative AMPs were measured by our transcriptome data. Two putative AMP genes (gapdh1 and gapdh2) were involved in glycolysis, which had extremely high expression levels in giant grouper muscle. As it has been reported that AMPs inhibit the growth of a broad spectrum of microbes and participate in regulating innate and adaptive immune responses, genome sequencing of this study provides a comprehensive cataloging of putative AMPs of groupers, supporting antimicrobial research and aquaculture therapy. These genomic resources will be beneficial to further molecular breeding of this economically important fish.
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Affiliation(s)
- Dengdong Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- Zhanjiang Bay Laboratory, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xiyang Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Yunhai Yi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- Zhanjiang Bay Laboratory, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Shuisheng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
- Zhanjiang Bay Laboratory, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
- Zhanjiang Bay Laboratory, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
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Zhang G, Li J, Zhang J, Liang X, Zhang X, Wang T, Yin S. Integrated Analysis of Transcriptomic, miRNA and Proteomic Changes of a Novel Hybrid Yellow Catfish Uncovers Key Roles for miRNAs in Heterosis. Mol Cell Proteomics 2019; 18:1437-1453. [PMID: 31092672 PMCID: PMC6601203 DOI: 10.1074/mcp.ra118.001297] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/09/2019] [Indexed: 01/14/2023] Open
Abstract
Heterosis is a complex biological phenomenon in which hybridization produces offspring that exhibit superior phenotypic characteristics compared with the parents. Heterosis is widely utilized in agriculture, for example in fish farming; however, its underlying molecular basis remains elusive. To gain a comprehensive and unbiased molecular understanding of fish heterosis, we analyzed the mRNA, miRNA, and proteomes of the livers of three catfish species, Pelteobagrus fulvidraco, P. vachelli, and their hybrid, the hybrid yellow catfish "Huangyou-1" (P. fulvidraco ♀ × P. vachelli ♂). Using next-generation sequencing and mass spectrometry, we show that the nonadditive, homoeolog expression bias and expression level dominance pattern were readily identified at the transcriptional, post-transcriptional, or protein levels, providing the evidence for the widespread presence of dominant models during hybridization. A number of predicted miRNA-mRNA-protein pairs were found and validated by qRT-PCR and PRM assays. Furthermore, several diverse key pathways were identified, including immune defense, metabolism, digestion and absorption, and cell proliferation and development, suggesting the vital mechanisms involved in the generation of the heterosis phenotype in progenies. We propose that the high parental expression of genes/proteins (growth, nutrition, feeding, and disease resistance) coupled with low parental miRNAs of the offspring, are inherited from the mother or father, thus indicating that the offspring were enriched with the advantages of the father or mother. We provide new and important information about the molecular mechanisms of heterosis, which represents a significant step toward a more complete elucidation of this phenomenon.
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Affiliation(s)
- Guosong Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; §Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong 274015, China
| | - Jie Li
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Jiajia Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Xia Liang
- §Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong 274015, China
| | - Xinyu Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Tao Wang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Shaowu Yin
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China.
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Divergence, evolution and adaptation in ray-finned fish genomes. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1003-1018. [PMID: 31098893 DOI: 10.1007/s11427-018-9499-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/12/2019] [Indexed: 02/06/2023]
Abstract
With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.
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Mohamad N, Mohd Roseli FA, Azmai MNA, Saad MZ, Md Yasin IS, Zulkiply NA, Nasruddin NS. Natural Concurrent Infection of Vibrio harveyi and V. alginolyticus in Cultured Hybrid Groupers in Malaysia. JOURNAL OF AQUATIC ANIMAL HEALTH 2019; 31:88-96. [PMID: 30536485 DOI: 10.1002/aah.10055] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/21/2018] [Indexed: 05/27/2023]
Abstract
In September 2016, a marine fish farm operator in Selangor, Malaysia, reported a disease outbreak affecting juvenile hybrid groupers (Camouflage Grouper Epinephelus polyphekadion × Tiger Grouper E. fuscoguttatus). The average daily mortality was 120 fish, resulting in a cumulative mortality rate of 29% within 10 d. The affected hybrid groupers displayed lethargy, excessive mucus production, rotten fins, congestion of livers and kidneys, and enlargement of spleens. Microscopically, general congestion of the brains and internal organs was evident. Vibrio harveyi and V. alginolyticus were successfully isolated from the diseased fish. The isolated pathogens were found to be sensitive to oxytetracycline and tetracycline, but resistant towards ampicillin and vancomycin. Experimental infections using the isolated V. harveyi (108 CFU/mL), V. alginolyticus (108 CFU/mL), and concurrent infection by V. harveyi (108 CFU/mL) and V. alginolyticus (108 CFU/mL) in juvenile Asian Seabass Lates calcarifer resulted in 60, 100, and 100% mortality, respectively, within 240 h postinfection. The experimentally infected Asian Seabass demonstrated similar clinical signs and histopathological changes as the naturally infected hybrid groupers. However, concurrently infected fish demonstrated severe clinical signs and histopathological changes compared with single infections. These results suggest that both isolates of Vibrio are pathogenic to fish and responsible for the disease outbreak. However, concurrent infection involving V. alginolyticus and V. harveyi leads to a more devastating impact to the cultured fish. This is the first report of concurrent Vibrio infection in cultured marine fish in Malaysia.
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Affiliation(s)
- Nurliyana Mohamad
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Fauzul Aidil Mohd Roseli
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Mohammad Noor Amal Azmai
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Mohd Zamri Saad
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Ina Salwany Md Yasin
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Nor Amalina Zulkiply
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Nurrul Shaqinah Nasruddin
- Department of Clinical Oral Biology, Faculty of Dentistry, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300, Kuala Lumpur, Malaysia
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22
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Insights into Body Size Evolution: A Comparative Transcriptome Study on Three Species of Asian Sisoridae Catfish. Int J Mol Sci 2019; 20:ijms20040944. [PMID: 30795590 PMCID: PMC6412271 DOI: 10.3390/ijms20040944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/06/2019] [Accepted: 02/18/2019] [Indexed: 12/13/2022] Open
Abstract
Body size is one of the most important attributes of a species, but the basic question of why and how each species reaches a different "right size" is still largely unknown. Herein, three phylogenetically closely related catfishes from Sisoridae, including one extraordinarily large-sized Bagarius yarrelli and two average-sized Glyptothorax macromaculatus and Oreoglanis setiger, were comparatively studied using RNA-Seq. Approximately 17,000 protein-coding genes were annotated for each of the three fishes, and 9509 genes were identified as high-confidence orthologous gene pairs. Comparative expressions uncovered a similar functional cluster about ribosome biogenesis was enriched in different tissues of the upregulated genes of Bagarius yarrelli. Moreover, differentially expressed genes and positively selected genes revealed that the glycolysis/pyruvate metabolism and cell cycle pathways have also greatly enhanced in this large-sized species. In total, 20 size-related candidate genes (including two growth modulators: the serine/threonine-protein kinases 3 (AKT3) and adaptor protein 1 (SH2B1), and a crucial pyruvate kinase (PKM2A)) were identified by multiplying comparative analyses along with gene functional screening, which would play major roles in enabling the large body size associated with Bagarius yarrelli and provide new insights into body size evolution. In conjunction with field observations and morphological comparisons, we hypothesize that habitat preferences promote size divergence of sisorids.
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Zhou S, Song D, Zhou X, Mao X, Zhou X, Wang S, Wei J, Huang Y, Wang W, Xiao SM, Qin Q. Characterization of Bacillus subtilis from gastrointestinal tract of hybrid Hulong grouper (Epinephelus fuscoguttatus × E. lanceolatus) and its effects as probiotic additives. FISH & SHELLFISH IMMUNOLOGY 2019; 84:1115-1124. [PMID: 30463174 DOI: 10.1016/j.fsi.2018.10.058] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/17/2018] [Accepted: 10/22/2018] [Indexed: 06/09/2023]
Abstract
Probiotics are widely used for the improvement of animals' growth and health. However, few marine aquatic probiotics are applied and licensed in China. In this study, a Bacillus spp. strain was isolated from the Hulong grouper gastrointestinal tract, which was identified as a new strain of Bacillus subtilis and was named as 7k. B. subtilis 7k showed desirable capability of sporulation and resistance to heat, simulated gastric juice and simulated duodenum juice, indicating its potential as probiotics. Seven antimicrobial chemicals were found in the secretion of the B. subtilis 7k. B. subtilis 7k addition in diet promoted the growth rate of Hulong groupers. Moreover, B. subtilis 7k can inhibit infection by iridovirus, making B. subtilis 7k a suitable kind of probiotic for maintaining fishes' health. Our results also revealed that B. subtilis 7k induced non-specific immune response in Hulong grouper under virus infection. Hulong grouper fed by diets containing B. subtilis 7k at 108 and 1010 cfu g-1 for 4-8 weeks were significantly strengthened in serum lysozyme activity, serum alternative complement activity (ACH50), serum bactericidal activity, respiratory burst, superoxide dismutase activity (SOD), and phagocytic activity of head kidney leucocytes when compared with those fed by control diets. In conclusion, B. subtilis 7k was isolated and characterized to be a kind of process enduring, growth stimulating, immunity enhancing and health promoting probiotic using in grouper culture.
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Affiliation(s)
- Sheng Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Deli Song
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China; Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xiaofeng Zhou
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xinliang Mao
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xuefeng Zhou
- Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Sunli Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jingguang Wei
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Youhua Huang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wenxiong Wang
- Department of Ocean Science, Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong
| | - Su-Mei Xiao
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Qiwei Qin
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Isolation and characterization of three skeletal troponin genes and association with growth-related traits in Exopalaemon carinicauda. Mol Biol Rep 2018; 46:705-718. [DOI: 10.1007/s11033-018-4526-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/23/2018] [Indexed: 12/15/2022]
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Shu Y, Xia J, Yu Q, Wang G, Zhang J, He J, Wang H, Zhang L, Wu H. Integrated analysis of mRNA and miRNA expression profiles reveals muscle growth differences between adult female and male Chinese concave-eared frogs (Odorrana tormota). Gene 2018; 678:241-251. [PMID: 30103010 DOI: 10.1016/j.gene.2018.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 07/24/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023]
Abstract
The Chinese concave-eared torrent frog (Odorrana tormota) is the first known non-mammalian vertebrate that can communicate using ultrasound. In this species, females are approximately four times as large as males, in which the female growth rate is obviously higher than that of male. Until now, the molecular mechanisms underlying muscle growth development differences between male and female frogs have not been reported. Here, we integrated mRNA and miRNA expression profiles to reveal growth differences in the hindlimb muscles of 2-year-old frogs. Among 569 differentially expressed genes (DEGs), 69 were associated with muscle growth and regeneration. Fifty-one up-regulated genes in females were potentially involved in promoting muscle growth and regeneration, whereas 18 up-regulated genes in males may lead to muscle growth inhibition and fast-twitch muscle fiber contraction. 244 DEGs were enriched in mTOR and other protein synthesis signaling pathways, and protein degradation pathways, including lysosomal protease, calpain, caspase, and ubiquitin-proteasome system pathways. It may interpret why female muscles grow faster than males. Based on expression differences of genes involved in glycolysis and oxidative metabolism, we speculated that the proportion of slow muscle fiber was higher and that of fast muscle fiber was lower in female compared with male muscle. Additionally, 767 miRNAs were identified, including 217 new miRNAs, and 6248 miRNA-negatively regulated mRNAs were predicted. The miRNA target genes were enriched in pathways related to muscle growth, protein synthesis, and degradation. Thus, in addition to the identified mRNA differential expressions, miRNAs may play other important roles in the differential regulation of hindlimb muscle growth between female and male O. tormota.
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Affiliation(s)
- Yilin Shu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jinquan Xia
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Qiang Yu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Gang Wang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jihui Zhang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jun He
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Huan Wang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ling Zhang
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University of Science and Technology, China; Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, China.
| | - Hailong Wu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
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Immunity, feed, and husbandry in fish health management of cultured Epinephelus fuscoguttatus with reference to Epinephelus coioides. AQUACULTURE AND FISHERIES 2018. [DOI: 10.1016/j.aaf.2018.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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