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Yao X, Zhou Y, Nyirenda K, Song Y, Ma C, Qian K, Zhao Y, Tang S, Zhao J. Characterization of sexual size dimorphism in mandarin fish and association with igfbp-5a/b regulation. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024:10.1007/s10695-024-01385-8. [PMID: 39096447 DOI: 10.1007/s10695-024-01385-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/22/2024] [Indexed: 08/05/2024]
Abstract
Mandarin fish (Siniperca chuatsi) is an important cultured fish in East Asia that shows sexual size dimorphism (SSD), with females growing faster than males when reaching marketable size. However, the regulatory mechanism of SSD is not clear. To characterize SSD of mandarin fish and its association with gh/igf1/igfbp-5 expression, gonadal developmental atlas of the females and the males were described, and growth parameters and serum levels of E2 and T, as well as the relative expression levels of gh, igf1, and igfbp-5a/b mRNAs, were determined. The results showed that the logistic growth equation of body mass and total length of female and male were W(♀) = 667.57/(1 + e^(4.19 - 1.24*t)), W(♂) = 582.71/(1 + e^(4.07 - 1.27*t)), L(♀) = 31.47/(1 + e^1.95 - 1.08*t)), L(♂) = 26.20/(1 + e^(2.56 - 1.5*t)). The month of inflection points for body mass for females and males were 3.37 mph and 3.20 mph, respectively, when the body mass were 333.79 g and 291.36 g. The month of inflection points for total length growth were 1.80 mph and 1.70 mph, respectively, when the total length were 18.52 cm and 16.28 cm. At 1.5-2.0 mph, SSD was not clearly demonstrated. At 3.0 mph, the body mass of the females was significantly higher than that of the males (P < 0.05), Serum E2, brain gh, and liver igf1 expression of the females was significantly higher than that of the males (P < 0.05); T content of the males was significantly higher than that of the females (P < 0.05). At 4.0 months of age, the body mass of the females was highly significantly higher than that of the males (P < 0.01), Serum E2, brain gh, and liver igf1 expression of the females was highly significantly higher than that of the males (P < 0.05); T content of the males was significantly higher than that of the females (P < 0.05). With the continuous development of gonads, muscle and liver igfbp-5a and -5b expression generally tend to increase in females and males, while igfbp-5a showed a gradual increasing trend, and igfbp-5b expression showed a trend of decreasing and then increasing. Male igfbp-5a/b expression was significantly higher than female at the age of 3.0-4.0 months (P < 0.05). This work verified that the females had faster growth rate since 3.0 mph compared to the males, which may be related to higher E2 levels in females leading to higher igf1 level, through inhibition of igfbp-5a/b expression.
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Affiliation(s)
- Xiaoli Yao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yunhong Zhou
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Kenneth Nyirenda
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yindu Song
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Chenxi Ma
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Kelin Qian
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
- Chuzhou Yangtze Aquaculture Breeding Farm, Chuzhou, 239000, Anhui, China
| | - Yan Zhao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Shoujie Tang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jinliang Zhao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China.
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
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Liu S, Han C, Huang J, Li M, Yang J, Li G, Lin H, Li S, Zhang Y. Genome-wide identification, evolution and expression of TGF-β signaling pathway members in mandarin fish (Siniperca chuatsi). Int J Biol Macromol 2023; 253:126949. [PMID: 37722635 DOI: 10.1016/j.ijbiomac.2023.126949] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 09/20/2023]
Abstract
Members of the transforming growth factor β (TGF-β) signaling pathway regulate diverse cellular biological processes in embryonic and tissue development. We took mandarin fish (Siniperca chuatsi) as the research object to identify all members of the TGF-β signaling pathway, measure their expression pattern in the key period post hatching, and further explore their possible role in the process of sex regulation. Herein, we identified eighty-three TGF-β signaling pathway members and located them on chromosomes based on the genome of mandarin fish. TGF-β signaling pathway members were highly conserved since each TGF-β subfamily clustered with orthologs from other species. Transcriptome analysis, qRT-PCR and in situ hybridization demonstrated that most mandarin fish TGF-β signaling pathway members presented stage-specific and/or sex-dimorphic expression during gonadal development, and different members of the TGF-β signaling pathway participated in different stages of gonadal development. Taken together, our results provide new insight into the role of TGF-β signaling pathway members in the sex regulation of mandarin fish.
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Affiliation(s)
- Shiyan Liu
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266373, China
| | - Chong Han
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China; School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jingjun Huang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China
| | - Meihui Li
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jiayu Yang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China
| | - Guifeng Li
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China
| | - Haoran Lin
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266373, China
| | - Shuisheng Li
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Yong Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266373, China.
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3
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Liu X, Zeng S, Liu S, Wang G, Lai H, Zhao X, Bi S, Guo D, Chen X, Yi H, Su Y, Zhang Y, Li G. Identifying the Related Genes of Muscle Growth and Exploring the Functions by Compensatory Growth in Mandarin Fish ( Siniperca chuatsi). Front Physiol 2020; 11:553563. [PMID: 33117188 PMCID: PMC7552573 DOI: 10.3389/fphys.2020.553563] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/31/2020] [Indexed: 01/16/2023] Open
Abstract
How organisms display many different biochemical, physiological processes through genes expression and regulatory mechanisms affecting muscle growth is a central issue in growth and development. In Siniperca chuatsi, the growth-related genes and underlying relevant mechanisms are poorly understood, especially for difference of body sizes and compensatory growth performance. Muscle from 3-month old individuals of different sizes was used for transcriptome analysis. Results showed that 8,942 different expression genes (DEGs) were identified after calculating the RPKM. The DEGs involved in GH-IGF pathways, protein synthesis, ribosome synthesis and energy metabolisms, which were expressed significantly higher in small individuals (S) than large fish (L). In repletion feeding and compensatory growth experiments, eight more significant DEGs were used for further research (GHR2, IGFR1, 4ebp, Mhc, Mlc, Myf6, MyoD, troponin). When food was plentiful, eight genes participated in and promoted growth and muscle synthesis, respectively. Starvation can be shown to inhibit the expression of Mhc, Mlc and troponin, and high expression of GHR2, IGFR1, and 4ebp inhibited growth. Fasting promoted the metabolic actions of GHR2, IGFR1, and 4ebp rather than the growth-promoting actions. MyoD can sense and regulate the hunger, which also worked with Mhc and Mlc to accelerate the compensatory growth of S. chuatsi. This study is helpful to understand the regulation mechanisms of muscle growth-related genes. The elected genes will contribute to the selective breeding in future as candidate genes.
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Affiliation(s)
- Xuange Liu
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Shuang Zeng
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Shuang Liu
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Gongpei Wang
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Han Lai
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Xiaopin Zhao
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Sheng Bi
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Dingli Guo
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Xiaoli Chen
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Huadong Yi
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Yuqin Su
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Yong Zhang
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Guifeng Li
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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4
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Zhang Y, Liang XF, He S, Chen X, Wang J, Li J, Zhu Q, Zhang Z, Li L, Alam MS. Effects of High Carbohydrate Diet-Modulated Microbiota on Gut Health in Chinese Perch. Front Microbiol 2020; 11:575102. [PMID: 33042089 PMCID: PMC7523390 DOI: 10.3389/fmicb.2020.575102] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
High carbohydrate diet-induced damage in gut is linked to changes in gut permeability and microbiota. However, the mechanisms of action are not clear, especially in non-mammals. We performed the gut microbiota profiling in Chinese perch fed with different content of starch diets (0, 10, and 20%) by 16S rRNA sequencing. The gut permeability, metabolites, histological analysis, and inflammatory infiltration were evaluated. We found that gut microbial diversity, beneficial bacteria quantity, and lactic acid content were higher in C10 group than in the other groups. The lower level of gut microbial diversity was observed in C20 group, and mycoplasma was the overwhelmingly dominant species, but the butyric acid-producing bacteria and butyric acid level were significantly reduced. The gut permeability in C20 group was also increased due to the decreased mRNA expression levels of tight junction proteins caused by the butyric acid deficiency and gut lipid droplets accumulation. Then a large amount of LPS penetrated into the plasma, resulting in inflammation. These results suggested that high carbohydrate diet-induced damage in gut could be attributed to the endotoxemia, permeability, and gut microbiota, especially the role of mycoplasma and butyric acid-producing bacteria. In addition, predictive functional profiling of microbial communities by PICRUSt showed that C10 group enriched pathway related to membrane transport and down-regulated the pathways related to energy, coenzyme factor and vitamin metabolism, while C20 group exhibited reversed results. These data showed that the high-carbohydrate diet reversed the beneficial changes in gut microbial metabolism resulted from the medium-carbohydrate diet, and further demonstrated that microbiota played a key role in the gut damage caused by the high-carbohydrate diet. Our findings provide a reference for the targeted regulation of gut microbiota to mitigate the damage caused by the increase in starch content in fish feed (cost saving).
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Affiliation(s)
- Yanpeng Zhang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Shan He
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Xu Chen
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Jie Wang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Jiao Li
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Qiangsheng Zhu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Zhen Zhang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Lu Li
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Muhammad Shoaib Alam
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
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5
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He S, Li L, Lv LY, Cai WJ, Dou YQ, Li J, Tang SL, Chen X, Zhang Z, Xu J, Zhang YP, Yin Z, Wuertz S, Tao YX, Kuhl H, Liang XF. Mandarin fish (Sinipercidae) genomes provide insights into innate predatory feeding. Commun Biol 2020; 3:361. [PMID: 32647268 PMCID: PMC7347838 DOI: 10.1038/s42003-020-1094-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/12/2020] [Indexed: 01/04/2023] Open
Abstract
Mandarin fishes (Sinipercidae) are piscivores that feed solely on live fry. Unlike higher vertebrates, teleosts exhibit feeding behavior driven mainly by genetic responses, with no modification by learning from parents. Mandarin fishes could serve as excellent model organisms for studying feeding behavior. We report a long-read, chromosomal-scale genome assembly for Siniperca chuatsi and genome assemblies for Siniperca kneri, Siniperca scherzeri and Coreoperca whiteheadi. Positive selection analysis revealed rapid adaptive evolution of genes related to predatory feeding/aggression, growth, pyloric caeca and euryhalinity. Very few gill rakers are observed in mandarin fishes; analogously, we found that zebrafish deficient in edar had a gill raker loss phenotype and a more predatory habit, with reduced intake of zooplankton but increased intake of prey fish. Higher expression of bmp4, which could inhibit edar expression and gill raker development through binding of a Xvent-1 site upstream of edar, may cause predatory feeding in Siniperca.
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Affiliation(s)
- Shan He
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Ling Li
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
- Department of Ecophysiology and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Li-Yuan Lv
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Wen-Jing Cai
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Ya-Qi Dou
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Jiao Li
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Shu-Lin Tang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Xu Chen
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Zhen Zhang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Jing Xu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Yan-Peng Zhang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Zhan Yin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Sven Wuertz
- Department of Ecophysiology and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology & Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Heiner Kuhl
- Department of Ecophysiology and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China.
- Innovation Base for Chinese Perch Breeding, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China.
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6
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Marnis H, Kania PW, Syahputra K, Zuo S, Dirks RP, Buchmann K. Transcriptomic analysis of Baltic cod (Gadus morhua) liver infected with Contracaecum osculatum third stage larvae indicates parasitic effects on growth and immune response. FISH & SHELLFISH IMMUNOLOGY 2019; 93:965-976. [PMID: 31419536 DOI: 10.1016/j.fsi.2019.08.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 06/10/2023]
Abstract
High infection levels due to third-stage larvae of the anisakid nematode Contracaecum osculatum have been documented in cod from the eastern part of the Baltic sea during the latest decades. The nematode larvae mainly infect the liver of Baltic cod and prevalence of infection has reached 100% with a mean intensity up to 80 parasites per host in certain areas and size classes. Low condition factors of the cod have been observed concomitant with the rise in parasite abundance suggesting a parasitic effect on growth parameters. To investigate any association between parasite infection and physiological status of the host we performed a comparative transcriptomic analysis of liver obtained from C. osculatum infected and non-infected cod. A total of 47,025 predicted gene models showed expression in cod liver and sequences corresponding to 2084 (4.43%) unigenes were differentially expressed in infected liver when compared to non-infected liver. Of the differentially expressed unigenes (DEGs) 1240 unigenes were up-regulated while 844 unigenes were down-regulated. The Gene Ontology (GO) enrichment analysis showed that 1304 DEGs were represented in cellular process and single-organism process, cell and cell part, binding and catalytic activity. As determined by the Kyoto Encyclopedia of Gene and Genomes (KEGG) Pathways analysis, 454 DEGs were involved in 138 pathways. Ninety-seven genes were related to metabolic pathways including carbohydrate, lipid, and amino acid metabolism. Thirteen regulated genes were playing a role in immune response such as Toll-like receptor signaling, NOD-like receptor signaling, RIG-I-like receptor signalling and thirty-six genes were associated with growth processes. This indicates that the nematode infection in Baltic cod may affect on molecular mechanisms involving metabolism, immune function and growth.
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Affiliation(s)
- Huria Marnis
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark.
| | - Per W Kania
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Khairul Syahputra
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Shaozhi Zuo
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Ron P Dirks
- Future Genomics Technologies B.V, Leiden, the Netherlands
| | - Kurt Buchmann
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Tu J, Tian C, Zhao P, Sun J, Wang M, Fan Q, Yuan Y. Identification and profiling of growth-related microRNAs in Chinese perch (Siniperca chuatsi). BMC Genomics 2017; 18:489. [PMID: 28659132 PMCID: PMC5490230 DOI: 10.1186/s12864-017-3851-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 06/07/2017] [Indexed: 12/17/2022] Open
Abstract
Background MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play important roles in the regulation of diverse biological processes in eukaryotes. Chinese perch (Siniperca chuatsi) is one of the most economically important fish species widely cultured in China. Growth is an extremely important characteristic in fish. Individual differences in body size are common in Siniperca chuatsi, which significantly influence the aquaculture production of Siniperca chuatsi. However, the underline growth-related regulatory factors, such as miRNAs, are still unknown. Results To investigate the growth-related miRNAs in Siniperca chuatsi, two RNA libraries from four growth-related tissues (brain, pituitary, liver, and muscle) of Siniperca chuatsi at 6-month stage with relatively high or low growth rates (big-size group or small-size group) were obtained and sequenced using Solexa sequencing. A total of 252 known miRNAs and 12 novel miRNAs were identified. The expression patterns of these miRNAs in big-size group and small-size group were compared, and the results showed that 31 known and 5 novel miRNAs were differently expressed (DE). Furthermore, to verify the Solexa sequencing, five DE miRNAs were randomly selected and quantified by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The results showed that their expression patterns were consistent with those of Solexa sequencing. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of target genes of DE miRNAs was performed. It showed that the target genes were involved in multiple biological processes including metabolic process, suggesting that metabolic process played an important role in growth of fish. Conclusions Siniperca chuatsi is a popular and economically important species in aquaculture. In this study, miRNAs in Siniperca chuatsi with different growth rates were identified, and their expression profiles were compared. The data provides the first large-scale miRNA profiles related to growth of Siniperca chuatsi, which is expected to contribute to a better understanding of the role of miRNAs in regulating the biological processes of growth and possibly useful for Siniperca chuatsi breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3851-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiagang Tu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Changxu Tian
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Peiqi Zhao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junxiao Sun
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Min Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qixue Fan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yongchao Yuan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. .,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, Hubei, 430070, China.
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Tian C, Guo W, Liang XF, Sun L, Lv L, Zhao C, Song Y, He S. Identification of species-specific microsatellite markers in three Siniperca species by RNA-Seq. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2016.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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