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Zhao C, Song Y, Zhang G, Zhang K, Yin S, Ji J. Multi-omics analysis identifies sex-specific hepatic protein-metabolite networks in yellow catfish (Pelteobagrus fulvidraco) exposed to chronic hypoxia. Int J Biol Macromol 2024; 268:131892. [PMID: 38677698 DOI: 10.1016/j.ijbiomac.2024.131892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Hypoxia disrupts the endocrine system of teleosts. The liver plays important roles in the endocrine system, energy storage, and metabolic processes. The aim of this study was to investigate the sex-specific hepatic response of yellow catfish under chronic hypoxia at the multi-omics level. Common hepatic responses in both sexes included the HIF-1 signaling pathway, glycolysis/gluconeogenesis, and steroid biosynthesis. Hypoxia dysregulated primary bile acid biosynthesis, lipid metabolism, and vitellogenin levels in female fish. Endoplasmic reticulum function in females also tended to be disrupted by hypoxia, as evidenced by significantly enriched pathways, including ribosome, protein processing in the endoplasmic reticulum, and RNA degradation. Other pathways, including the TCA cycle, oxidative phosphorylation, and Parkinson's and Huntington's disease, were highly enriched by hypoxia in male fish, suggesting that mitochondrial function was dysregulated. In both sexes of yellow catfish, the cell cycle was arrested and apoptosis was inhibited under chronic hypoxia. Multi-omics suggested that SLC2A5, CD209, LGMN, and NEDD8 served as sex-specific markers in these fish under chronic hypoxia. Our results provide insights into hepatic adaptation to chronic hypoxia and facilitate our understanding of sex-specific responses in fish.
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Affiliation(s)
- Cheng Zhao
- College of Marine Science and Engineering, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, Jiangsu, China
| | - Yufeng Song
- College of Marine Science and Engineering, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Guosong Zhang
- School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Kai Zhang
- College of Marine Science and Engineering, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, Jiangsu, China
| | - Shaowu Yin
- College of Marine Science and Engineering, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, Jiangsu, China.
| | - Jie Ji
- College of Marine Science and Engineering, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, Jiangsu, China.
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Li L, Li X, Chen Y, Yang Y, Wang N, Xu W. Identification and Functional Analysis of Cynoglossus semilaevis Z-Linked E3 Ubiquitin Ligase rnf34. Animals (Basel) 2024; 14:311. [PMID: 38275772 PMCID: PMC10812492 DOI: 10.3390/ani14020311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
The high proportion of males in C. semilaevis hinders their industrial development. The genetic ZW individual can become a pseudomale by sex reversal. And the pseudomale can produce Z-sperm (with epigenetic information to cause sex reversal) while W-sperm is absent, which leads to an even higher male proportion in offspring. Recently, with the development of transcriptomic technologies, research on spermatogenesis in C. semilaevis has been focused on the ubiquitination pathway. In this study, we analyzed the function of the ubiquitin ligase rnf34 gene on the Z chromosome. A qPCR experiment showed that its expression level in the gonad was the highest among different tissues. In the ovary, the expression gradually increased with development from 40 days post-hatching (dph) to 1.5 years post-hatching (yph). In the testis, rnf34 showed increased expression from 40 dph to 6 months post-hatching (mpf) and stabilized up until 1.5 ypf. In situ hybridization showed that the mRNA of rnf34 was mainly distributed in the germ cells of the testis and the ovary. In vivo siRNA-mediated knockdown of the rnf34 gene in male fish affected the expression of a series of genes related to sex differentiation and spermatogenesis. These results provide genetic data on the molecular mechanisms of gonadal development and spermatogenesis in C. semilaevis.
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Affiliation(s)
- Lu Li
- School of Fishery, Zhejiang Ocean University, Zhoushan 316022, China
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Xihong Li
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Yadong Chen
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Yingming Yang
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Na Wang
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Wenteng Xu
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
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Du M, Jiang Z, Wang C, Wei C, Li Q, Cong R, Wang W, Zhang G, Li L. Genome-Wide Association Analysis of Heat Tolerance in F 2 Progeny from the Hybridization between Two Congeneric Oyster Species. Int J Mol Sci 2023; 25:125. [PMID: 38203295 PMCID: PMC10778899 DOI: 10.3390/ijms25010125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
As the world's largest farmed marine animal, oysters have enormous economic and ecological value. However, mass summer mortality caused by high temperature poses a significant threat to the oyster industry. To investigate the molecular mechanisms underlying heat adaptation and improve the heat tolerance ability in the oyster, we conducted genome-wide association analysis (GWAS) analysis on the F2 generation derived from the hybridization of relatively heat-tolerant Crassostrea angulata ♀ and heat-sensitive Crassostrea gigas ♂, which are the dominant cultured species in southern and northern China, respectively. Acute heat stress experiment (semi-lethal temperature 42 °C) demonstrated that the F2 population showed differentiation in heat tolerance, leading to extremely differentiated individuals (approximately 20% of individuals die within the first four days with 10% survival after 14 days). Genome resequencing and GWAS of the two divergent groups had identified 18 significant SNPs associated with heat tolerance, with 26 candidate genes located near these SNPs. Eleven candidate genes that may associate with the thermal resistance were identified, which were classified into five categories: temperature sensor (Trpm2), transcriptional factor (Gata3), protein ubiquitination (Ube2h, Usp50, Uchl3), heat shock subfamily (Dnajc17, Dnaja1), and transporters (Slc16a9, Slc16a14, Slc16a9, Slc16a2). The expressional differentiation of the above genes between C. gigas and C. angulata under sublethal temperature (37 °C) further supports their crucial role in coping with high temperature. Our results will contribute to understanding the molecular mechanisms underlying heat tolerance, and provide genetic markers for heat-resistance breeding in the oyster industry.
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Affiliation(s)
- Mingyang Du
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zhuxiang Jiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chaogang Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chenchen Wei
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
| | - Qingyuan Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Rihao Cong
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Wei Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266100, China
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Wuhan 430072, China
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- University of Chinese Academy of Sciences, Beijing 101408, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266100, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Wuhan 430072, China
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Gong G, Ke W, Liao Q, Xiong Y, Hu J, Mei J. A chromosome-level genome assembly of the darkbarbel catfish Pelteobagrus vachelli. Sci Data 2023; 10:598. [PMID: 37684295 PMCID: PMC10491679 DOI: 10.1038/s41597-023-02509-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
The darkbarbel catfish (Pelteobagrus vachelli), an economically important aquaculture species in China, is extensively employed in hybrid yellow catfish production due to its superior growth rate. However, information on its genome has been limited, constraining further genetic studies and breeding programs. Leveraging the power of PacBio long-read sequencing and Hi-C technologies, we present a high-quality, chromosome-level genome assembly for the darkbarbel catfish. The resulting assembly spans 692.10 Mb, with an impressive 99.9% distribution over 26 chromosomes. The contig N50 and scaffold N50 are 13.30 Mb and 27.55 Mb, respectively. The genome is predicted to contain 22,109 protein-coding genes, with 96.1% having functional annotations. Repeat elements account for approximately 35.79% of the genomic landscape. The completeness of darkbarbel catfish genome assembly is highlighted by a BUSCO score of 99.07%. This high-quality genome assembly provides a critical resource for future hybrid catfish breeding, comparative genomics, and evolutionary studies in catfish and other related species.
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Affiliation(s)
- Gaorui Gong
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wensi Ke
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qian Liao
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yang Xiong
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jingqi Hu
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Mei
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
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Luo LF, Xu ZS, Li DY, Hu Z, Gao ZX. Comparative transcriptome profiles of four sexually size dimorphic fish. Sci Data 2022; 9:774. [PMID: 36528628 PMCID: PMC9759545 DOI: 10.1038/s41597-022-01887-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Sexual size dimorphism is widespread in fish species. Although sex growth differences in multiple species have been studied successively, the commonalities of regulatory mechanisms across sexually dimorphic species are unknown. In this study, we performed RNA-seq analysis of four representative fish (loach, half-smooth tongue sole, yellow catfish, and Nile tilapia) with significant growth differences between females and males. Clean reads were identified from four fish species, ranging from 45,718,052 to 57,733,120. Following comparison transcriptome analysis, there were 1,132 and 1,108, 1,290 and 1,102, 4,732 and 4,266, 748 and 192 differentially expressed genes (DEGs) in the brain and muscle of loach, half-smooth tongue sole, yellow catfish, and Nile tilapia, respectively. Furthermore, the expression levels were validated by quantitative real-time PCR (qRT-PCR). Comparative transcriptome profiles of four fish described here will provide fundamental information for further studies on the commonalities of sexually size dimorphic fish in regulating growth differences between females and males.
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Affiliation(s)
- Li-Fei Luo
- grid.35155.370000 0004 1790 4137College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Zi-Sheng Xu
- grid.35155.370000 0004 1790 4137College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Dan-Yang Li
- grid.35155.370000 0004 1790 4137College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Zhen Hu
- Hubei Aquatic Products Technology Promotion Station, Wuhan, 430060 China
| | - Ze-Xia Gao
- grid.35155.370000 0004 1790 4137College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China ,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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