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Liu X, Gao J, Zhang P, Shi T, Yan B, Azra MN, Baloch WA, Wang P, Gao H. De novo transcriptional analysis of the response to starvation stress in the white ridgetail prawn, Exopalaemon carinicauda. Genomics 2023; 115:110746. [PMID: 37977333 DOI: 10.1016/j.ygeno.2023.110746] [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: 10/03/2023] [Revised: 10/27/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
To study the mechanism of the biomolecular response in Exopalaemon carinicauda to starvation stress, we subjected muscle tissue RNA samples from four stress points, including 0 d(control group), 10 d, 20 d, and 30 d, to starvation stress on white ridgetail prawn with a body weight of 1.41 + 0.42 g, aquaculture water temperature of 23-25 °C, salinity of 26, dissolved oxygen ≥5 mg/L, and pH 8-8.5, Then performed de novo transcriptome assembly and gene expression analysis using BGISEQ-500 with a tag-based digital gene expression (DGE) system. By de novo assembling at the four times, we obtained 28,167, 21,115, 24,497, and 27,080 reads, respectively. The results showed that the stress at 10 d led to no significant difference in the expressed genes, while the stress at 20 d and 30 d showed a significant increase (or decrease) in the expression of 97 (276) and 143 (410) genes, respectively, which were involved in 8 different metabolic pathways. In addition, we detected 2647 unigene transcription factors. Eleven upregulated and sixteen downregulated genes from the different starvation stress groups were choose to verify the reliability of the transcriptome data, and the results showed that the expression trends of these genes were consistent with the results shown by the transcriptome. The analysis of the experimental data and our discussion of the response mechanism of white ridgetail prawn under starvation stress provides a foundation for further screening of the key genes of starvation stress and may help to elucidate their functions.
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Affiliation(s)
- Xue Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China
| | - Jiayi Gao
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China
| | - Pei Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China
| | - Tingting Shi
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China
| | - Binlun Yan
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Lianyungang, Jiangsu 222005, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, Jiangsu 210014, China
| | - Mohamad Nor Azra
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
| | - Wazir Ali Baloch
- Department of Freshwater Biology and Fisheries, University of Sindh, Jamshoro 76080, Pakistan.
| | - Panpan Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Lianyungang, Jiangsu 222005, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, Jiangsu 210014, China
| | - Huan Gao
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Lianyungang, Jiangsu 222005, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, Jiangsu 210014, China.
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Wang J, Li J, Ge Q, Li J. A potential negative regulation of myostatin in muscle growth during the intermolt stage in Exopalaemon carinicauda. Gen Comp Endocrinol 2021; 314:113902. [PMID: 34529998 DOI: 10.1016/j.ygcen.2021.113902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
Muscle growth in crustacean is a complicated process where the muscle grows and develops through muscle restoration, and the growth rate depends on the net muscle gain during molting. Myostatin (MSTN) is a conserved inhibitor of muscle growth in vertebrates, but until now solid evidence supporting a similar function of MSTN in invertebrates has been lacking. In this study, we identified and characterized MSTN from the shrimp Exopalaemon carinicauda (EcMSTN) to better understand its biological function. The full-length cDNA of EcMSTN was 1,518 bp, encoding 428 amino acid residues, and the genomic sequence was 1,851 bp, including three exons and two introns. EcMSTN was expressed in a wide range of tissues, but predominantly detected in the abdominal muscle (P < 0.05). Low expression was detected in the cleavage, blastula and gastrula stages in the early development stages, increasing after the nauplius stage. EcMSTN expression was negatively correlated with the growth traits. After EcMSTN knockdown using RNA interference, EcMSTN expression was down-regulated in the abdominal muscle and up-regulated the expression of growth-related genes, including fast myosin heavy chain and skeletal muscle actin 3. After inhibiting EcMSTN for 5 weeks, the RNAi-treated shrimp with reduced EcMSTN levels exhibited a dramatically higher body weight compared with that of the control group. Association analysis revealed that two SNP loci g.Mstn220 and g.Mstn567 were markedly associated with both body weight and body length. The results would clarify the negative role of EcMSTN in regulating muscle growth during the intermolt stage and provide growth-related markers for molecular marker assisted breeding of E. carinicauda.
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Affiliation(s)
- Jiajia Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jitao Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Qianqian Ge
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Lv J, Lu X, Ti X, Liu P, Li J, Li J. QTL mapping and marker identification for sex determination in the ridgetail white prawn, Exopalaemon carinicauda. Genomics 2020; 112:5240-5247. [PMID: 32956845 DOI: 10.1016/j.ygeno.2020.09.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/25/2022]
Abstract
Sex determination is an important and intriguing research topic in the field of evolutionary and developmental biology. Quantitative trait locus (QTL) mapping for sex is helpful in clarifying the sex determination system of species. In this study, a second high-resolution genetic linkage map was constructed for the ridgetail white prawn, Exopalaemon carinicauda, which included 9280 markers, covering 99.98% of the complete genome. Based on the linkage map, a highly significant sex-related QTL was first mapped to a single linkage group (LG3, LOD > 55.6). Fifty-two markers in the QTL region were significantly associated with sex (p ≤ 10-40), of which heterogametic genotypes in females supported the ZW sex determination mechanism. Six markers were verified to be significantly associated with sex in the wild population. Some sex-related genes were identified, including phospholipase D, protein kinase shaggy, and longitudinals lacking protein. These results inform our understanding of the mechanisms of sex determination in E. carinicauda.
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Affiliation(s)
- Jianjian Lv
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Xuan Lu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xingbin Ti
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Ping Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jitao Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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