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Liu C, Zhang W, Dong Q, Liu H. Exoskeleton protein repertoires in decapod crustaceans revealed distinct biomineralization evolution with molluscs. J Proteomics 2024; 291:105046. [PMID: 37981007 DOI: 10.1016/j.jprot.2023.105046] [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: 09/01/2023] [Revised: 10/29/2023] [Accepted: 11/03/2023] [Indexed: 11/21/2023]
Abstract
Crustaceans are the champions of mineral mobilization and deposition in the animal kingdom due to their unique ability to rapidly and periodically mineralize and demineralize their exoskeletons. They are commonly covered with mineralized exoskeletons for protection and regularly molt throughout their lives. Mineralized crustacean exoskeletons are formed under the control of macromolecules especially matrix proteins but the types of matrix proteins are understudied compared to those in molluscan shells. This gap hinders our understanding of their evolutionary paths compared with those of molluscs. Here, we comprehensively analyzed matrix proteins in the exoskeleton of two crabs, one shrimp, and one crayfish and resulted in a major improvement (∼10-fold) in the identification of biomineralization proteins compared to conventional methods for decapod crustaceans. By a comparison with well-studied molluscan biomineralization proteins, we found that decapod crustaceans evolved novel proteins to form mineralized exoskeletons while sharing some proteins with those of molluscs. Our study sheds light on their evolution and adaption to different environment for exoskeleton formation and provides a foundation for further studies of mineralization in crustaceans under normal and climate-changed conditions. SIGNIFICANCE: Most crustaceans have mineralized exoskeletons as protection. How they form these hierarchical structures is still unclear. This is due partially to the understudied matrix proteins in the minerals. This study filled such a gap by using proteomic analysis of matrix proteins from four decapod crustacean exoskeletons. Many novel proteins were discovered which enabled a solid comparison with those of molluscs. By comparison, we proposed that crustaceans evolved novel proteins to form mineralized exoskeletons while sharing some proteins with those of molluscs. This is useful for us to understand the evolution of two major biomineralized phylum.
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Affiliation(s)
- Chuang Liu
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing 210024, China.
| | - Wenjing Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing 210024, China
| | - Qianli Dong
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing 210024, China
| | - Haipeng Liu
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing 210024, China
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Fu Y, Zhang F, Wang W, Xu J, Zhao M, Ma C, Cheng Y, Chen W, Su Z, Lv X, Liu Z, Ma K, Ma L. Temporal and Spatial Signatures of Scylla paramamosain Transcriptome Reveal Mechanistic Insights into Endogenous Ovarian Maturation under Risk of Starvation. Int J Mol Sci 2024; 25:700. [PMID: 38255774 PMCID: PMC10815400 DOI: 10.3390/ijms25020700] [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: 11/18/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Variability in food availability leads to condition-dependent investments in reproduction. This study is aimed at understanding the metabolic response and regulatory mechanism of female Scylla paramamosain in response to starvation in a temporal- and tissue-specific manner. The mud crabs were starved for 7 (control), 14, 28, and 40 days for histological and biochemical analysis in the hepatopancreas, ovary, and serum, as well as for RNA sequencing on the hepatopancreas and ovary. We further highlighted candidate gene modules highly linked to physiological traits. Collectively, our observations suggested that starvation triggered endogenous ovarian maturation at the expense of hepatopancreas mass, with both metabolic adjustments to optimize energy and fatty acid supply from hepatopancreas to ovary in the early phase, followed by the activation of autophagy-related pathways in both organs over prolonged starvation. These specific adaptive responses might be considered efficient strategies to stimulate ovarian maturation of Scylla paramamosain under fasting stress, which improves the nutritional value of female mud crabs and other economically important crustaceans.
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Affiliation(s)
- Yin Fu
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; (Y.F.)
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Fengying Zhang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; (Y.F.)
| | - Wei Wang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; (Y.F.)
| | - Jiayuan Xu
- Experimental Base of East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ningbo 315604, China
| | - Ming Zhao
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; (Y.F.)
| | - Chunyan Ma
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; (Y.F.)
| | - Yongxu Cheng
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Wei Chen
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; (Y.F.)
| | - Zhixing Su
- Experimental Base of East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ningbo 315604, China
| | - Xiaokang Lv
- Experimental Base of East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ningbo 315604, China
| | - Zhiqiang Liu
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; (Y.F.)
| | - Keyi Ma
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; (Y.F.)
| | - Lingbo Ma
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; (Y.F.)
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Yang N, Li W, Feng W, Wang M, Liu A, Tang Y, Su S. Genomics and transcriptomics of the Chinese mitten crabs (Eriocheir sinensis). Sci Data 2023; 10:843. [PMID: 38036563 PMCID: PMC10689444 DOI: 10.1038/s41597-023-02761-4] [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: 05/24/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023] Open
Abstract
To gain a deeper understanding of the genetic factors influencing the growth and development of Eriocheir sinensis, a well-known species of hairy crab found in Yangcheng Lake, this study focused on the de novo genome and full-length transcriptome information of the selected subjects. Specifically, Yangcheng Lake hairy crabs were chosen as the experimental samples. Initially, a genome analysis was performed, resulting in the identification of gene fragments with a combined length of 1266,092,319 bp. Subsequently, a transcriptome analysis was conducted on a mixture of tissues from four different sites, namely muscle, brain, eye, and heart, to further investigate the genetic characteristics at the transcriptome level. The Pacific Biosciences (Pacio) single-molecule real-time sequencing system generated a total of 36.93 G sub-fragments and 175,90041 effective inserts. This research contributes to the indirect comprehension of genetic variations underlying individual traits. Furthermore, a comparison of the obtained data with relevant literature emphasizes the advantages of this study and establishes a basis for further investigations on the Chinese mitten crab.
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Affiliation(s)
- Nan Yang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
| | - Wenjing Li
- Jiangsu Haorun Biological Industry Group Co., Ltd, Taizhou, 225309, China
| | - Wenrong Feng
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Meiyao Wang
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Aimin Liu
- Jiangsu Haorun Biological Industry Group Co., Ltd, Taizhou, 225309, China
| | - Yongkai Tang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China.
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Shengyan Su
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China.
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
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Sun X, Wang G, Yang J, Yu W, Xu J, Tang B, Ding G, Zhang D. Whole genome evaluation analysis and preliminary Assembly of Oratosquilla oratoria (Stomatopoda: Squillidae). Mol Biol Rep 2023; 50:4165-4173. [PMID: 36894769 DOI: 10.1007/s11033-023-08356-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND As the dominant species of Stomatopoda, Oratosquilla oratoria has not been fully cultivated artificially, and the fishery production mainly depends on marine fishing. Due to the lack of stomatopod genome, the development of molecular breeding of mantis shrimps still lags behind. METHODS AND RESULTS A survey analysis was performed to obtain the genome size, GC content and heterozygosity ratio in order to provide a fundation for subsequent whole-genome sequencing. The results showed that the estimated genome size of the O. oratoria was about 2.56 G, and the heterozygosity ratio was 1.81%, indicating that it is a complex genome. Then the sequencing data was preliminarily assembled with k-mer = 51 by SOAPdenovo software to obtain a genome size of 3.01G and GC content of 40.37%. According to ReapeatMasker and RepeatModerler analysis, the percentage of repeats in O. oratoria was 45.23% in the total genome, similar to 44% in Survey analysis. The MISA tool was used to analyze the simple sequence repeat (SSR) characteristics of genome sequences including Oratosquilla oratoria, Macrobrachium nipponense, Fenneropenaeus chinensis, Eriocheir japonica sinensis, Scylla paramamosain and Paralithodes platypus. All crustacean genomes showed similar SSRs characteristics, with the highest proportion of di-nucleotide repeat sequences. And AC/GT and AGG/CCT repeats were the main types of di-nucleotide and tri-nucleotide repeats in O. oratoria. CONCLUSION This study provided a reference for the genome assembly and annotation of the O. oratoria, and also provided a theoretical basis for the development of molecular markers of O. oratoria.
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Affiliation(s)
- Xiaoli Sun
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Jie Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Wei Yu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Jiayue Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Ge Ding
- Chemical and Biological Engineering College, Yancheng Institute of Technology, Yancheng, 224003, China
| | - Daizhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China.
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Wang Y, Yang LG, Feng GP, Yao ZL, Li SH, Zhou JF, Fang WH, Chen YH, Li XC. PvML1 suppresses bacterial infection by recognizing LPS and regulating AMP expression in shrimp. Front Immunol 2022; 13:1088862. [PMID: 36643915 PMCID: PMC9832027 DOI: 10.3389/fimmu.2022.1088862] [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: 11/03/2022] [Accepted: 12/06/2022] [Indexed: 12/29/2022] Open
Abstract
Toll and Toll-like receptors (TLRs) play essential roles in the innate immunity of Drosophila and mammals. Recent studies have revealed the presence of Toll-mediated immune signaling pathways in shrimp. However, the recognition and activation mechanism of Toll signaling pathways in crustaceans remain poorly understood due to the absence of key recognition molecules, such as peptidoglycan recognition proteins. Here, a novel MD2-related lipid-recognition (ML) member named PvML1 was characterized in Penaeus vannamei. We found that PvML1 shared a similar 3D structure with human MD2 that could specifically recognize lipopolysaccharides (LPS) participating in LPS-mediated TLR4 signaling. PvML1 was highly expressed in hemocytes and remarkably upregulated after Vibrio parahemolyticus challenge. Furthermore, the binding and agglutinating assays showed that PvML1 possessed strong binding activities to LPS and its key portion lipid A as well as Vibrio cells, and the binding of PvML1 with bacterial cells led to the agglutination of bacteria, suggesting PvML1 may act as a potential pathogen recognition protein upon interaction with LPS. Besides, coating V. parahemolyticus with recombinant PvML1 promoted bacterial clearance in vivo and increased the survival rate of bacterium-challenged shrimp. This result was further confirmed by RNAi experiments. The knockdown of PvML1 remarkably suppressed the clearance of bacteria in hemolymph and decreased the survival rate of infected shrimp. Meanwhile, the silencing of PvML1 severely impaired the expression of a few antimicrobial peptides (AMPs). These results demonstrated the significant correlation of bacterial clearance mediated by PvML1 with the AMP expression. Interestingly, we found that PvML1 interacted with the extracellular region of PvToll2, which had been previously shown to participate in bacterial clearance by regulating AMP expression. Taken together, the proposed antibacterial model mediated by PvML1 might be described as follows. PvML1 acted as a potential recognition receptor for Gram-negative bacteria by binding to LPS, and then it activated PvToll2-mediated signaling pathway by interacting with PvToll2 to eliminate invading bacteria through producing specific AMPs. This study provided new insights into the recognition and activation mechanism of Toll signaling pathways of invertebrates and the defense functions of ML members.
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Affiliation(s)
- Yue Wang
- Key Laboratory of Inland Saline-alkaline Aquaculture, Ministry of Agriculture and Rural Affairs, Shanghai, China,East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China,Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Li-Guo Yang
- Key Laboratory of Inland Saline-alkaline Aquaculture, Ministry of Agriculture and Rural Affairs, Shanghai, China,East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Guang-Peng Feng
- Key Laboratory of Inland Saline-alkaline Aquaculture, Ministry of Agriculture and Rural Affairs, Shanghai, China,East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Zong-Li Yao
- Key Laboratory of Inland Saline-alkaline Aquaculture, Ministry of Agriculture and Rural Affairs, Shanghai, China,East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Shou-Hu Li
- Key Laboratory of Inland Saline-alkaline Aquaculture, Ministry of Agriculture and Rural Affairs, Shanghai, China,East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Jun-Fang Zhou
- Key Laboratory of Inland Saline-alkaline Aquaculture, Ministry of Agriculture and Rural Affairs, Shanghai, China,East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Wen-Hong Fang
- Key Laboratory of Inland Saline-alkaline Aquaculture, Ministry of Agriculture and Rural Affairs, Shanghai, China,East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Yi-Hong Chen
- Key Laboratory for Healthy and Safe Aquaculture, Institute of Modern Aquaculture Science and Engineering (IMASE), College of Life Science, South China Normal University, Guangzhou, China,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China,*Correspondence: Yi-Hong Chen, ; Xin-Cang Li,
| | - Xin-Cang Li
- Key Laboratory of Inland Saline-alkaline Aquaculture, Ministry of Agriculture and Rural Affairs, Shanghai, China,East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China,*Correspondence: Yi-Hong Chen, ; Xin-Cang Li,
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Ren Y, Wang W, Liu Z, Luo M, Fu Y, Zhang F, Ma C, Zhao M, Chen W, Jiang K, Ma L. Insight of vitellogenesis patterns: A comparative analysis of the differences between the primary and secondary vitellogenesis period in the ovary, hepatopancreas, and muscle of mud crab, scylla paramamosain. Front Genet 2022; 13:965070. [PMID: 36105103 PMCID: PMC9465302 DOI: 10.3389/fgene.2022.965070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/05/2022] [Indexed: 12/04/2022] Open
Abstract
The mud crab, Scylla paramamosain, has abundant nutrients in its edible parts, ovary, hepatopancreas, and muscle during the ovarian maturation stage. The ovary of S. paramamosain can re-mature after spawning during the secondary ovarian maturation period. We aimed to analyze the characteristics of the first vitellogenesis period (FVP)1 and second vitellogenesis period (SVP)2 of S. paramamosain during ovarian maturation to understand the differences in vitellogenesis patterns between the first and second ovarian maturation periods. Accordingly, the gonadosomatic index (GSI) and hepatopancreatic index (HSI), the external and histological characteristics of the ovary and hepatopancreas, the Sp-Vg (vitellogenin, Vg) expression levels in the hepatopancreas and ovary, and the dynamics of the biochemical components in the ovary, hepatopancreas, and muscle were determined. Based on the results, the GSI was significantly positively correlated with HSI during the FVP and significantly negatively correlated with HSI from stage Ⅳ to stage Ⅴ of the SVP. A significant difference was found between the FVP and SVP in the hepatopancreas. Notably, the hepatopancreas displayed a gradual degeneration trend during the SVP. The expression level of Sp-Vg was significantly higher in the hepatopancreas than that in the ovary during the FVP and SVP. Seventeen amino acids were detected in the hepatopancreas, ovary, and muscle during the FVP and SVP, with glutamate as the predominant amino acid. During the FVP and SVP, the C16:0 and C18:1n9c were the dominant fatty acids in the hepatopancreas and ovary, the MUFA gradually increased in the ovary and hepatopancreas, and a significant difference was found in the dynamic trend of the HUFA and SFA contents from stage Ⅳ to stage Ⅴ between the FVP and SVP. These findings indicate that the ovary can re-mature after spawning in S. paramamosain and can maintain the status of the first ovarian maturation; however, the hepatopancreas gradually degenerate during the SVP.
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Affiliation(s)
- Yuanhao Ren
- Key Laboratory of East China Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Wei Wang
- Key Laboratory of East China Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
| | - Zhiqiang Liu
- Key Laboratory of East China Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
| | - Minghao Luo
- Key Laboratory of East China Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Yin Fu
- Key Laboratory of East China Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Fengying Zhang
- Key Laboratory of East China Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
| | - Chunyan Ma
- Key Laboratory of East China Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
| | - Ming Zhao
- Key Laboratory of East China Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
| | - Wei Chen
- Key Laboratory of East China Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
| | - Keji Jiang
- Key Laboratory of East China Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
| | - Lingbo Ma
- Key Laboratory of East China Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
- *Correspondence: Lingbo Ma,
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Identification and Evolution Analysis of the Complete Methyl Farnesoate Biosynthesis and Related Pathway Genes in the Mud Crab, Scylla paramamosain. Int J Mol Sci 2022; 23:ijms23169451. [PMID: 36012717 PMCID: PMC9409210 DOI: 10.3390/ijms23169451] [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: 07/24/2022] [Revised: 08/13/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
The sesquiterpenoid hormone methyl farnesoate (MF) plays a vital role during crustacean development, which is mainly evidenced by its varied titers during different developmental stages. However, the biosynthesis pathways of MF remain obscure to some extent. In this study, we identified the complete MF biosynthesis and related pathway genes in Scylla paramamosain, including three involved in acetyl-CoA metabolism, eight in the mevalonate pathway, five in the sesquiterpenoids synthesis pathway, and five in the methionine cycle pathway. Bioinformatics, genomic structure, and phylogenetic analysis indicated that the JH biosynthesis genes might have experienced evolution after species differentiation. The mRNA tissue distribution analysis revealed that almost all genes involving in or relating to MF syntheses were highly expressed in the mandibular organ (MO), among which juvenile hormone acid methyltransferase was exclusively expressed in the MO, suggesting that most of these genes might mainly function in MF biosynthesis and that the methionine cycle pathway genes might play a crucial regulatory role during MF synthesis. In addition, the phylogenetic and tissue distribution analysis of the cytochrome P450 CYP15-like gene suggested that the epoxidized JHs might exist in crustaceans, but are mainly synthesized in hepatopancreas rather than the MO. Finally, we also found that betaine-homocysteine S-methyltransferase genes were lost in insects while methionine synthase was probably lost in most insects except Folsomia candida, indicating a regulatory discrepancy in the methionine cycle between crustaceans and insects. This study might increase our understanding of synthetic metabolism tailored for sesquiterpenoid hormones in S. paramamosain and other closely related species.
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Ye S, Yu X, Chen H, Zhang Y, Wu Q, Tan H, Song J, Saqib HSA, Farhadi A, Ikhwanuddin M, Ma H. Full-Length Transcriptome Reconstruction Reveals the Genetic Mechanisms of Eyestalk Displacement and Its Potential Implications on the Interspecific Hybrid Crab (Scylla serrata ♀ × S. paramamosain ♂). BIOLOGY 2022; 11:biology11071026. [PMID: 36101407 PMCID: PMC9312322 DOI: 10.3390/biology11071026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022]
Abstract
Simple Summary The eyestalk is a key organ in crustaceans that produces neurohormones and regulates a range of physiological functions. Eyestalk displacement was discovered in some first-generation (F1) offspring of the novel interspecific hybrid crab (Scylla serrata ♀ × S. paramamosain ♂). To uncover the genetic mechanism underlying eyestalk displacement and its potential implications, high-quality transcriptome was reconstructed using single-molecule real-time (SMRT) sequencing. A total of 37 significantly differential alternative splicing (DAS) events (17 up-regulated and 20 down-regulated) and 1475 significantly differential expressed transcripts (DETs) (492 up-regulated and 983 down-regulated) were detected in hybrid crabs with displaced eyestalks (DH). The most significant DAS events and DETs were annotated as being endoplasmic reticulum chaperone BiP and leucine-rich repeat protein lrrA-like isoform X2. In addition, the top ten significant gene ontology (GO) terms were related to the cuticle or chitin. Overall, this study highlights the underlying genetic mechanisms of eyestalk displacement and provide useful knowledge for mud crab (Scylla spp.) crossbreeding. Abstract The lack of high-quality juvenile crabs is the greatest impediment to the growth of the mud crab (Scylla paramamosain) industry. To obtain high-quality hybrid offspring, a novel hybrid mud crab (S. serrata ♀ × S. paramamosain ♂) was successfully produced in our previous study. Meanwhile, an interesting phenomenon was discovered, that some first-generation (F1) hybrid offspring’s eyestalks were displaced during the crablet stage I. To uncover the genetic mechanism underlying eyestalk displacement and its potential implications, both single-molecule real-time (SMRT) and Illumina RNA sequencing were implemented. Using a two-step collapsing strategy, three high-quality reconstructed transcriptomes were obtained from purebred mud crabs (S. paramamosain) with normal eyestalks (SPA), hybrid crabs with normal eyestalks (NH), and hybrid crabs with displaced eyestalks (DH). In total, 37 significantly differential alternative splicing (DAS) events (17 up-regulated and 20 down-regulated) and 1475 significantly differential expressed transcripts (DETs) (492 up-regulated and 983 down-regulated) were detected in DH. The most significant DAS events and DETs were annotated as being endoplasmic reticulum chaperone BiP and leucine-rich repeat protein lrrA-like isoform X2. In addition, the top ten significant GO terms were related to the cuticle or chitin. Overall, high-quality reconstructed transcriptomes were obtained for the novel interspecific hybrid crab and provided valuable insights into the genetic mechanisms of eyestalk displacement in mud crab (Scylla spp.) crossbreeding.
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Affiliation(s)
- Shaopan Ye
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Xiaoyan Yu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Huiying Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Qingyang Wu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Huaqiang Tan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Jun Song
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Hafiz Sohaib Ahmed Saqib
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Ardavan Farhadi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Mhd Ikhwanuddin
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Correspondence: ; Tel.: +86-754-86503471
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9
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Fu Y, Zhang F, Ma C, Wang W, Liu Z, Chen W, Zhao M, Ma L. Comparative Metabolomics and Lipidomics of Four Juvenoids Application to Scylla paramamosain Hepatopancreas: Implications of Lipid Metabolism During Ovarian Maturation. Front Endocrinol (Lausanne) 2022; 13:886351. [PMID: 35574001 PMCID: PMC9094423 DOI: 10.3389/fendo.2022.886351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
This study was the first to evaluate multiple hormonal manipulations to hepatopancreas over the ovarian development stages of the mud crab, Scylla paramamosain. A total of 1258 metabolites in 75 hepatopancreas explants from five female crabs were induced by juvenile hormone III (JH III), methyl farnesoate (MF), farnesoic acid (FA) and methoprene (Met), as identified from combined metabolomics and lipidomics (LC-MS/MS). 101 significant metabolites and 47 significant pathways were selected and compared for their comprehensive effects to ovarian maturation. While MF played an extensive role in lipid accumulation, JH III and Met shared similar effects, especially in the commonly and significantly elevated triglycerides and lysophospholipids (fold change≥2 and ≤0.5, VIP≥1). The significant upregulation of β-oxidation and key regulators in lipid degradation by FA (P ≤ 0.05) resulted in less lipid accumulation from this treatment, with a shift toward lipid export and energy consumption, unlike the effects of MF, JH III and Met. It was possible that MF and FA played their own unique roles and acted in synergy to modulate lipid metabolism during crab ovarian maturation. Our study yielded insights into the MF-related lipid metabolism in crustacean hepatopancreas for the overall regulation of ovarian maturation, and harbored the potential use of juvenoids to induce reproductive maturity of this economic crab species.
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Affiliation(s)
- Yin Fu
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Fengying Zhang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Chunyan Ma
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wei Wang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Zhiqiang Liu
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Wei Chen
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Ming Zhao
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- *Correspondence: Lingbo Ma, ; Ming Zhao,
| | - Lingbo Ma
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- *Correspondence: Lingbo Ma, ; Ming Zhao,
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10
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Wolfe JM, Luque J, Bracken-Grissom HD. How to become a crab: Phenotypic constraints on a recurring body plan. Bioessays 2021; 43:e2100020. [PMID: 33751651 DOI: 10.1002/bies.202100020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
A fundamental question in biology is whether phenotypes can be predicted by ecological or genomic rules. At least five cases of convergent evolution of the crab-like body plan (with a wide and flattened shape, and a bent abdomen) are known in decapod crustaceans, and have, for over 140 years, been known as "carcinization." The repeated loss of this body plan has been identified as "decarcinization." In reviewing the field, we offer phylogenetic strategies to include poorly known groups, and direct evidence from fossils, that will resolve the history of crab evolution and the degree of phenotypic variation within crabs. Proposed ecological advantages of the crab body are summarized into a hypothesis of phenotypic integration suggesting correlated evolution of the carapace shape and abdomen. Our premise provides fertile ground for future studies of the genomic and developmental basis, and the predictability, of the crab-like body form.
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Affiliation(s)
- Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Javier Luque
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Smithsonian Tropical Research Institute, Balboa-Ancon, Panama.,Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, USA
| | - Heather D Bracken-Grissom
- Institute of Environment and Department of Biological Sciences, Florida International University, North Miami, Florida, USA
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11
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Toyota K, Miyakawa H, Hiruta C, Sato T, Katayama H, Ohira T, Iguchi T. Sex Determination and Differentiation in Decapod and Cladoceran Crustaceans: An Overview of Endocrine Regulation. Genes (Basel) 2021; 12:genes12020305. [PMID: 33669984 PMCID: PMC7924870 DOI: 10.3390/genes12020305] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
Mechanisms underlying sex determination and differentiation in animals are known to encompass a diverse array of molecular clues. Recent innovations in high-throughput sequencing and mass spectrometry technologies have been widely applied in non-model organisms without reference genomes. Crustaceans are no exception. They are particularly diverse among the Arthropoda and contain a wide variety of commercially important fishery species such as shrimps, lobsters and crabs (Order Decapoda), and keystone species of aquatic ecosystems such as water fleas (Order Branchiopoda). In terms of decapod sex determination and differentiation, previous approaches have attempted to elucidate their molecular components, to establish mono-sex breeding technology. Here, we overview reports describing the physiological functions of sex hormones regulating masculinization and feminization, and gene discovery by transcriptomics in decapod species. Moreover, this review summarizes the recent progresses of studies on the juvenile hormone-driven sex determination system of the branchiopod genus Daphnia, and then compares sex determination and endocrine systems between decapods and branchiopods. This review provides not only substantial insights for aquaculture research, but also the opportunity to re-organize the current and future trends of this field.
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Affiliation(s)
- Kenji Toyota
- Marine Biological Station, Sado Center for Ecological Sustainability, Niigata University, Sado, Niigata 952-2135, Japan
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa 259-1293, Japan;
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
- Correspondence: (K.T.); (T.S.); (T.I.)
| | - Hitoshi Miyakawa
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi 321-8505, Japan;
| | - Chizue Hiruta
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan;
| | - Tomomi Sato
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa 236-0027, Japan
- Correspondence: (K.T.); (T.S.); (T.I.)
| | - Hidekazu Katayama
- Department of Applied Biochemistry, School of Engineering, Tokai University, Kanagawa 259-1292, Japan;
| | - Tsuyoshi Ohira
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa 259-1293, Japan;
| | - Taisen Iguchi
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa 236-0027, Japan
- Correspondence: (K.T.); (T.S.); (T.I.)
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