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Duan Z, Wang J, Liu S, Xu Q, Chen H, Li C, Hui M, Chen N. Positive selection in cilia-related genes may facilitate deep-sea adaptation of Thermocollonia jamsteci. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175358. [PMID: 39127215 DOI: 10.1016/j.scitotenv.2024.175358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Deep-sea hydrothermal vents are characterized by high hydrostatic pressure, hypoxia, darkness and toxic substances. However, how organisms adapt to such extreme marine ecosystems remain poorly understood. We hypothesize that adaptive evolution plays an essential role in generating novelty for evolutionary adaptation to the deep-sea environment because adaptive evolution has been found to be critical for species origin and evolution. In this project, the chromosome-level genome of the deep-sea hydrothermal vent gastropod T. jamsteci was constructed for the first time to examine molecular mechanisms of its adaptation to the deep-sea environment. The genome size was large (2.54 Gb), ranking at the top of all species in the Vetigastropoda subclass, driven primarily by the bursts of transposable elements (TEs). The transposition of TEs may also trigger chromosomal changes including both inter-chromosomal fusions and intra-chromosomal activities involving chromosome inversions, rearrangements and fusions, as revealed by comparing the genomes of T. jamsteci and its closely related shallow-sea species Gibbula magus. Innovative changes including the expansion of the ABC transporter gene family that may facilitate detoxification, duplication of genes related to endocytosis, immunity, apoptosis, and anti-apoptotic domains that may help T. jamsteci fight against microbial pathogens, were identified. Furthermore, comparative analysis identified positive selection signals in a large number of genes including the hypoxia up-regulated protein 1, which is a chaperone that may promote adaptation of the T. jamsteci to hypoxic deepsea environments, hox2, Rx2, Pax6 and cilia-related genes BBS1, BBS2, BBS9 and RFX4. Notably, because of the critical importance of cilia and IFT in development, positive selection in cilia-related genes may play a critical role in facilitating T. jamsteci to adapt to the high-pressure deep-sea ecosystem. Results from this study thus revealed important molecular clues that may facilitate further research on the adaptation of molluscs to deep-sea hydrothermal vents.
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Affiliation(s)
- Zelin Duan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laoshan Laboratory, Qingdao 266237, China; Laboratory of Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jing Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shuya Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Qing Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; College of Basic Medical Sciences, China Three Gorges University, Yichang 443000, China
| | - Hao Chen
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chaolun Li
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Min Hui
- Laoshan Laboratory, Qingdao 266237, China; Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laoshan Laboratory, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; College of Basic Medical Sciences, China Three Gorges University, Yichang 443000, China.
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2
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Yan C, Wu Z, Liu Y, Sun Y, Zhang J. Comparative transcriptomic analysis primarily explores the molecular mechanism of compound eye formation in Neocaridina denticulata sinensis. BMC Genomics 2024; 25:570. [PMID: 38844864 PMCID: PMC11155044 DOI: 10.1186/s12864-024-10453-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/24/2024] [Indexed: 06/10/2024] Open
Abstract
Compound eyes formation in decapod crustaceans occurs after the nauplius stage. However, the key genes and regulatory mechanisms of compound eye development during crustacean embryonic development have not yet been clarified. In this study, RNA-seq was used to investigate the gene expression profiles of Neocaridina denticulata sinensis from nauplius to zoea stage. Based on RNA-seq data analysis, the phototransduction and insect hormone biosynthesis pathways were enriched, and molting-related neuropeptides were highly expressed. There was strong cell proliferation in the embryo prior to compound eye development. The formation of the visual system and the hormonal regulation of hatching were the dominant biological events during compound eye development. The functional analysis of DEGs across all four developmental stages showed that cuticle formation, muscle growth and the establishment of immune system occurred from nauplius to zoea stage. Key genes related to eye development were discovered, including those involved in the determination and differentiation of the eye field, eye-color formation, and visual signal transduction. In conclusion, the results increase the understanding of the molecular mechanism of eye formation in crustacean embryonic stage.
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Affiliation(s)
- Congcong Yan
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding, 071002, China
- Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Zixuan Wu
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding, 071002, China
| | - Yujie Liu
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding, 071002, China
| | - Yuying Sun
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding, 071002, China.
- Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.
| | - Jiquan Zhang
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding, 071002, China.
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3
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Wang J, Lv J, Shi M, Ge Q, Wang Q, He Y, Li J, Li J. Chromosome-level genome assembly of ridgetail white shrimp Exopalaemon carinicauda. Sci Data 2024; 11:576. [PMID: 38834644 DOI: 10.1038/s41597-024-03423-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024] Open
Abstract
Exopalaemon carinicauda, a eurythermal and euryhaline shrimp, contributes one third of the total biomass production of polyculture ponds in eastern China and is considered as a potential ideal experimental animal for research on crustaceans. We conducted a high-quality chromosome-level genome assembly of E. carinicauda combining PacBio HiFi and Hi-C sequencing data. The total assembly size was 5.86 Gb, with a contig N50 of 235.52 kb and a scaffold N50 of 138.24 Mb. Approximately 95.29% of the assembled sequences were anchored onto 45 pseudochromosomes. BUSCO analysis revealed that 92.89% of 1,013 single-copy genes were highly conserved orthologs. A total of 44, 288 protein-coding genes were predicted, of which 70.53% were functionally annotated. Given its high heterozygosity (2.62%) and large proportion of repeat sequences (71.49%), it is one of the most complex genome assemblies. This chromosome-scale genome will be a valuable resource for future molecular breeding and functional genomics research on E. carinicauda.
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Affiliation(s)
- Jiajia Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Jianjian Lv
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Miao Shi
- Berry Genomics Co., Ltd., Beijing, China
| | - Qianqian Ge
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Qiong Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Yuying He
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Jian Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Jitao Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China.
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Li W, Wang J, Li J, Liu P, Fei F, Liu B, Li J. The effect of astaxanthin on the alkalinity stress resistance of Exopalaemon carinicauda. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170415. [PMID: 38278276 DOI: 10.1016/j.scitotenv.2024.170415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Astaxanthin (Axn), a feed additive, can improve growth performance and enhance the environmental stress tolerance of shrimp at all growth stages. High carbonate alkalinity is considered a major stressor that affects the survival, growth, and reproduction of aquatic animals in saline-alkaline waters. In this study, a combined analysis of physiology, transcriptomics, and metabolomics was performed to explore the effected mechanism of Axn on Exopalaemon carinicauda (E. carinicauda) under alkalinity stress. The results revealed that dietary Axn can inhibit oxidative stress damage caused by alkalinity stress and maintain the normal cell structure and mitochondrial membrane potential. Transcriptomic data indicated that differentially expressed genes (DEGs) under alkalinity stress and those under alkalinity stress after Axn feeding were associated with apoptosis. The metabolic data suggested that alkalinity stress has adverse effects on ammonia metabolism, unsaturated fatty acid metabolism, and TCA cycle, and dietary Axn can improve the metabolic processes in E. carinicauda. In addition, transcriptomics and metabolomics analyses showed that Axn could help maintain the cytoskeletal structure and inhibit apoptosis under alkalinity stress; a TUNEL assay further confirmed these effects. Lastly, metabolic responses to alkalinity stress included changes in multiple amino acids and unsaturated fatty acids, and pathways related to energy metabolism were downregulated in the hepatopancreas of E. carinicauda under alkalinity stress. Collectively, all these results provide new insights into the molecular mechanisms underlying alkalinity stress tolerance in E. carinicauda after Axn feeding.
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Affiliation(s)
- Wenyang Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Jiajia Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Jitao Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Ping Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Fan Fei
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Baoliang Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Jian Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China.
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Wang J, Tang S, Ge Q, Wang Q, He Y, Ren X, Li J, Li J. Genome-Wide Identification of Vitellogenin Gene Family and Comparative Analysis of Their Involvement in Ovarian Maturation in Exopalaemon carinicauda. Int J Mol Sci 2024; 25:1089. [PMID: 38256163 PMCID: PMC10815947 DOI: 10.3390/ijms25021089] [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: 11/21/2023] [Revised: 12/29/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Vitellogenin (Vtg) is a precursor of yolk proteins in egg-laying vertebrates and invertebrates and plays an important role in vitellogenesis and embryonic development. However, the Vtg family remains poorly characterized in Exopalaemon carinicauda, a major commercial mariculture species found along the coasts of the Yellow and Bohai Seas. In this study, 10 Vtg genes from the genomes of E. carinicauda were identified and characterized. Phylogenetic analyses showed that the Vtg genes in crustaceans could be classified into four groups: Astacidea, Brachyra, Penaeidae, and Palaemonidae. EcVtg genes were unevenly distributed on the chromosomes of E. carinicauda, and a molecular evolutionary analysis showed that the EcVtg genes were primarily constrained by purifying selection during evolution. All putative EcVtg proteins were characterized by the presence of three conserved functional domains: a lipoprotein N-terminal domain (LPD_N), a domain of unknown function (DUF1943), and a von Willebrand factor type D domain (vWD). All EcVtg genes exhibited higher expression in the female hepatopancreas than in other tissues, and EcVtg gene expression during ovarian development suggested that the hepatopancreas is the main synthesis site in E. carinicauda. EcVtg1a, EcVtg2, and EcVtg3 play major roles in exogenous vitellogenesis, and EcVtg3 also plays a major role in endogenous vitellogenesis. Bilateral ablation of the eyestalk significantly upregulates EcVtg mRNA expression in the female hepatopancreas, indicating that the X-organ/sinus gland complex plays an important role in ovarian development, mostly by inducing Vtg synthesis. These results could improve our understanding of the function of multiple Vtg genes in crustaceans and aid future studies on the function of EcVtg genes during ovarian development in 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 266071, China; (J.W.); (S.T.); (Q.W.); (Y.H.); (X.R.); (J.L.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China;
| | - Shuai Tang
- 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 266071, China; (J.W.); (S.T.); (Q.W.); (Y.H.); (X.R.); (J.L.)
| | - Qianqian Ge
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China;
| | - Qiong 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 266071, China; (J.W.); (S.T.); (Q.W.); (Y.H.); (X.R.); (J.L.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China;
| | - Yuying He
- 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 266071, China; (J.W.); (S.T.); (Q.W.); (Y.H.); (X.R.); (J.L.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China;
| | - Xianyun Ren
- 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 266071, China; (J.W.); (S.T.); (Q.W.); (Y.H.); (X.R.); (J.L.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, 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 266071, China; (J.W.); (S.T.); (Q.W.); (Y.H.); (X.R.); (J.L.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, 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 266071, China; (J.W.); (S.T.); (Q.W.); (Y.H.); (X.R.); (J.L.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China;
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Miao M, Li S, Yuan J, Liu P, Fang X, Zhang C, Zhang X, Li F. CRISPR/Cas9-mediated gene mutation of EcIAG leads to sex reversal in the male ridgetail white prawn Exopalaemon carinicauda. Front Endocrinol (Lausanne) 2023; 14:1266641. [PMID: 38075036 PMCID: PMC10703455 DOI: 10.3389/fendo.2023.1266641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
In the culture of crustaceans, most species show sexual dimorphism. Monosex culture is an effective approach to achieve high yield and economic value, especially for decapods of high value. Previous studies have developed some sex control strategies such as manual segregation, manipulation of male androgenic gland and knockdown of the male sexual differentiation switch gene encoding insulin-like androgenic gland hormone (IAG) in decapods. However, these methods could not generate hereditable changes. Genetic manipulation to achieve sex reversal individuals is absent up to now. In the present study, the gene encoding IAG (EcIAG) was identified in the ridgetail white prawn Exopalaemon carinicauda. Sequence analysis showed that EcIAG encoded conserved amino acid structure like IAGs in other decapod species. CRISPR/Cas9-mediated genome editing technology was used to knock out EcIAG. Two sgRNAs targeting the second exon of EcIAG were designed and microinjected into the prawn zygotes or the embryos at the first cleavage with commercial Cas9 protein. EcIAG in three genetic males was knocked out in both chromosome sets, which successfully generated sex reversal and phenotypic female characters. The results suggest that CRISPR/Cas9-mediated genome editing technology is an effective way to develop sex manipulation technology and contribute to monosex aquaculture in crustaceans.
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Affiliation(s)
- Miao Miao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Peipei Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaochen Fang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chengsong Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, China
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7
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Shi XZ, Yang MC, Kang XL, Li YX, Hong PP, Zhao XF, Vasta G, Wang JX. Scavenger receptor B2, a type III membrane pattern recognition receptor, senses LPS and activates the IMD pathway in crustaceans. Proc Natl Acad Sci U S A 2023; 120:e2216574120. [PMID: 37276415 PMCID: PMC10268257 DOI: 10.1073/pnas.2216574120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/24/2023] [Indexed: 06/07/2023] Open
Abstract
The immune deficiency (IMD) pathway is critical for elevating host immunity in both insects and crustaceans. The IMD pathway activation in insects is mediated by peptidoglycan recognition proteins, which do not exist in crustaceans, suggesting a previously unidentified mechanism involved in crustacean IMD pathway activation. In this study, we identified a Marsupenaeus japonicus B class type III scavenger receptor, SRB2, as a receptor for activation of the IMD pathway. SRB2 is up-regulated upon bacterial challenge, while its depletion exacerbates bacterial proliferation and shrimp mortality via abolishing the expression of antimicrobial peptides. The extracellular domain of SRB2 recognizes bacterial lipopolysaccharide (LPS), while its C-terminal intracellular region containing a cryptic RHIM-like motif interacts with IMD, and activates the pathway by promoting nuclear translocation of RELISH. Overexpressing shrimp SRB2 in Drosophila melanogaster S2 cells potentiates LPS-induced IMD pathway activation and diptericin expression. These results unveil a previously unrecognized SRB2-IMD axis responsible for antimicrobial peptide induction and restriction of bacterial infection in crustaceans and provide evidence of biological diversity of IMD signaling in animals. A better understanding of the innate immunity of crustaceans will permit the optimization of prevention and treatment strategies against the arising shrimp diseases.
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Affiliation(s)
- Xiu-Zhen Shi
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, 266237, Qingdao, Shandong, China
| | - Ming-Chong Yang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, 266237, Qingdao, Shandong, China
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, China
| | - Xin-Le Kang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, 266237, Qingdao, Shandong, China
| | - Yan-Xue Li
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, 266237, Qingdao, Shandong, China
| | - Pan-Pan Hong
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, 266237, Qingdao, Shandong, China
| | - Xiao-Fan Zhao
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, 266237, Qingdao, Shandong, China
| | - Gerardo R. Vasta
- Department of Microbiology and Immunology, School of Medicine, Institute of Marine and Environmental Technology, University of Maryland Baltimore, Baltimore, MD21202
| | - Jin-Xing Wang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, 266237, Qingdao, Shandong, China
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, China
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8
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Gao Y, Zhang X, Yuan J, Zhang C, Li S, Li F. CRISPR/Cas9-mediated mutation on an insulin-like peptide encoding gene affects the growth of the ridgetail white prawn Exopalaemon carinicauda. Front Endocrinol (Lausanne) 2022; 13:986491. [PMID: 36246877 PMCID: PMC9556898 DOI: 10.3389/fendo.2022.986491] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/15/2022] [Indexed: 11/25/2022] Open
Abstract
Insulin-like peptides (ILPs) play key roles in animal growth, metabolism and reproduction in vertebrates. In crustaceans, one type of ILPs, insulin-like androgenic gland hormone (IAG) had been reported to be related to the sex differentiations. However, the function of other types of ILPs is rarely reported. Here, we identified another type of ILPs in the ridgetail white prawn Exopalaemon carinicauda (EcILP), which is an ortholog of Drosophila melanogaster ILP7. Sequence characterization and expression analyses showed that EcILP is similar to vertebrate insulin/IGFs and insect ILPs in its heterodimeric structure and expression profile. Using CRISPR/Cas9 genome editing technology, we generated EcILP knockout (KO) prawns. EcILP-KO individuals have a significant higher growth-inhibitory trait and mortality than those in the normal group. In addition, knockdown of EcILP by RNA interference (RNAi) resulted in slower growth rate and higher mortality. These results indicated that EcILP was an important growth regulator in E. carinicauda.
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Affiliation(s)
- Yi Gao
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Xiaojun Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jianbo Yuan
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Chengsong Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shihao Li
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Fuhua Li
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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9
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Zhou Y, Song Q, Liu Y, Sun Y, Zhang J. A novel type I Crustin from Exopalaemon carinicauda: Antimicrobial ability related to conserved cysteine. FISH & SHELLFISH IMMUNOLOGY 2022; 127:948-955. [PMID: 35661815 DOI: 10.1016/j.fsi.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Crustins are a kind of antibacterial peptides (AMP) existing in crustaceans, and their antibacterial abilities are considered to be related to the conserved WAP domain. In this study, a novel type I Crustin gene was identified in Exopalaemon carinicauda, named EcCru. The deduced amino acid sequence revealed that the conserved cysteine at position 7 in the WAP domain was replaced by aspartic acid. The gene is 405 bp in length, encoding 134 amino acids, and is mainly distributed in gills and hepatopancreas. After Vibrio parahaemolyticus and Aeromonas hydrophila stimulation, the expression of EcCru was significantly up-regulated within 12 h, and then returned to normal levels. The recombinant protein was obtained using the Pichia pastoris expression system, and the recombinant protein had neither antibacterial activity against gram-positive or gram-negative bacteria. But the antibacterial ability emerged when Asp101 was mutated to Cys. Notably, we also obtained a mutant that had a deletion at the 6 th conserved Cys in the WAP domain, and this mutant had antibacterial ability against gram-positive bacteria Bacillus subtilis and B. cereus. This indicates that the conserved cysteine with different positions in WAP domain can have different effects on the antibacterial ability of Crustins.
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Affiliation(s)
- Yongzhao Zhou
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Qinghua Song
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China; Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Hebei University, Baoding, 071002, China
| | - Yujie Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Yuying Sun
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China; Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Hebei University, Baoding, 071002, China.
| | - Jiquan Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China.
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10
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Jaramillo ML, Ammar D, Quispe RL, Bonatto Paese CL, Gruendling AP, Müller YM, Nazari EM. Identification of Hox genes and their expression profiles during embryonic development of the emerging model organism, Macrobrachium olfersii. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:292-300. [PMID: 35037742 DOI: 10.1002/jez.b.23118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/13/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
Hox genes encode transcription factors that specify the body segment identity during development, including crustaceans, such as amphipods and decapods, that possess a remarkable diversity of segments and specialized appendages. In amphipods, alterations of specialized appendages have been obtained using knockout experiment of Hox genes, which suggests that these genes are involved in the evolution of morphology within crustaceans. However, studies of Hox genes in crustaceans have been limited to a few species. Here, we identified the homeodomain of nine Hox genes: labial (lab), proboscipedia (pb), Deformed (Dfd), Sex combs reduced (Scr), fushi tarazu (ftz), Antennapedia (Antp), Ultrabithorax (Ubx), abdominal-A (abdA), and Abdominal-B (AbdB), and evaluated their expression by RT-qPCR and RT-PCR in the ovary, during embryonic development, and at the first larval stage (Zoea I) of the decapod Macrobrachium olfersii. The transcript levels of lab, Dfd, and ftz decreased and transcripts of pb, Scr, Antp, Ubx, abdA, and AbdB increased during embryonic development. Hox genes were expressed in mature ovaries and Zoea I larval stages, except Scr and ftz, respectively. In addition, isoforms of Dfd, Scr, Ubx, and abdA, which have been scarcely reported in crustaceans, were described. New partial sequences of 87 Hox genes from other crustaceans were identified from the GenBank database. Our results are interesting for future studies to determine the specific function of Hox genes and their isoforms in the freshwater prawn M. olfersii and to contribute to the understanding of the diversity and evolution of body plans and appendages in Crustaceans.
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Affiliation(s)
- Michael L Jaramillo
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Dib Ammar
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Ruth L Quispe
- Departamento de Bioquímica, Campus Universitário, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Christian L Bonatto Paese
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Ana P Gruendling
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Yara M Müller
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Evelise M Nazari
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
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11
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Schultz JA, Hebert PDN. Do pseudogenes pose a problem for metabarcoding marine animal communities? Mol Ecol Resour 2022; 22:2897-2914. [PMID: 35700118 DOI: 10.1111/1755-0998.13667] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 06/01/2022] [Indexed: 11/30/2022]
Abstract
Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658 bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. NUMTs were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 309 NUMTs ≥ 150 bp were detected, with an average of 1.98 per species (range = 0-33) and a mean length of 391 bp ± 200 bp. Among this total, 75 (24.3 %) lacked indels or stop codons. NUMTs appear to pose the greatest interpretational risk when short (< 313 bp) amplicons are used, such as in eDNA studies, dietary analyses, or processed fish identification. Employing the standard amplicon length (313 bp) for marine metabarcoding, NUMTs could potentially inflate the OTU count by 21% above the true species count while also raising intraspecific variation at COI by 15%. However, when both amplicon length and position are considered, inflation in OTU counts and in barcode variation were just 9% and 10%, respectively, suggesting NUMTs will not seriously distort biodiversity assessments. There was a weak positive correlation between genome size and NUMT count but no variation among phyla or trophic groups. Until bioinformatic advances improve NUMT detection, the best defense involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives.
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Affiliation(s)
- Jessica A Schultz
- Department of Integrative Biology, University of Guelph, Guelph, ON, CANADA.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, CANADA
| | - Paul D N Hebert
- Department of Integrative Biology, University of Guelph, Guelph, ON, CANADA.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, CANADA
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12
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Liu Y, Wu Z, Guo K, Zhou Y, Xing K, Zheng J, Sun Y, Zhang J. Metallothionein-1 gene from Exopalaemon carinicauda and its response to heavy metal ions challenge. MARINE POLLUTION BULLETIN 2022; 175:113324. [PMID: 35051848 DOI: 10.1016/j.marpolbul.2022.113324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 12/09/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Metallothioneins (MTs) belong to a conserved low-molecular-weight protein family that participates in heavy metal binding and detoxification. EcMT-1 was amplified by PCR from genomic DNA of Exopalaenon carinicauda. It contained a 180 bp open reading frame and encoded 59 amino acids. A total of 18 cysteine (Cys) residues were found in the deduced amino acid sequence, which was consistent with the Cys-rich characteristics of MTs. EcMT-1 was mainly expressed in hepatopancreas, followed by stomach and gill. The expression profiles of EcMT-1 indicated that EcMT-1 was significantly increased at 24, 48 h and 12, 24, and 48 h under the treatment of 2.5 μmol/L CdCl2 and 50 μmol/L CuSO4. The expression of EcMT-1 at gastrula stage was very low; it was detectable until nauplius stage, and the highest expression level appeared in the postlarvae stage.
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Affiliation(s)
- Yujie Liu
- School of Life Sciences, Institute of Life and Green Development, Hebei University, Baoding 071002, China
| | - Zixuan Wu
- School of Life Sciences, Institute of Life and Green Development, Hebei University, Baoding 071002, China
| | - Kun Guo
- School of Life Sciences, Institute of Life and Green Development, Hebei University, Baoding 071002, China
| | - Yongzhao Zhou
- School of Life Sciences, Institute of Life and Green Development, Hebei University, Baoding 071002, China
| | - Kefan Xing
- School of Life Sciences, Institute of Life and Green Development, Hebei University, Baoding 071002, China
| | - Jiaqi Zheng
- School of Life Sciences, Institute of Life and Green Development, Hebei University, Baoding 071002, China
| | - Yuying Sun
- School of Life Sciences, Institute of Life and Green Development, Hebei University, Baoding 071002, China.
| | - Jiquan Zhang
- School of Life Sciences, Institute of Life and Green Development, Hebei University, Baoding 071002, China.
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13
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Uengwetwanit T, Pootakham W, Nookaew I, Sonthirod C, Angthong P, Sittikankaew K, Rungrassamee W, Arayamethakorn S, Wongsurawat T, Jenjaroenpun P, Sangsrakru D, Leelatanawit R, Khudet J, Koehorst JJ, Schaap PJ, Martins dos Santos V, Tangy F, Karoonuthaisiri N. A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes. Mol Ecol Resour 2021; 21:1620-1640. [PMID: 33586292 PMCID: PMC8197738 DOI: 10.1111/1755-0998.13357] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 01/31/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022]
Abstract
To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.
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Affiliation(s)
- Tanaporn Uengwetwanit
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Wirulda Pootakham
- National Omics CenterNational Science and Technology Development AgencyPathum ThaniThailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Chutima Sonthirod
- National Omics CenterNational Science and Technology Development AgencyPathum ThaniThailand
| | - Pacharaporn Angthong
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Kanchana Sittikankaew
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Wanilada Rungrassamee
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Sopacha Arayamethakorn
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
- Division of Bioinformatics and Data Management for ResearchDepartment of Research and DevelopmentFaculty of MedicineSiriraj HospitalMahidol UniversityBangkokThailand
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
- Division of Bioinformatics and Data Management for ResearchDepartment of Research and DevelopmentFaculty of MedicineSiriraj HospitalMahidol UniversityBangkokThailand
| | - Duangjai Sangsrakru
- National Omics CenterNational Science and Technology Development AgencyPathum ThaniThailand
| | - Rungnapa Leelatanawit
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Jutatip Khudet
- Shrimp Genetic Improvement CenterIntegrative Aquaculture Biotechnology Research GroupSurat ThaniThailand
| | - Jasper J. Koehorst
- Laboratory of Systems and Synthetic BiologyDepartment of Agrotechnology and Food SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic BiologyDepartment of Agrotechnology and Food SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Vitor Martins dos Santos
- Laboratory of Systems and Synthetic BiologyDepartment of Agrotechnology and Food SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Frédéric Tangy
- Viral Genomics and Vaccination UnitUMR3569 CNRSVirology DepartmentInstitut PasteurParisFrance
| | - Nitsara Karoonuthaisiri
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
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14
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Catalán-García M, Chauvigné F, Stavang JA, Nilsen F, Cerdà J, Finn RN. Lineage-level divergence of copepod glycerol transporters and the emergence of isoform-specific trafficking regulation. Commun Biol 2021; 4:643. [PMID: 34059783 PMCID: PMC8167128 DOI: 10.1038/s42003-021-01921-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/26/2021] [Indexed: 02/04/2023] Open
Abstract
Transmembrane conductance of small uncharged solutes such as glycerol typically occurs through aquaglyceroporins (Glps), which are commonly encoded by multiple genes in metazoan organisms. To date, however, little is known concerning the evolution of Glps in Crustacea or what forces might underly such apparent gene redundancy. Here, we show that Glp evolution in Crustacea is highly divergent, ranging from single copy genes in species of pedunculate barnacles, tadpole shrimps, isopods, amphipods and decapods to up to 10 copies in diplostracan water fleas although with monophyletic origins in each lineage. By contrast the evolution of Glps in Copepoda appears to be polyphyletic, with surprisingly high rates of gene duplication occurring in a genera- and species-specific manner. Based upon functional experiments on the Glps from a parasitic copepod (Lepeophtheirus salmonis), we show that such lineage-level gene duplication and splice variation is coupled with a high rate of neofunctionalization. In the case of L. salmonis, splice variation of a given gene resulted in tissue- or sex-specific expression of the channels, with each variant evolving unique sites for protein kinase C (PKC)- or protein kinase A (PKA)-regulation of intracellular membrane trafficking. The combined data sets thus reveal that mutations favouring a high fidelity control of intracellular trafficking regulation can be a selection force for the evolution and retention of multiple Glps in copepods.
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Affiliation(s)
- Marc Catalán-García
- Department of Biological Sciences, Bergen High Technology Centre, University of Bergen, Bergen, Norway
- IRTA-Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain
| | - François Chauvigné
- IRTA-Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain
| | - Jon Anders Stavang
- Department of Biological Sciences, Bergen High Technology Centre, University of Bergen, Bergen, Norway
| | - Frank Nilsen
- Department of Biological Sciences, Bergen High Technology Centre, University of Bergen, Bergen, Norway
| | - Joan Cerdà
- IRTA-Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain.
| | - Roderick Nigel Finn
- Department of Biological Sciences, Bergen High Technology Centre, University of Bergen, Bergen, Norway.
- IRTA-Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain.
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15
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A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni. Genes (Basel) 2021; 12:genes12030401. [PMID: 33799706 PMCID: PMC7998251 DOI: 10.3390/genes12030401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/02/2021] [Accepted: 03/06/2021] [Indexed: 11/17/2022] Open
Abstract
How asexual reproduction shapes transposable element (TE) content and diversity in eukaryotic genomes remains debated. We performed an initial survey of TE load and diversity in the putative ancient asexual ostracod Darwinula stevensoni. We examined long contiguous stretches of DNA in clones from a genomic fosmid library, totaling about 2.5 Mb, and supplemented these data with results on TE abundance and diversity from an Illumina draft genome. In contrast to other TE studies in putatively ancient asexuals, which revealed relatively low TE content, we found that at least 19% of the fosmid dataset and 26% of the genome assembly corresponded to known transposons. We observed a high diversity of transposon families, including LINE, gypsy, PLE, mariner/Tc, hAT, CMC, Sola2, Ginger, Merlin, Harbinger, MITEs and helitrons, with the prevalence of DNA transposons. The predominantly low levels of sequence diversity indicate that many TEs are or have recently been active. In the fosmid data, no correlation was found between telomeric repeats and non-LTR retrotransposons, which are present near telomeres in other taxa. Most TEs in the fosmid data were located outside of introns and almost none were found in exons. We also report an N-terminal Myb/SANT-like DNA-binding domain in site-specific R4/Dong non-LTR retrotransposons. Although initial results on transposable loads need to be verified with high quality draft genomes, this study provides important first insights into TE dynamics in putative ancient asexual ostracods.
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16
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Wu Z, Liu Y, Zheng J, Zhou Y, Xing K, Sun Y, Zhang J. Genomic structure, expression and functional characterization of arginine kinase (EcAK) from Exopalaemon carinicauda. FISH & SHELLFISH IMMUNOLOGY 2021; 109:82-86. [PMID: 33352337 DOI: 10.1016/j.fsi.2020.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/10/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Arginine kinase (AK, EC 2.7.3.3) plays an important role in cells with high, fluctuating energy requirements. In invertebrates, AK is the major phosphagen kinase that modulates the energy metabolism. Here, the full-length cDNA sequence encoding arginine kinase (EcAK) was obtained from the Exopalaemon carinicauda. The complete nucleotide sequence of EcAK contained a 1068 bp open reading frame (ORF) encoding EcAK precursor of 355 amino acids. The genomic DNA fragment of EcAK with the corresponding cDNA sequence is composed of 4 exons and 3 introns. The domain architecture of the deduced EcAK protein contained an ATP-gua_PtransN domain and an ATP-gua_Ptrans domain. EcAK mRNA was predominantly expressed in the muscle. The expression of EcAK in the prawns challenged with Vibrio parahaemolyticus and Aeromonas hydrophila changed in a time-dependent manner. Then, EcAK was recombinantly expressed in Pichia pastoris and the purified recombinant EcAK had the same enzymatic characterization as AK from the muscle of Euphausia superba. In conclusion, EcAK may play the same biological activity in E. carinicauda as those from other crustaceans.
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Affiliation(s)
- Zixuan Wu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, China
| | - Yujie Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, China
| | - Jiaqi Zheng
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, China
| | - Yongzhao Zhou
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, China
| | - Kefan Xing
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, China
| | - Yuying Sun
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, China.
| | - Jiquan Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, China.
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17
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Jin S, Bian C, Jiang S, Han K, Xiong Y, Zhang W, Shi C, Qiao H, Gao Z, Li R, Huang Y, Gong Y, You X, Fan G, Shi Q, Fu H. A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense. Gigascience 2021; 10:giaa160. [PMID: 33459341 PMCID: PMC7812440 DOI: 10.1093/gigascience/giaa160] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/01/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The oriental river prawn, Macrobrachium nipponense, is an economically important shrimp in China. Male prawns have higher commercial value than females because the former grow faster and reach larger sizes. It is therefore important to reveal sex-differentiation and development mechanisms of the oriental river prawn to enable genetic improvement. RESULTS We sequenced 293.3 Gb of raw Illumina short reads and 405.7 Gb of Pacific Biosciences long reads. The final whole-genome assembly of the Oriental river prawn was ∼4.5 Gb in size, with predictions of 44,086 protein-coding genes. A total of 49 chromosomes were determined, with an anchor ratio of 94.7% and a scaffold N50 of 86.8 Mb. A whole-genome duplication event was deduced to have happened 109.8 million years ago. By integration of genome and transcriptome data, 21 genes were predicted as sex-related candidate genes. CONCLUSION The first high-quality chromosome-level genome assembly of the oriental river prawn was obtained. These genomic data, along with transcriptome sequences, are essential for understanding sex-differentiation and development mechanisms in the oriental river prawn, as well as providing genetic resources for in-depth studies on developmental and evolutionary biology in arthropods.
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Affiliation(s)
- Shubo Jin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Sufei Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Kai Han
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Yiwei Xiong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Wenyi Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | | | - Hui Qiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Zijian Gao
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Ruihan Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Yongsheng Gong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Hongtuo Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
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18
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Veenstra JA. Gonadulins, the fourth type of insulin-related peptides in decapods. Gen Comp Endocrinol 2020; 296:113528. [PMID: 32526328 DOI: 10.1016/j.ygcen.2020.113528] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/04/2020] [Accepted: 06/03/2020] [Indexed: 12/30/2022]
Abstract
Insulin and related peptides play important roles in the regulation of growth and reproduction. Until recently three different types of insulin-related peptides had been identified from decapod crustaceans. The identification of two novel insulin-related peptides from Sagmariasus verreauxi and Cherax quadricarinatus suggested that there might a fourth type. Publicly available short read archives show that orthologs of these peptides are commonly present in these animals. Most decapods have two genes coding such peptides, but Penaeus species have likely only one and some palaemonids have three. Interestingly, expression levels can vary more than thousand-fold in the gonads of Portunus trituberculatus, where gonadulin 1 is expressed by the testis and gonadulin 2 by the ovary. Although these peptides are also expressed in other tissues, the occasionally very high expression in the gonads led to them being called gonadulins.
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Affiliation(s)
- Jan A Veenstra
- INCIA UMR 5287 CNRS, University of Bordeaux, Pessac, France.
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19
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Gao Y, Zhang X, Zhang X, Yuan J, Xiang J, Li F. CRISPR/Cas9-mediated mutation reveals Pax6 is essential for development of the compound eye in Decapoda Exopalaemon carinicauda. Dev Biol 2020; 465:157-167. [PMID: 32702356 DOI: 10.1016/j.ydbio.2020.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 12/01/2022]
Abstract
The compound eye in crustaceans is a main eye type in the animal kingdom, knowledge about the mechanism to determine the development of compound eye is very limited. Paired box protein 6 (Pax6) is generally regarded as a master regulator for eye development. In the present study, a genome-based analysis of the Pax6 gene in the ridge tail white prawn Exopalaemon carinicauda was performed and two members of Pax6 homologs, named Ec-Eyeless (EcEy) and Ec-Twin of eyeless (EcToy) were identified. To understand the function of these two homologs of Pax6 gene in the prawn, the CRISPR/Cas9 genome editing technique was applied to generate EcEy and EcToy knock-out (KO) prawns and their phenotypes were analyzed. The surviving EcEy-KO embryos and larvae exhibited severe abnormal eye morphology, suggesting that EcEy is necessary for the compound eye development in prawn, while no mutant phenotype was found in EcToy-KO individuals. These findings highlighted the conservative role of Pax6 gene in the compound eye formation, and the functional differentiation between EcEy and EcToy gene may reveal a novel regulating mechanism of Pax6 on the compound eye development in the decapods. These data will provide important information for understanding the regulation mechanism for crustacean compound eye development.
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Affiliation(s)
- Yi Gao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiaoxi Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jianbo Yuan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266237, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
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20
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Ovarian development pattern and vitellogenesis of ridgetail white prawn, Exopalaemon carinicauda. Cell Tissue Res 2020; 382:367-379. [PMID: 32556723 DOI: 10.1007/s00441-020-03223-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/24/2020] [Indexed: 10/24/2022]
Abstract
The ridgetail white prawn Exopalaemon carinicauda has the potential to be used as a model organism in crustacean research because it has a transparent body, available draft genome, and short life cycle. However, their ovarian development pattern remains unclear under laboratory culture conditions. This study investigated the changes of ovarian external feature, ovarian histology, gonadosomatic index (GSI), and hepatosomatic index (HSI), as well as the expression and localization of vitellogenin in the ovary and the hepatopancreas during the first ovarian development cycle of E. carinicauda under laboratory-reared condition. The results demonstrated that (1) the first ovarian development cycle of E. carinicauda could be divided into 5 different stages in which the ovary changes its color from white to yellow during the vitellogenesis process in parallel with increasing GSI. (2) After pubertal molt, most females reached ovarian stage II while the females reached stage V after premating molt. (3) During the ovarian development, GSI increased smoothly and HSI relatively stable during the period of stages I to IV, while GSI increased but HSI decreased significantly from stages IV to V. (4) In situ hybridization (ISH) revealed that EcVg was slightly expressed in the oocyte cytoplasm of previtellogenic oocytes. The positive signal was mainly detected in hepatopancreatic fibrillar cells, and a strong signal was found in the hepatopancreas at stage IV. Moreover, the expression level of EcVg-mRNA in the hepatopancreas is stage-specific, and the hepatopancreas contributes majority of vitellin precursor protein to support the ovarian development of E. carinicauda.
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21
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Sun Y, Liu M, Yan C, Yang H, Wu Z, Liu Y, Su N, Hou J, Zhang J, Yang F, Zhang J. CRISPR/Cas9-mediated deletion of β, β-carotene 9', 10'-oxygenase gene (EcBCO2) from Exopalaemon carinicauda. Int J Biol Macromol 2020; 151:168-177. [PMID: 32057858 DOI: 10.1016/j.ijbiomac.2020.02.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/01/2020] [Accepted: 02/09/2020] [Indexed: 01/16/2023]
Abstract
CRISPR/Cas9 technology is an efficient genome editing tool for producing genetically modified animals. Carotenoids color the world around us and their accumulation in animals could be used to culture colorful new verities in animal breeding. β, β-carotene 9', 10'-oxygenase (BCO2) is an important enzyme during β-carotene metabolism. In this research, one full-length cDNA sequence encoding BCO2 (named EcBCO2) were obtained from Exopalaemon carinicauda. The genomic structure analysis showed that EcBCO2 gene was composed of 9 exons and 8 introns. Then, the CRISPR/Cas9-mediated deletion of EcBCO2 gene was generated by co-microinjection of Cas9 mRNA and EcBCO2 sgRNA into one-cell stage embryos of E. carinicauda. Subsequently, the phenotype of EcBCO2-KO prawns was compared with that of wild-type prawns, which showed that EcBCO2-KO resulted in the color change in the hepatopancreas of prawns. In addition, the EcBCO2-KO prawns had a higher survival rate than wild-type prawns when the prawns were challenged with Vibrio parahaemolyticus or Aeromonas hydrophila. These results indicate that BCO2 gene could be used as a candidate gene in molecular marker-assistant breeding of prawns.
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Affiliation(s)
- Yuying Sun
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Mengfei Liu
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Congcong Yan
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Hao Yang
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Zixuan Wu
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Yujie Liu
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Naike Su
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Jiale Hou
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Jiahao Zhang
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Fusheng Yang
- Xiaoshan Donghai Aquaculture Co., Ltd, Xiaoshan 310012, China
| | - Jiquan Zhang
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China; Xiaoshan Donghai Aquaculture Co., Ltd, Xiaoshan 310012, China.
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22
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Molina WF, Costa GWWF, Cunha IMC, Bertollo LAC, Ezaz T, Liehr T, Cioffi MB. Molecular Cytogenetic Analysis in Freshwater Prawns of the Genus Macrobrachium (Crustacea: Decapoda: Palaemonidae). Int J Mol Sci 2020; 21:ijms21072599. [PMID: 32283616 PMCID: PMC7178241 DOI: 10.3390/ijms21072599] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 01/18/2023] Open
Abstract
Freshwater prawns of the genus Macrobrachium are one of the important components of circumtropical marine, estuarine, and freshwater environments. They have been extensively exploited for human consumption for many years. More than 250 species reflect the evolutionary success of this highly diversified group, with a complex and challenging taxonomy due to morphological variations and vast geographical distribution. Although genetic approaches have been used to clarify phylogenetic and taxonomic aspects of Macrobrachium species, cytogenetic information is still very scarce and mostly focused on chromosome number and morphology. Here, we present chromosome data for three species from the Neotropical region, M. carcinus,M. acanthurus, and M. amazonicum, and one species from the Oriental region, M. rosenbergii. Using conventional cytogenetic approaches and chromosome mapping of repetitive DNAs by fluorescence in situ hybridization (FISH), we identified numerical diversification of the diploid set, within and between both zoogeographic regions. These included M. acanthurus and M. amazonicum sharing diploid chromosomes of 98, while M. carcinus has 94, and M. rosenbergii has 118 chromosomes. Argentophilic sites are also variable in number, but they occur in a much higher number than 18S rDNA, representing two to 10 sites within the study species. Microsatellites repeat motifs are also abundant in the chromosomes, with a co-localization and uniform distribution along the chromosome arms, but completely absent in the AT-rich centromeric regions. As a whole, our study suggests that the 2n divergence was followed by a considerable rDNA diversification. The abundance of the exceptional amount of microsatellite sequences in the chromosomes also suggests that they are essential components of the Macrobrachium genome and, therefore, maintained as a shared feature by the species, the reason for which is yet unknown.
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Affiliation(s)
- Wagner F. Molina
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59078970, Brazil; (W.F.M.); (G.W.W.F.C.); (I.M.C.C.)
| | - Gideão W. W. F. Costa
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59078970, Brazil; (W.F.M.); (G.W.W.F.C.); (I.M.C.C.)
| | - Inailson M. C. Cunha
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59078970, Brazil; (W.F.M.); (G.W.W.F.C.); (I.M.C.C.)
| | - Luiz A. C. Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP C.P. 676, Brazil; (L.A.C.B.); (M.B.C.)
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia;
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 7747 Jena, Germany
- Correspondence:
| | - Marcelo B. Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP C.P. 676, Brazil; (L.A.C.B.); (M.B.C.)
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23
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Van Quyen D, Gan HM, Lee YP, Nguyen DD, Nguyen TH, Tran XT, Nguyen VS, Khang DD, Austin CM. Improved genomic resources for the black tiger prawn (Penaeus monodon). Mar Genomics 2020; 52:100751. [PMID: 32033920 DOI: 10.1016/j.margen.2020.100751] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/24/2019] [Accepted: 01/03/2020] [Indexed: 12/20/2022]
Abstract
World production of farmed crustaceans was 7.8 million tons in 2016. While only making up approximately 10% of world aquaculture production, crustaceans are generally high-value species and can earn significant export income for producing countries. Viet Nam is a major seafood producing country earning USD 7.3 billion in 2016 in export income with shrimp as a major commodity. However, there is a general lack of genomic resources available for shrimp species, which is challenging to obtain due to the need to deal with large repetitive genomes, which characterize many decapod crustaceans. The first tiger prawn (P. monodon) genome assembly was assembled in 2016 using the standard Illumina PCR-based pair-end reads and a computationally-efficient but relatively suboptimal assembler, SOAPdenovo v2. As a result, the current P. monodon draft genome is highly fragmented (> 2 million scaffolds with N50 length of <1000 bp), exhibiting only moderate genome completeness (< 35% BUSCO complete single-copy genes). We sought to improve upon the recently published P. monodon genome assembly and completeness by generating Illumina PCR-free pair-end sequencing reads to eliminate genomic gaps associated with PCR-bias and performing de novo assembly using the updated MaSurCA de novo assembler. Furthermore, we scaffolded the assembly with low coverage Nanopore long reads and several recently published deep Illumina transcriptome paired-end sequencing data, producing a final genome assembly of 1.6 Gbp (1,211,364 scaffolds; N50 length of 1982 bp) with an Arthropod BUSCO completeness of 96.8%. Compared to the previously published P. monodon genome assembly from China (NCBI Accession Code: NIUS01), this represents an almost 20% increase in the overall BUSCO genome completeness that now consists of more than 90% of Arthropod BUSCO single-copy genes. The revised P. monodon genome assembly (NCBI Accession Code: VIGR01) will be a valuable resource to support ongoing functional genomics and molecular-based breeding studies in Vietnam.
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Affiliation(s)
- Dong Van Quyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam; University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia; Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia; Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Dinh Duy Nguyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Thi Hoa Nguyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Xuan Thach Tran
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Van Sang Nguyen
- Institute for Aquaculture No.2 (RIA2), 116 Nguyen Dinh Chieu St., Dist. 1, Ho Chi Minh City, Viet Nam
| | - Dinh Duy Khang
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam.
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia; Deakin Genomics Centre, Deakin University, Geelong, Australia.
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24
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Sun Y, Yan C, Liu M, Liu Y, Wang W, Cheng W, Yang F, Zhang J. CRISPR/Cas9-mediated deletion of one carotenoid isomerooxygenase gene (EcNinaB-X1) from Exopalaemon carinicauda. FISH & SHELLFISH IMMUNOLOGY 2020; 97:421-431. [PMID: 31846777 DOI: 10.1016/j.fsi.2019.12.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/09/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
During the immune defense reaction of invertebrate, a plenty of reactive oxygen species (ROS) could be induced to product. Though ROS can kill foreign invaders, the accumulation of these reactive molecules in animals will cause serious cell damage. Carotenoids could function as scavengers of oxygen radicals. In this research, cDNA and genomic DNA of one carotenoid isomerooxygenase gene (named EcNinaB-X1) were cloned from Exopalaemon carinicauda. EcNinaB-X1 gene was composed of 12 exons and 11 introns. EcNinaB-X1 knock-out (KO) prawns were produced via CRISPR/Cas9 technology and the change of their phenotypes were analyzed. Of the 400 injected one-cell stage embryos with cas9 mRNA and one sgRNA targeting the first exon of EcNinaB-X1 gene, 26 EcNinaB-X1-KO prawns were generated and the mutant rate reached 6.5% after embryo injection. The EcNinaB-X1-KO prawns had significant lower mortality than those in wild-type group when the prawns were challenged with Vibrio parahaemolyticus or Aeromonas hydrophila. In conclusion, we first demonstrate the function of the carotenoid isomerooxygenase gene in immune defense of E. carinicauda by performing directed, heritable gene mutagenesis.
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Affiliation(s)
- Yuying Sun
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Congcong Yan
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Mengfei Liu
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Yujie Liu
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Wenzheng Wang
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Wei Cheng
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Fusheng Yang
- Xiaoshan Donghai Aquaculture Co., Ltd, Xiaoshan, 310012, China
| | - Jiquan Zhang
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China; Xiaoshan Donghai Aquaculture Co., Ltd, Xiaoshan, 310012, China.
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25
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Effects of Inbreeding on Genetic Characteristic, Growth, Survival Rates, and Immune Responses of a New Inbred Line of Exopalaemon carinicauda. Int J Genomics 2020; 2020:5735968. [PMID: 31998771 PMCID: PMC6964724 DOI: 10.1155/2020/5735968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/16/2019] [Accepted: 12/12/2019] [Indexed: 11/17/2022] Open
Abstract
The Exopalaemon carinicauda could be a useful crustacean laboratory animal in many research fields. We newly established an inbred line of Exopalaemon carinicauda named EC4 inbred line by brother×sister mating and keeping to F11 generation. Trends in heterozygosity in the process of producing EC4 inbred line were examined through the characterization of polymorphisms based on gene frequencies of SNP and EST-SSR loci. The results demonstrated that the number of alleles (N), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) gradually decreased with the increase of inbreeding generations. The genetic detection results indicated that 9 (29.03%, 9/31) of the SNP loci and 15 (32.61%, 15/46) of the EST-SSR loci were homozygous in F11 generation of EC4 inbred line. The variation of the growth-related traits, the immune responses, and antioxidant status were described in experimental full-sibling inbred populations of E. carinicauda at five levels of inbreeding coefficient (F = 0.785, F = 0.816, F = 0.859, F = 0.886, F = 0.908) under controlled laboratory conditions. The body weight, body length, and survival rate in EC4 inbred line of all generations were less than the control population. Inbreeding affected the antibacterial activity, phenoloxidase (PO) activity, and superoxide dismutase (SOD) which decreased at the eleventh generation of EC4 inbred line. This study demonstrated that inbreeding had a negative effect on the economic traits and immune response, but our inbred line was established successfully until F11 and confirmed by genetic detection using SNP and EST-SSR loci.
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26
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Apitanyasai K, Huang SW, Ng TH, He ST, Huang YH, Chiu SP, Tseng KC, Lin SS, Chang WC, Baldwin-Brown JG, Long AD, Lo CF, Yu HT, Wang HC. The gene structure and hypervariability of the complete Penaeus monodon Dscam gene. Sci Rep 2019; 9:16595. [PMID: 31719551 PMCID: PMC6851185 DOI: 10.1038/s41598-019-52656-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/17/2019] [Indexed: 12/19/2022] Open
Abstract
Using two advanced sequencing approaches, Illumina and PacBio, we derive the entire Dscam gene from an M2 assembly of the complete Penaeus monodon genome. The P. monodon Dscam (PmDscam) gene is ~266 kbp, with a total of 44 exons, 5 of which are subject to alternative splicing. PmDscam has a conserved architectural structure consisting of an extracellular region with hypervariable Ig domains, a transmembrane domain, and a cytoplasmic tail. We show that, contrary to a previous report, there are in fact 26, 81 and 26 alternative exons in N-terminal Ig2, N-terminal Ig3 and the entirety of Ig7, respectively. We also identified two alternatively spliced exons in the cytoplasmic tail, with transmembrane domains in exon variants 32.1 and 32.2, and stop codons in exon variants 44.1 and 44.2. This means that alternative splicing is involved in the selection of the stop codon. There are also 7 non-constitutive cytoplasmic tail exons that can either be included or skipped. Alternative splicing and the non-constitutive exons together produce more than 21 million isoform combinations from one PmDscam locus in the P. monodon gene. A public-facing database that allows BLAST searches of all 175 exons in the PmDscam gene has been established at http://pmdscam.dbbs.ncku.edu.tw/.
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Affiliation(s)
- Kantamas Apitanyasai
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan.,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Shiao-Wei Huang
- Department of Life Sciences, National Taiwan University, Taipei, Taiwan
| | - Tze Hann Ng
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan.,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Shu-Ting He
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan.,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Hsun Huang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan.,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Shen-Po Chiu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Kuan-Chien Tseng
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Wen-Chi Chang
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
| | - James G Baldwin-Brown
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
| | - Chu-Fang Lo
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan.,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Hon-Tsen Yu
- Department of Life Sciences, National Taiwan University, Taipei, Taiwan
| | - Han-Ching Wang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan. .,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan.
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27
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Zhang J, Liu Y, Zhou Y, Wang W, Su N, Sun Y. Cloning of a trehalose-6-phosphate synthase gene from Exopalaemon carinicauda and its expression response to bacteria challenge. FISH & SHELLFISH IMMUNOLOGY 2019; 93:387-394. [PMID: 31326590 DOI: 10.1016/j.fsi.2019.07.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/13/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Trehalose, a nonreducing disaccharide, is present in a wide variety of organisms and plays a key role in many organisms under different stress conditions. In the study, the full-length cDNA sequence encoding trehalose-6-phosphate synthase (EcTPS) was obtained from Exopalaemon carinicauda. The complete nucleotide sequence of EcTPS contained a 2532 bp open reading frame (ORF) encoding a putative protein of 843 amino acids. The domain architecture of the deduced EcTPS contained a glycol_transf_20 domain and a trehalose_PPase domain. EcTPS mRNA was predominantly expressed in the hepatopancreas. The expression of EcTPS in the prawns challenged with Vibrio parahaemolyticus and Aeromonas hydrophila changed in a time-dependent manner. The function of EcTPS was also studied by double-strand RNA interference. The results showed that the knock-down of EcTPS increased the mortality of the Vibrio-challenged group and Aeromonas-challenged group compared with the control group. The present study provides some new insight into the immune function of the trehalose-6-phosphate synthase in prawns.
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Affiliation(s)
- Jiquan Zhang
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China.
| | - Yujie Liu
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Yongzhao Zhou
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Wenzheng Wang
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Naike Su
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Yuying Sun
- Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China.
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Levy T, Rosen O, Manor R, Dotan S, Azulay D, Abramov A, Sklarz MY, Chalifa-Caspi V, Baruch K, Shechter A, Sagi A. Production of WW males lacking the masculine Z chromosome and mining the Macrobrachium rosenbergii genome for sex-chromosomes. Sci Rep 2019; 9:12408. [PMID: 31455815 PMCID: PMC6712010 DOI: 10.1038/s41598-019-47509-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022] Open
Abstract
The cultivation of monosex populations is common in animal husbandry. However, preselecting the desired gender remains a major biotechnological and ethical challenge. To achieve an efficient biotechnology for all-female aquaculture in the economically important prawn (Macrobrachium rosenbergii), we achieved – for the first time – WW males using androgenic gland cells transplantation which caused full sex-reversal of WW females to functional males. Crossing the WW males with WW females yielded all-female progeny lacking the Z chromosome. We now have the ability to manipulate – by non-genomic means – all possible genotype combinations (ZZ, WZ and WW) to retain either male or female phenotypes and hence to produce monosex populations of either gender. This calls for a study of the genomic basis underlying this striking sexual plasticity, questioning the content of the W and Z chromosomes. Here, we report on the sequencing of a high-quality genome exhibiting distinguishable paternal and maternal sequences. This assembly covers ~ 87.5% of the genome and yielded a remarkable N50 value of ~ 20 × 106 bp. Genomic sex markers were used to initiate the identification and validation of parts of the W and Z chromosomes for the first time in arthropods.
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Affiliation(s)
- Tom Levy
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410501, Israel
| | - Ohad Rosen
- Enzootic HK, Ltd., Unit 1109, 11/F, Kowloon Centre, 33 Ashley Road, Tsimshatsui, Kowloon, Hong Kong
| | - Rivka Manor
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410501, Israel
| | - Shahar Dotan
- Enzootic HK, Ltd., Unit 1109, 11/F, Kowloon Centre, 33 Ashley Road, Tsimshatsui, Kowloon, Hong Kong
| | - Dudu Azulay
- Enzootic HK, Ltd., Unit 1109, 11/F, Kowloon Centre, 33 Ashley Road, Tsimshatsui, Kowloon, Hong Kong
| | - Anna Abramov
- Enzootic HK, Ltd., Unit 1109, 11/F, Kowloon Centre, 33 Ashley Road, Tsimshatsui, Kowloon, Hong Kong
| | - Menachem Y Sklarz
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410501, Israel
| | - Vered Chalifa-Caspi
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410501, Israel
| | | | - Assaf Shechter
- Enzootic HK, Ltd., Unit 1109, 11/F, Kowloon Centre, 33 Ashley Road, Tsimshatsui, Kowloon, Hong Kong
| | - Amir Sagi
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410501, Israel. .,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410501, Israel.
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Li J, Lv J, Liu P, Chen P, Wang J, Li J. Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits. BMC Genomics 2019; 20:598. [PMID: 31331278 PMCID: PMC6647322 DOI: 10.1186/s12864-019-5981-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/16/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND High-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species. RESULTS In the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73 cM and 0.55 cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8-15.7% of the total growth-traits variation. CONCLUSIONS The genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growth traits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps.
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Affiliation(s)
- Jitao Li
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Jianjian Lv
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Ping Liu
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Ping Chen
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Jiajia Wang
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Jian Li
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China. .,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China.
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30
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Waiho K, Shi X, Fazhan H, Li S, Zhang Y, Zheng H, Liu W, Fang S, Ikhwanuddin M, Ma H. High-Density Genetic Linkage Maps Provide Novel Insights Into ZW/ZZ Sex Determination System and Growth Performance in Mud Crab ( Scylla paramamosain). Front Genet 2019; 10:298. [PMID: 31024620 PMCID: PMC6459939 DOI: 10.3389/fgene.2019.00298] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
Mud crab, Scylla paramamosain is one of the most important crustacean species in global aquaculture. To determine the genetic basis of sex and growth-related traits in S. paramamosain, a high-density genetic linkage map with 16,701 single nucleotide polymorphisms (SNPs) was constructed using SLAF-seq and a full-sib family. The consensus map has 49 linkage groups, spanning 5,996.66 cM with an average marker-interval of 0.81 cM. A total of 516 SNP markers, including 8 female-specific SNPs segregated in two quantitative trait loci (QTLs) for phenotypic sex were located on LG32. The presence of female-specific SNP markers only on female linkage map, their segregation patterns and lower female: male recombination rate strongly suggest the conformation of a ZW/ZZ sex determination system in S. paramamosain. The QTLs of most (90%) growth-related traits were found within a small interval (25.18–33.74 cM) on LG46, highlighting the potential involvement of LG46 in growth. Four markers on LG46 were significantly associated with 10–16 growth-related traits. BW was only associated with marker 3846. Based on the annotation of transcriptome data, 11 and 2 candidate genes were identified within the QTL regions of sex and growth-related traits, respectively. The newly constructed high-density genetic linkage map with sex-specific SNPs, and the identified QTLs of sex- and growth-related traits serve as a valuable genetic resource and solid foundation for marker-assisted selection and genetic improvement of crustaceans.
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Affiliation(s)
- Khor Waiho
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Shaobin Fang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Mhd Ikhwanuddin
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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31
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Molt-dependent transcriptome analysis of claw muscles in Chinese mitten crab Eriocheir sinensis. Genes Genomics 2019; 41:515-528. [DOI: 10.1007/s13258-019-00787-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 01/17/2019] [Indexed: 01/16/2023]
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32
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Zenger KR, Khatkar MS, Jones DB, Khalilisamani N, Jerry DR, Raadsma HW. Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters. Front Genet 2019; 9:693. [PMID: 30728827 PMCID: PMC6351666 DOI: 10.3389/fgene.2018.00693] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/11/2018] [Indexed: 11/20/2022] Open
Abstract
Within aquaculture industries, selection based on genomic information (genomic selection) has the profound potential to change genetic improvement programs and production systems. Genomic selection exploits the use of realized genomic relationships among individuals and information from genome-wide markers in close linkage disequilibrium with genes of biological and economic importance. We discuss the technical advances, practical requirements, and commercial applications that have made genomic selection feasible in a range of aquaculture industries, with a particular focus on molluscs (pearl oysters, Pinctada maxima) and marine shrimp (Litopenaeus vannamei and Penaeus monodon). The use of low-cost genome sequencing has enabled cost-effective genotyping on a large scale and is of particular value for species without a reference genome or access to commercial genotyping arrays. We highlight the pitfalls and offer the solutions to the genotyping by sequencing approach and the building of appropriate genetic resources to undertake genomic selection from first-hand experience. We describe the potential to capture large-scale commercial phenotypes based on image analysis and artificial intelligence through machine learning, as inputs for calculation of genomic breeding values. The application of genomic selection over traditional aquatic breeding programs offers significant advantages through being able to accurately predict complex polygenic traits including disease resistance; increasing rates of genetic gain; minimizing inbreeding; and negating potential limiting effects of genotype by environment interactions. Further practical advantages of genomic selection through the use of large-scale communal mating and rearing systems are highlighted, as well as presenting rate-limiting steps that impact on attaining maximum benefits from adopting genomic selection. Genomic selection is now at the tipping point where commercial applications can be readily adopted and offer significant short- and long-term solutions to sustainable and profitable aquaculture industries.
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Affiliation(s)
- Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
| | - Mehar S Khatkar
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - David B Jones
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Nima Khalilisamani
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Tropical Futures Institute, James Cook University Singapore, Singapore, Singapore
| | - Herman W Raadsma
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
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Zhang J, Liu Y, Li Y, Su N, Zhou Y, Xiang J, Sun Y. Biological function of a gC1qR homolog (EcgC1qR) of Exopalaemon carinicauda in defending bacteria challenge. FISH & SHELLFISH IMMUNOLOGY 2018; 82:378-385. [PMID: 30144564 DOI: 10.1016/j.fsi.2018.08.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/15/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
The gC1qR is a ubiquitously expressed cell protein that interacts with the globular heads of C1q (gC1q) and many other ligands. In this study, one gC1qR homolog gene was obtained from Exopalaemon carinicauda and named EcgC1qR. The complete nucleotide sequence of EcgC1qR contained a 774 bp open reading frame (ORF) encoding EcgC1qR precursor of 257 amino acids. The deduced amino acid sequence of EcgC1qR revealed a 55-amino-acid-long mitochondrial targeting sequence at the N-terminal and a mitochondrial acidic matrix protein of 33 kDa (MAM33) domain. The genomic organization of EcgC1qR gene showed that EcgC1qR gene contained five exons and four introns. EcgC1qR could express in all of the detected tissues and its expression was much higher in hepatopancreas and hemocytes. The expression of EcgC1qR in the hepatopancreas of prawns challenged with Vibrio parahaemolyticus and Aeromonas hydrophila changed in a time-dependent manner. The expression of EcgC1qR in prawns challenged with V. parahaemolyticus was up-regulated at 6 h (p < 0.05), and significantly up-regulated at 12 h and 24 h (p < 0.01), and then returned to the control levels at 48 h post-challenge (p > 0.05). At the same time, the expression in Aeromonas-challenged group was significantly up-regulated at 6, 12 and 24 h. The recombinant EcgC1qR could inhibit the growth of two tested bacteria. In addition, we successfully deleted EcgC1qR gene through CRISPR/Cas9 technology and it was the first time to obtain the mutant of gC1qR homolog gene in crustacean. It's a great progress to study the biological function of gC1qR in crustacean in future.
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Affiliation(s)
- Jiquan Zhang
- College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China; Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yujie Liu
- College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Yanyan Li
- College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Naike Su
- College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Yaru Zhou
- College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Jianhai Xiang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China; Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yuying Sun
- College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China.
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34
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Zhang J, Song F, Sun Y, Yu K, Xiang J. CRISPR/Cas9-mediated deletion of EcMIH shortens metamorphosis time from mysis larva to postlarva of Exopalaemon carinicauda. FISH & SHELLFISH IMMUNOLOGY 2018; 77:244-251. [PMID: 29621632 DOI: 10.1016/j.fsi.2018.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/29/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
The recently emerged CRISPR/Cas9 technology is the most flexible means to produce targeted mutations at the genomic loci in a variety of organisms. In Crustaceans, molt-inhibiting hormone (MIH) is an important negative-regulatory factor and plays a key role in suppressing the molting process. However, whether precise disruption of MIH in crustacean can be achieved and successfully used to improve the development and growth has not been proved. In this research, the complementary DNA (cDNA) and genomic DNA, including flanking regions of the MIH gene (EcMIH) of ridgetail white prawn Exopalaemon carinicauda, were cloned and sequenced. Sequence analysis revealed that EcMIH was composed of three exons and two introns. Analysis by RT-PCR showed that EcMIH mainly expressed in eyestalks. During different development periods, EcMIH was highest in juvenile stage and extremely low in others but adult prawns eyestalks. In addition, we applied CRISPR/Cas9 technology to generate EcMIH knock-out (KO) prawns and then analyzed the changes in their phenotypes. We efficiently generated 12 EcMIH-KO prawns out of 250 injected one-cell stage embryos and the mutant rate reached 4.8% after embryo injection with one sgRNA targeting the second exon of EcMIH. The EcMIH-KO prawns exhibited increased the body length and shortened the metamorphosis time of larvae from mysis larva to postlarva. Meanwhile, EcMIH-KO did not cause the health problems such as early stage death or deformity. In conclusion, we successfully obtained EcMIH gene and generated EcMIH-KO prawns using CRISPR/Cas9 technology. This study will certainly lead to a wide application prospect of MIH gene in prawns breeding.
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Affiliation(s)
- Jiquan Zhang
- College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China; CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Fengge Song
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yuying Sun
- College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China.
| | - Kuijie Yu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Jianhai Xiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
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35
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Yuan J, Zhang X, Liu C, Yu Y, Wei J, Li F, Xiang J. Genomic resources and comparative analyses of two economical penaeid shrimp species, Marsupenaeus japonicus and Penaeus monodon. Mar Genomics 2018. [DOI: 10.1016/j.margen.2017.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Sun Y, Zhang J, Xiang J. Immune function against bacteria of chitin deacetylase 1 (EcCDA1) from Exopalaemon carinicauda. FISH & SHELLFISH IMMUNOLOGY 2018; 75:115-123. [PMID: 29421585 DOI: 10.1016/j.fsi.2018.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/25/2018] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
Chitin deacetylase (CDA, EC 3.5.1.41), belonging to a family of extracellular chitin-modifying enzymes, can catalyze the deacetylation of chitin. In this study, the full-length cDNA sequence encoding chitin deacetylase 1 (EcCDA1) was obtained fromExopalaemon carinicauda. The complete nucleotide sequence of EcCDA1 contained a 1611 bp open reading frame (ORF) encoding EcCDA1 precursor of 536 amino acids. The domain architecture of the deduced EcCDA1 protein contained a signal peptide, a chitin-binding peritrophin-A domain (ChtBD2), a low-density lipoprotein receptor class A domain (LDLa) and a Polysacc_deac_1 domain. EcCDA1 mRNA was predominantly expressed in the gills. The expression of EcCDA1 in the prawns challenged with Vibrio parahaemolyticus and Aeromonas hydrophila changed in a time-dependent manner. The expression of EcCDA1 in the prawns challenged with V. parahaemolyticus was up-regulated at 12 h (p < 0.05), and significantly up-regulated at 24 h and 48 h (p < 0.01), and then returned to the control levels at 96 h post-challenge (p > 0.05). At the same time, the expression in Aeromonas-challenged group was significantly up-regulated at 12, 24 and 48 h (p < 0.01) and returned to the control levels at 120 h post-challenge (p > 0.05). Then, EcCDA1 was recombinantly expressed in Pichia pastoris and the purified recombinant EcCDA1 could not inhibit the growth of V. parahaemolyticus or A. hydrophila, which indicated that the CDA1 may play its biological activity in immune defense by deacetylation from chitin.
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Affiliation(s)
- Yuying Sun
- College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Jiquan Zhang
- College of Life Sciences, Hebei University, Baoding, Hebei 071002, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China; Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Jianhai Xiang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China; Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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37
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Vogt G. Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives. J Biosci 2018; 43:189-223. [PMID: 29485126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In the last 15 years, considerable attempts have been undertaken to develop the obligately parthenogenetic marbled crayfish Procambarus virginalis as a new model in biology. Its main advantage is the production of large numbers of offspring that are genetically identical to the mother, making this crustacean particularly suitable for research in epigenetics. Now, a draft genome, transcriptome and genome-wide methylome are available opening new windows for research. In this article, I summarize the biological advantages and genomic and epigenetic features of marbled crayfish and, based on first promising data, discuss what this new model could contribute to answering of ''big'' biological questions. Genome mining is expected to reveal new insights into the genetic specificities of decapod crustaceans, the genetic basis of arthropod reproduction, moulting and immunity, and more general topics such as the genetic underpinning of adaptation to fresh water, omnivory, biomineralization, sexual system change, behavioural variation, clonal genome evolution, and resistance to cancer. Epigenetic investigations with the marbled crayfish can help clarifying the role of epigenetic mechanisms in gene regulation, tissue specification, adult stem cell regulation, cell ageing, organ regeneration and disease susceptibility. Marbled crayfish is further suitable to elucidate the relationship between genetic and epigenetic variation, the transgenerational inheritance of epigenetic signatures and the contribution of epigenetic phenotype variation to the establishment of social hierarchies, environmental adaptation and speciation. These issues can be tackled by experiments with highly standardized laboratory lineages, comparison of differently adapted wild populations and the generation of genetically and epigenetically edited strains.
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Affiliation(s)
- Gunter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany,
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Vogt G. Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives. J Biosci 2018. [DOI: 10.1007/s12038-018-9741-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Molecular characterization and function of β-N-acetylglucosaminidase from ridgetail white prawn Exopalaemon carinicauda. Gene 2018; 648:12-20. [PMID: 29339067 DOI: 10.1016/j.gene.2018.01.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/04/2017] [Accepted: 01/11/2018] [Indexed: 01/16/2023]
Abstract
Chitin degradation is catalyzed by a two-component chitinolytic enzyme system, chitinase and β-N-acetylglucosaminidase (NAGase). In this paper, the full-length cDNA sequence encoding NAGase (EcNAG) was obtained from Exopalaemon carinicauda. The deduced amino acid sequence of EcNAG open reading frame (ORF) contained one Glycohydro_20b2 domain and one Glyco_hydro_20 domain. Based on the cDNA sequence, the genomic structure of EcNAG was characterized and it was composed of six exons and five introns. EcNAG mRNA majorly expressed in the hepatopancreas and epidermis. During the molting stages, EcNAG mRNA expression was well-regulated and its expression reached the highest level at the molting stage E. In addition, EcNAG was recombinant expressed in Pichia pastoris and the partial enzymatic characterization of recombinant EcNAG was confirmed. After being challenged with Vibrio parahaemolyticus and Aeromonas hydrophila, the expression of EcNAG was up-regulated significantly at 6 h and reached the peak at 12 h. And then, the expression began to down-regulated and came to the normal level at 72 h. It is helpful to research the relationship between the molt-related hormones and chitinlytic enzymes.
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Sun Y, Zhang J, Xiang J. A CRISPR/Cas9-mediated mutation in chitinase changes immune response to bacteria in Exopalaemon carinicauda. FISH & SHELLFISH IMMUNOLOGY 2017; 71:43-49. [PMID: 28962883 DOI: 10.1016/j.fsi.2017.09.065] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/15/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Chitinase, belonging to family 18 glycosyl hydrolase, is a multi-gene family and it has many functions. Generation of loss-of-function mutant targeting an interesting gene is a common way to clarify its function based on reverse genetics. In this study, we first reported the immune defense of a chitinase gene (EcChi4) in Exopalaemon carinicauda using its EcChi4-deletion mutant. EcChi4 was predominantly expressed in hepatopancreas and was upregulated after challenge with Vibrio parahaemolyticus or Aeromonas hydrophila. After knockout EcChi4 gene using CRISPR/Cas9 tool, the prawns in EcChi4-deletion group had significant higher mortality than those in wild-type group when the prawns were challenged with V. parahaemolyticus or A. hydrophila. In conclusion, we first demonstrate the function of a chitinase gene in immune defense of E. carinicauda by performing directed, heritable gene mutagenesis. In the future, CRISPR/Cas9 should be widely applicable as a feasible means for gene editing in E. carinicauda for the study of important biological questions that cannot be easily addressed in other decapods.
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Affiliation(s)
- Yuying Sun
- College of Marine Life and Fisheries, Huaihai Institute of Technology, 59 Cangwu Road, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China
| | - Jiquan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China.
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
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