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Phonsiri K, Mavichak R, Panserat S, Boonanuntanasarn S. Differential responses of hepatopancreas transcriptome between fast and slow growth in giant freshwater prawns (Macrobrachium rosenbergii) fed a plant-based diet. Sci Rep 2024; 14:4957. [PMID: 38418833 PMCID: PMC10902295 DOI: 10.1038/s41598-024-54349-6] [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: 02/01/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Efficient utilisation of plant-based diets in the giant freshwater prawn, Marcrobrachium rosenbergii, varies according to individual, suggesting that it might be associated with differences in physiological and metabolic responses. Therefore, we aimed to investigate the individual differences in the growth response of shrimp fed to a soybean-based diet (SBM). Two hundred shrimp were fed SBM for 90 days, and specific growth rate (SGR) was determined individually. Fast- and slow-growing shrimp (F-shrimp vs. S-shrimp), with the highest and lowest 5% SGRs, respectively, were sampled to determine haemolymph chemistry and carcass composition. The hepatopancreas of these shrimps were used for transcriptome analysis through RNA sequencing (RNA-Seq). The results showed no significant differences in haemolymph chemistry parameters. In terms of carcass proximate composition, F-shrimp exhibited higher protein composition than did S-shrimp, suggesting that F-shrimp have higher protein anabolism. Using RNA-seq and real-time reverse transcription polymerase chain reaction (qRT-PCR), the expression levels of several genes encoding physiologic and metabolic enzymes were found to be upregulated in F-shrimp compared to in S-shrimp, suggesting that these enzymes/proteins mediated the efficient use of SBM-based diets for growth promotion in shrimp. Various DEGs associated with the immune system were observed, indicating a difference in immune processes between F- and S-shrimp. The expression of several housekeeping genes was found to be upregulated in S-shrimp. Collectively, the upregulated expression of several enzymes associated with physiological and/or metabolic processes and increased protein anabolism may be attributed to the efficient use of SBM for maximal growth in shrimp.
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Affiliation(s)
- Khanakorn Phonsiri
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Muang, Nakhon Ratchasima, 30000, Thailand
| | - Rapeepat Mavichak
- Aquatic Animal Health Research Center, Charoen Pokphand Co. Ltd., Rama 2 Rd., Km 41.5, Bangtorat, Muang Samutsakorn, Samutsakorn, 74000, Thailand
| | - Stephane Panserat
- INRAE, Université de Pau et des Pays de l'Adour, E2S UPPA, NuMéA, Saint-Pée-Sur-Nivelle, France
| | - Surintorn Boonanuntanasarn
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Muang, Nakhon Ratchasima, 30000, Thailand.
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Ma X, Yan X, Ke R, Shan H, Rehman SU, Feng T, Zheng Y, Chuang C, Zhou W, Liu Q, Zheng J. Comparative Transcriptome Sequencing Analysis of Hirudo nipponia in Different Growth Periods. Front Physiol 2022; 13:873831. [PMID: 35812329 PMCID: PMC9259933 DOI: 10.3389/fphys.2022.873831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Hirudo nipponia is the only blood-sucking leech included in Chinese Pharmacopoeia having distinct features of anticoagulation, exorcizing blood stasis, and promoting menstruation. Despite such significant characteristics, very little is known about its molecular genetics and related physiological mechanisms. In this study, the transcriptomes of H. nipponia at three developmental stages (larvae, young, and adults), revealed a total of 1,348 differentially expressed genes (DEGs), 223 differentially expressed lncRNAs, and 88 novel mRNAs. A significant diverse gene expression patterns were observed at different developmental stages which were analyzed by differential gene expression trends, and the overall gene expression trends consist of three overall down-regulated trends, and two overall up-regulated trends. Furthermore, the GO and KEGG enrichment functional annotation analysis revealed that these DEGs were mainly associated with protein hydrolysis, signal transduction, energy metabolism, and lipid metabolism while growth, development, metabolism, and reproduction-related DEGs were also found. Additionally, real-time quantitative PCR results confirmed deep sequencing results based on the relative expression levels of nine randomly selected genes. This is the first transcriptome-based comprehensive study of H. irudo nipponia at different developmental stages which provided considerable deep understanding related to gene expression patterns and their relevant developmental pathways, neurodevelopmental and reproductive characteristics of the leech.
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Affiliation(s)
- Xiaocong Ma
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Xiuying Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Ren Ke
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Huiquan Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Yalin Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Chen Chuang
- Guangxi Medical University Cancer Hospital, Nanning, China
| | - Weiguan Zhou
- Thai Natural Hirudin Co, Ltd., Bangkok, Thailand
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
- *Correspondence: Qingyou Liu, ; Jinghui Zheng,
| | - Jinghui Zheng
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
- *Correspondence: Qingyou Liu, ; Jinghui Zheng,
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Chitin Synthesis and Degradation in Crustaceans: A Genomic View and Application. Mar Drugs 2021; 19:md19030153. [PMID: 33804177 PMCID: PMC8002005 DOI: 10.3390/md19030153] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/29/2022] Open
Abstract
Chitin is among the most important components of the crustacean cuticular exoskeleton and intestinal peritrophic matrix. With the progress of genomics and sequencing technology, a large number of gene sequences related to chitin metabolism have been deposited in the GenBank database in recent years. Here, we summarized the genes and pathways associated with the biosynthesis and degradation of chitins in crustaceans based on genomic analyses. We found that chitin biosynthesis genes typically occur in single or two copies, whereas chitin degradation genes are all multiple copies. Moreover, the chitinase genes are significantly expanded in most crustacean genomes. The gene structure and expression pattern of these genes are similar to those of insects, albeit with some specific characteristics. Additionally, the potential applications of the chitin metabolism genes in molting regulation and immune defense, as well as industrial chitin degradation and production, are also summarized in this review.
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Zhang X, Yuan J, Zhang X, Xiang J, Li F. Genomic Characterization and Expression of Juvenile Hormone Esterase-Like Carboxylesterase Genes in Pacific White Shrimp, Litopenaeus vannamei. Int J Mol Sci 2020; 21:ijms21155444. [PMID: 32751646 PMCID: PMC7432913 DOI: 10.3390/ijms21155444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/02/2022] Open
Abstract
The sesquiterpenoid methyl farnesoate (MF), a juvenile hormone (JH) analog, plays important roles in many physiological processes of crustaceans, such as morphogenesis, molting and reproduction. Juvenile hormone esterase-like (JHE-like) carboxylesterase (CXE) is a key enzyme in MF degradation, playing a significant role in regulating MF titer. However, its function is barely known in shrimp. In this study, a total of 21 JHE-like CXEs (LvCXEs) were characterized in Pacific white shrimp Litopenaeus vannamei, based on the full genome and multi-transcriptomic data. LvCXE has a conserved triplet catalytic site (Ser-Glu-His) and a characteristic GxSxG motif. Most LvCXEs were highly expressed in the hepatopancreas, which was the main site for MF degradation. LvCXEs containing a GESAG motif showed a specific expansion in the L. vannamei genome. Those GESAG-containing LvCXEs presented differential expressions at different larvae stages and different molting stages of L. vannamei, which suggested their potential functions in development and molting. Additionally, when the transcription level of CXEs was inhibited, it could lead to failed molt and death of L. vannamei. When we further detected the expression levels of the key ecdysone responsive transcription factors including LvE75, LvBr-C, LvHr3 and LvFtz-f1 after the CXE inhibitor was injected into L. vannamei, they all showed apparent down-regulation. These results suggested that the expansion of LvCXEs in the L. vannamei genome should contribute to the regulation of metamorphosis at larvae stages and frequent molting during the growth of L. vannamei.
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Affiliation(s)
- Xiaoxi Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbo Yuan
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Correspondence: (J.Y.); (X.Z.)
| | - Xiaojun Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Correspondence: (J.Y.); (X.Z.)
| | - Jianhai Xiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Fuhua Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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Zhang X, Yuan J, Zhang X, Liu C, Xiang J, Li F. Genome-Wide Analysis of Alternative Splicing Provides Insights Into Stress Response of the Pacific White Shrimp Litopenaeus vanname. Front Genet 2019; 10:845. [PMID: 31572450 PMCID: PMC6752684 DOI: 10.3389/fgene.2019.00845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/14/2019] [Indexed: 01/15/2023] Open
Abstract
Alternative splicing (AS) can enhance transcript diversity dramatically and play an important role in stress adaptation. Limited researches of AS have been reported in the Pacific white shrimp (Litopenaeus vannamei), which is an important aquaculture species in the world. Here, we performed a genome-wide identification of AS events in L. vannamei based on eight transcriptomes. We identified 38,781 AS events in the shrimp genome, and some of them were validated by polymerase chain reaction experiments. These AS events correspond to 9,209 genes, accounting for 36% of protein-coding genes in the shrimp genome. The number of AS events increased after virus or bacteria infection and low salinity stress. Type 1 AS genes (AS was initially activated) were mainly enriched in substance and energy metabolism, such as carbon metabolism and amino metabolism. However, type 2 AS genes (AS events changed) displayed specific enrichment under different stress challenges. Specifically, type 2 AS genes under biotic stresses were mainly enriched in the pathogenic pathway and immune network, and the AS genes under low salinity stress were significantly enriched for betalain biosynthesis. In summary, our study indicates that AS events are complex in shrimp and may be related to stress adaptation. These results will provide valuable resource for functional genomic studies on crustaceans.
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Affiliation(s)
- Xiaoxi Zhang
- 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, Institute of Oceanology Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianbo Yuan
- 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, Institute of Oceanology Chinese Academy of Sciences, Qingdao, China
| | - Xiaojun Zhang
- 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, Institute of Oceanology Chinese Academy of Sciences, Qingdao, China
| | - Chengzhang Liu
- 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, Institute of Oceanology Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Sciences, Chinese Academy of Sciences, Qingdao, China
| | - Jianhai Xiang
- 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, Institute of Oceanology Chinese Academy of Sciences, Qingdao, China
| | - Fuhua Li
- 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, Institute of Oceanology Chinese Academy of Sciences, Qingdao, China
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Li Y, Li X, Xu W, Han Z, Zhao Y, Dong J, Wei H, Chen Q. Comparative iTRAQ-based quantitative proteomic analysis of the Chinese grass shrimp (Palaemonetes sinensis) infected with the isopod parasite Tachaea chinensis. Parasit Vectors 2019; 12:415. [PMID: 31443734 PMCID: PMC6708196 DOI: 10.1186/s13071-019-3675-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/19/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Although parasitic isopods can negatively affect the reproduction and ingestion of several commercially important crustaceans, little is known regarding the mechanisms that underlie these effects. METHODS In the present study, the iTRAQ (isobaric tags for relative and absolute quantification) approach was applied to identify differentially expressed proteins in the Chinese grass shrimp Palaemonetes sinensis infected with the parasitic isopod Tachaea chinensis. RESULTS On the basis of our analysis, we identified 1262 proteins from a total of 4292 peptides. There was a significant difference in the expression of 182 proteins between the control and infected groups, among which 69 were upregulated and 113 were downregulated after T. chinensis infection. The differentially expressed proteins revealed that parasitism may inhibit the immune response, thereby increasing host vulnerability to additional lethal infection. Furthermore, T. chinensis may secrete anticoagulants to inhibit hemolymph clotting. Moreover, the isopod parasite placed a heavy metabolic burden on the host, particularly with respect to glucose metabolism. CONCLUSIONS Our study is the first to use the iTRAQ-based proteomic approach to analyze the effects of an isopod parasite on its host. The results we obtained using this approach will make a valuable contribution to understanding the molecular mechanisms underlying isopod parasitism on crustaceans.
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Affiliation(s)
- Yingdong Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China
| | - Xin Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China
| | - Weibin Xu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China
| | - Zhibin Han
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China
| | - Yingying Zhao
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China
| | - Jing Dong
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China
| | - Hua Wei
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China
| | - Qijun Chen
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China.
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Zhang X, Yuan J, Zhang X, Liu C, Li F, Xiang J. Genome-Wide Identification and Expression Profiles of Myosin Genes in the Pacific White Shrimp, Litopenaeus vannamei. Front Physiol 2019; 10:610. [PMID: 31178751 PMCID: PMC6537884 DOI: 10.3389/fphys.2019.00610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/29/2019] [Indexed: 12/18/2022] Open
Abstract
As the main structural protein of muscle fiber, myosin is essential for multiple cellular processes or functions, especially for muscle composition and development. Although the shrimp possess a well-developed muscular system, the knowledge about the myosin family in shrimp is far from understood. In this study, we performed comprehensive analysis on the myosin genes in the genome of the Pacific white shrimp, Litopenaeus vannamei. A total of 29 myosin genes were identified, which were classified into 14 subfamilies. Among them, Myo2 subfamily was significantly expanded in the penaeid shrimp genome. Most of the Myo2 subfamily genes were primarily expressed in abdominal muscle, which suggested that Myo2 subfamily genes might be responsible for the well-developed muscular system of the penaeid shrimp. In situ hybridization detection showed that the slow-type muscle myosin gene was mainly localized in pleopod muscle and superficial ventral muscle of the shrimp. This study provides valuable insights into the evolutionary and functional characterization of myosin genes in shrimps, which provides clues for us to understand the well-developed muscular system of shrimp.
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Affiliation(s)
- Xiaoxi Zhang
- 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.,University of Chinese Academy of Sciences, Beijing, China
| | - Jianbo Yuan
- 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
| | - Xiaojun Zhang
- 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
| | - Chengzhang Liu
- 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
| | - Fuhua Li
- 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
| | - Jianhai Xiang
- 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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