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Xu M, Li F, Zhang X, Chen B, Geng Y, Ouyang P, Chen D, Li L, Huang X. Microbiome analysis reveals the intestinal microbiota characteristics and potential impact of Procambarus clarkii. Appl Microbiol Biotechnol 2024; 108:77. [PMID: 38204126 PMCID: PMC10781845 DOI: 10.1007/s00253-023-12914-5] [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: 07/19/2023] [Revised: 11/06/2023] [Accepted: 11/17/2023] [Indexed: 01/12/2024]
Abstract
The intestinal microbiota interacts with the host and plays an important role in the immune response, digestive physiology, and regulation of body functions. In addition, it is also well documented that the intestinal microbiota of aquatic animals are closely related to their growth rate. However, whether it resulted in different sizes of crayfish in the rice-crayfish coculture model remained vague. Here, we analyzed the intestinal microbiota characteristics of crayfish of three sizes in the same typical rice-crayfish coculture field by high-throughput sequencing technology combined with quantitative real-time polymerase chain reaction (qRT-PCR) and enzyme activity, investigating the relationship between intestinal microbiota in crayfish and water and sediments. The results showed that the dominant intestinal microbiota of crayfish was significantly different between the large size group (BS), normal size group (NS), and small size group (SS), where Bacteroides and Candidatus_Bacilloplasma contributed to the growth of crayfish by facilitating food digestion through cellulolysis, which might be one of the potential factors affecting the difference in sizes. Follow-up experiments confirmed that the activity of lipase (LPS) and protease was higher in BS, and the relative expression of development-related genes, including alpha-amylase (α-AMY), myocyte-specific enhancer factor 2a (MEF2a), glutathione reductase (GR), chitinase (CHI), and ecdysone receptor (EcR), in BS was significantly higher than that in SS. These findings revealed the intestinal microbiota characteristics of crayfish of different sizes and their potential impact on growth, which is valuable for managing and manipulating the intestinal microbiota in crayfish to achieve high productivity in practice. KEY POINTS: • Significant differences in the dominant microflora of BS, NS, and SS in crayfish. • Cellulolysis might be a potential factor affecting different sizes in crayfish. • Adding Bacteroides and Candidatus_Bacilloplasma helped the growth of crayfish.
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Affiliation(s)
- Ming Xu
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Fulong Li
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoli Zhang
- Fishery Research Institute, Chengdu Academy of Agriculture and Forestry Sciences, Wenjiang, Sichuan, China
| | - Baipeng Chen
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi Geng
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ping Ouyang
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Defang Chen
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Liangyu Li
- Fishery Research Institute, Chengdu Academy of Agriculture and Forestry Sciences, Wenjiang, Sichuan, China
| | - Xiaoli Huang
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Xia Y, Zhang X, Zhang X, Zhu H, Zhong X, Song W, Yuan J, Sha Z, Li F. Gene structure, expression and function analysis of the MyoD gene in the Pacific white shrimp Litopenaeus vannamei. Gene 2024; 921:148523. [PMID: 38703863 DOI: 10.1016/j.gene.2024.148523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/14/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
The Pacific white shrimp Litopenaeus vannamei is a representative species of decapod crustacean and an economically important marine aquaculture species worldwide. However, research on the genes involved in muscle growth and development in shrimp is still lacking. MyoD is recognized as a crucial regulator of myogenesis and plays an essential role in muscle growth and differentiation in various animals. Nonetheless, little information is available concerning the function of this gene among crustaceans. In this study, we identified a sequence of the MyoD gene (LvMyoD) with a conserved bHLH domain in the L. vannamei genome. Phylogenetic analysis revealed that both the overall protein sequence and specific functional sites of LvMyoD are highly conserved with those of other crustacean species and that they are evolutionarily closely related to vertebrate MyoD and Myf5. LvMyoD expression is initially high during early muscle development in shrimp and gradually decreases after 40 days post-larval development. In adults, the muscle-specific expression of LvMyoD was confirmed through RT-qPCR analysis. Knockdown of LvMyoD inhibited the growth of the shrimp in body length and weight. Histological observation and transcriptome sequencing of muscle samples after RNA interference (RNAi) revealed nuclear agglutination and looseness in muscle fibers. Additionally, we observed significant effects on the expression of genes involved in heat shock proteins, myosins, actins, protein synthesis, and glucose metabolism. These findings suggest that LvMyoD plays a critical role in regulating muscle protein synthesis and muscle cell differentiation. Overall, this study highlights the involvement of LvMyoD in myogenesis and muscle growth, suggesting that it is a potentially important regulatory target for shrimp breeding efforts.
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Affiliation(s)
- Yanting Xia
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Institute of Aquatic Biotechnology, Collage of Life Sciences, Qingdao University, Qingdao 266071, 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 266071, China; Institute of Aquatic Biotechnology, Collage of Life Sciences, Qingdao University, Qingdao 266071, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Xiaoxi Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Haochen Zhu
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Institute of Aquatic Biotechnology, Collage of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Xiaoyun Zhong
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, 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 266071, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhenxia Sha
- Institute of Aquatic Biotechnology, Collage of Life Sciences, Qingdao University, Qingdao 266071, 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 266071, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
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Bao S, Wang W, Deng Z, Zhou R, Zeng S, Hou D, He J, Huang Z. Changes of bacterial communities and bile acid metabolism reveal the potential "intestine-hepatopancreas axis" in shrimp. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 938:173384. [PMID: 38815838 DOI: 10.1016/j.scitotenv.2024.173384] [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: 03/27/2024] [Revised: 05/11/2024] [Accepted: 05/18/2024] [Indexed: 06/01/2024]
Abstract
The interaction between the gut and the liver plays a significant role in individual health and diseases. Mounting evidence supports that bile acids are important metabolites in the bidirectional communication between the gut and the liver. Most of the current studies on the "gut-liver axis" have focused on higher vertebrates, however, few was reported on lower invertebrates such as shrimp with an open circulatory system. Here, microbiomic and metabolomic analyses were conducted to investigate the bacterial composition and bile acid metabolism in intestine, hemolymph and hepatopancreas of Penaeus vannamei fed diets supplemented with octanoic acid and oleic acid. After six days of feeding, the bacterial composition in intestine, hemolymph and hepatopancreas changed at different stages, with significant increases in the relative abundance of several genera such as Pseudomonas and Rheinheimera in intestine and hepatopancreas. Notably, there was a more similar bacterial composition in intestine and hepatopancreas at the genus level, which indicated the close communication between shrimp intestine and hepatopancreas. Meanwhile, higher content of some bile acids such as lithocholic acid (LCA) and α-muricholic acid (α-MCA) in intestine and lower content of some bile acids such as taurohyocholic acids (THCA) and isolithocholic acid (IsoLCA) in hepatopancreas were detected. Furthermore, Spearman correlation analysis revealed a significant correlation between bacterial composition and bile acid metabolism in intestine and hepatopancreas. The microbial source tracking analysis showed that there was a high proportion of intestine and hepatopancreas bacterial community as the source of each other. Collectively, these results showed a strong crosstalk between shrimp intestine and hepatopancreas, which suggests a unique potential "intestine-hepatopancreas axis" in lower invertebrate shrimp with an open circulatory system. Our finding contributed to the understanding of the interplay between shrimp intestine and hepatopancreas in the view of microecology and provided new ideas for shrimp farming and disease control.
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Affiliation(s)
- Shicheng Bao
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Wenjun Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Zhixuan Deng
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Renjun Zhou
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Shenzheng Zeng
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Dongwei Hou
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Jianguo He
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China; Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Zhuhai 519082, China; State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhijian Huang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China; Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Zhuhai 519082, China; State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China.
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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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Goldberg JK, Godfrey RK, Barrett M. A long-read draft assembly of the Chinese mantis (Mantodea: Mantidae: Tenodera sinensis) genome reveals patterns of ion channel gain and loss across Arthropoda. G3 (BETHESDA, MD.) 2024; 14:jkae062. [PMID: 38517310 DOI: 10.1093/g3journal/jkae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 01/29/2024] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
Praying mantids (Mantodea: Mantidae) are iconic insects that have captivated biologists for decades, especially the species with cannibalistic copulatory behavior. This behavior has been cited as evidence that insects lack nociceptive capacities and cannot feel pain; however, this behaviorally driven hypothesis has never been rigorously tested at the genetic or functional level. To enable future studies of nociceptive capabilities in mantids, we sequenced and assembled a draft genome of the Chinese praying mantis (Tenodera sinensis) and identified multiple classes of nociceptive ion channels by comparison to orthologous gene families in Arthropoda. Our assembly-produced using PacBio HiFi reads-is fragmented (total size = 3.03 Gb; N50 = 1.8 Mb; 4,966 contigs), but is highly complete with respect to gene content (BUSCO complete = 98.7% [odb10_insecta]). The size of our assembly is substantially larger than that of most other insects, but is consistent with the size of other mantid genomes. We found that most families of nociceptive ion channels are present in the T. sinensis genome; that they are most closely related to those found in the damp-wood termite (Zootermopsis nevadensis); and that some families have expanded in T. sinensis while others have contracted relative to nearby lineages. Our findings suggest that mantids are likely to possess nociceptive capabilities and provide a foundation for future experimentation regarding ion channel functions and their consequences for insect behavior.
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Affiliation(s)
- Jay K Goldberg
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E Lowell St, Tucson, AZ 85741, USA
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Ln, Norwich, Norfolk NR4 7UH, UK
| | - R Keating Godfrey
- Department of Biological Sciences, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA
| | - Meghan Barrett
- Department of Biology, Indiana University Purdue University Indianapolis, 420 University Blvd, Indianapolis, IN 46202, USA
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Wu B, Zhao C, Zheng X, Peng Z, Liu M. Observation of Agonistic Behavior in Pacific White Shrimp ( Litopenaeus vannamei) and Transcriptome Analysis. Animals (Basel) 2024; 14:1691. [PMID: 38891739 PMCID: PMC11171402 DOI: 10.3390/ani14111691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Agonistic behavior has been identified as a limiting factor in the development of intensive L. vannamei aquaculture. However, the characteristics and molecular mechanisms underlying agonistic behavior in L. vannamei remain unclear. In this study, we quantified agonistic behavior through a behavioral observation system and generated a comprehensive database of eyestalk and brain ganglion tissues obtained from both aggressive and nonaggressive L. vannamei employing transcriptome analysis. The results showed that there were nine behavior patterns in L. vannamei which were correlated, and the fighting followed a specific process. Transcriptome analysis revealed 5083 differentially expressed genes (DEGs) in eyestalk and 1239 DEGs in brain ganglion between aggressive and nonaggressive L. vannamei. Moreover, these DEGs were primarily enriched in the pathways related to the energy metabolism process and signal transduction. Specifically, the phototransduction (dme04745) signaling pathway emerges as a potential key pathway for the adjustment of the L. vannamei agonistic behavior. The G protein-coupled receptor kinase 1-like (LOC113809193) was screened out as a significant candidate gene within the phototransduction pathway. Therefore, these findings contribute to an enhanced comprehension of crustacean agonistic behavior and provide a theoretical basis for the selection and breeding of L. vannamei varieties suitable for high-density aquaculture environments.
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Affiliation(s)
- Bo Wu
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo 315000, China; (B.W.); (C.Z.); (X.Z.)
| | - Chenxi Zhao
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo 315000, China; (B.W.); (C.Z.); (X.Z.)
| | - Xiafei Zheng
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo 315000, China; (B.W.); (C.Z.); (X.Z.)
| | - Zhilan Peng
- Zhejiang Engineering Research Center for Aquacultural Seeds Industry and Green Cultivation Technologies, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315000, China;
| | - Minhai Liu
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo 315000, China; (B.W.); (C.Z.); (X.Z.)
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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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Xiong X, Xie C, Li S, Wang Y, Jiang J, Xie D, Chen S, Xiong Y, Gan L. PvGeneExpDB: An integrative gene expression database for in-depth understanding on the Pacific white shrimp (Litopenaeus vannamei). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101227. [PMID: 38518736 DOI: 10.1016/j.cbd.2024.101227] [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: 01/12/2024] [Revised: 02/27/2024] [Accepted: 03/17/2024] [Indexed: 03/24/2024]
Abstract
The Pacific white shrimp (Litopenaeus vannamei) is a high-valued economic farming species. With the development of high-throughput sequencing technology, cumulative large-scale transcriptomic studies have been revealing molecular landscape of various biological conditions including genetic selection, breeding, evolution, disease landscape, etc. However, no single experiment or databases allow thorough investigations of transcriptomic dynamics for these progressions. Meanwhile, the available datasets are often scattered and lack management. Here, we have established PvGeneExpDB, the first gene expression database for L. vannamei (www.bio-marine-scau.com/pv_ex/), which encompasses gene expression profiles, differential expression, and co-expression analyses under various biological conditions. Based on the analyses of 7 datasets, which include 53 samples with accurate and detailed records, PvGeneExpDB identifies 20,599 novel transcripts, shows expression profiles of a total of 20,817 genes, and implements Gene Ontology (GO) reconstruction of 76.7 % of these genes. Besides, 26 co-expressed groups were first identified by large-scale, cross-sample Weighted Gene Co-expression Network Analysis (WGCNA). By integrating the gene expression data in the database, our goal is to deepen the biological understanding of L. vannamei.
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Affiliation(s)
- Xi Xiong
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China
| | - Chun Xie
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Sijun Li
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun-Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yanzhi Wang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun-Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Junyang Jiang
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China
| | - Dizhi Xie
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China
| | - Shijun Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China.
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun-Yat-sen University, Guangzhou, Guangdong 510006, China.
| | - Lian Gan
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China.
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Lin J, Wan H, Xue H, He Y, Peng B, Zhang Z, Wang Y. Transcriptomics reveals different response mechanisms of Litopenaeus vannamei hemocytes to injection of Vibrio parahaemolyticus and WSSV. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101201. [PMID: 38340389 DOI: 10.1016/j.cbd.2024.101201] [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: 10/05/2023] [Revised: 01/21/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024]
Abstract
As the most important cultural crustacean species worldwide, studies about Pacific white shrimp (Litopenaeus vannamei) have received more attention. It has been well-documented that various pathogens could infect L. vannamei, resulting in huge economic losses. The studies about the responding mechanism of L. vannamei to sole pathogens such as Vibrio parahaemolyticus and white spot virus (WSSV) have been extensively reported, while the studies about the differently responding mechanisms remain unclear. In the present study, we identified the differently expressed genes (DEGs) of L. vannamei hemocytes post V. parahaemolyticus and WSSV infection with RNA-seq technology and compared the DEGs between the two groups. The results showed 2672 DEGs post the V. parahaemolyticus challenge (1079 up-regulated and 1593 down-regulated genes), while 1146 DEGs post the WSSV challenge (1067 up-regulated and 513 down-regulated genes). In addition, we screened the genes that simultaneously respond to WSSV and V. parahaemolyticus (434), solely respond to WSSV (1146), and V. parahaemolyticus challenge (2238), respectively. Six DEGs involved in innate immunity were quantified to validate the RNA-seq results, and the results confirmed the high consistency of both methods. Furthermore, we found plenty of innate immunity-related genes that responded to V. parahaemolyticus and WSSV infection, including pattern recognition receptors (PRRs), the proPO activating system, antimicrobial peptides (AMPs), and other immunity-related proteins. The results revealed that they were differently expressed after different pathogen challenges, demonstrating the complex and specific recognition systems involved in defending against the invasion of different pathogens in the environment. The present study improved our understanding of the molecular response of hemocytes of L. vannamei to V. parahaemolyticus and WSSV stimulation.
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Affiliation(s)
- Jiaming Lin
- College of Marine Biology, Xiamen Ocean Vocational College, Xiamen 361100, China; Xiamen Key Laboratory of Intelligent Fishery, Xiamen 361100, China
| | - Haifu Wan
- Fisheries College, Jimei University, Xiamen 361021, China; Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Xiamen 361021, China
| | - Haibo Xue
- College of Marine Biology, Xiamen Ocean Vocational College, Xiamen 361100, China; Xiamen Key Laboratory of Intelligent Fishery, Xiamen 361100, China
| | - Yibin He
- College of Marine Biology, Xiamen Ocean Vocational College, Xiamen 361100, China; Xiamen Key Laboratory of Intelligent Fishery, Xiamen 361100, China
| | - Bohao Peng
- Fisheries College, Jimei University, Xiamen 361021, China; Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Xiamen 361021, China
| | - Ziping Zhang
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yilei Wang
- Fisheries College, Jimei University, Xiamen 361021, China; Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Xiamen 361021, China.
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10
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Zhang Y, Chen Z, Wang Y, Dong H, Sun J, Li J, Mao X. Molecular modelling studies reveal cryoprotective mechanism of L-Proline during the frozen storage of shrimp (Litopenaeus vannamei). Food Chem 2024; 441:138259. [PMID: 38185047 DOI: 10.1016/j.foodchem.2023.138259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/27/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
This study aimed to investigate the cryoprotective properties of proline (1% and 3% (w/v)) on shrimp. The cryoprotective mechanism was studied using physico-chemical experiments and molecular simulations. Proline had a notable positive impact on the thawing loss and texture of shrimp in comparison to the control. The denaturation of myosin in frozen shrimp was delayed by proline. Microscopy analysis demonstrated that proline effectively lowered the harm caused by ice crystals to shrimp muscle. Molecular simulations indicated that proline potentially exerted a cryoprotective effect primarily through the "water substitution" and "glassy state" hypotheses. Proline formed hydrogen bonds with myosin to replace the water molecules around myosin. Additionally, proline interacted with water molecules to form a glassy state, impeding the growth of ice crystals. Consequently, the stability of shrimp myosin was enhanced during freezing. In conclusion, proline demonstrated promise as an efficacious cryoprotectant for aquatic products.
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Affiliation(s)
- Yejun Zhang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Zhaohui Chen
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Yongzhen Wang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Hao Dong
- Shandong Meijia Group Co. Ltd., Rizhao 276800, PR China
| | - Jianan Sun
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China.
| | - Jiao Li
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China.
| | - Xiangzhao Mao
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
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11
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Perez-Enriquez R, Juárez OE, Galindo-Torres P, Vargas-Aguilar AL, Llera-Herrera R. Improved genome assembly of the whiteleg shrimp Penaeus (Litopenaeus) vannamei using long- and short-read sequences from public databases. J Hered 2024; 115:302-310. [PMID: 38451162 DOI: 10.1093/jhered/esae015] [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: 12/20/2023] [Accepted: 02/28/2024] [Indexed: 03/08/2024] Open
Abstract
The Pacific whiteleg shrimp Penaeus (Litopenaeus) vannamei is a highly relevant species for the world's aquaculture development, for which an incomplete genome is available in public databases. In this work, PacBio long-reads from 14 publicly available genomic libraries (131.2 Gb) were mined to improve the reference genome assembly. The libraries were assembled, polished using Illumina short-reads, and scaffolded with P. vannamei, Feneropenaeus chinensis, and Penaeus monodon genomes. The reference-guided assembly, organized into 44 pseudo-chromosomes and 15,682 scaffolds, showed an improvement from previous reference genomes with a genome size of 2.055 Gb, N50 of 40.14 Mb, L50 of 21, and the longest scaffold of 65.79 Mb. Most orthologous genes (92.6%) of the Arthropoda_odb10 database were detected as "complete," and BRAKER predicted 21,816 gene models; from these, we detected 1,814 single-copy orthologues conserved across the genomic references for Marsupenaeus japonicus, F. chinensis, and P. monodon. Transcriptomic-assembly data aligned in more than 99% to the new reference-guided assembly. The collinearity analysis of the assembled pseudo-chromosomes against the P. vannamei and P. monodon reference genomes showed high conservation in different sets of pseudo-chromosomes. In addition, more than 21,000 publicly available genetic marker sequences were mapped to single-site positions. This new assembly represents a step forward to previously reported P. vannamei assemblies. It will be helpful as a reference genome for future studies on the evolutionary history of the species, the genetic architecture of physiological and sex-determination traits, and the analysis of the changes in genetic diversity and composition of cultivated stocks.
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Affiliation(s)
- Ricardo Perez-Enriquez
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, B.C.S., Mexico
| | - Oscar E Juárez
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, B.C.S., Mexico
- Dirección de Investigación en Acuacultura, Programa de Recursos Genéticos, Instituto Mexicano de Investigación en Pesca y Acuacultura Sustentables, Coyoacán, Ciudad de México, Mexico
| | - Pavel Galindo-Torres
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, B.C.S., Mexico
| | - Ana Luisa Vargas-Aguilar
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, B.C.S., Mexico
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados, Unidad Mérida, Mérida, Yucatán, Mexico
| | - Raúl Llera-Herrera
- Functional Genomics Laboratory, Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mazatlán, Sinaloa, Mexico
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12
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Mangabeira-Silva IS, Soares PET, Vieira da Silva YT, Rodrigues de Albuquerque BHD, Câmera de Oliveira MTF, Ferreira LAH, Bezerra de Souza MF, Vieira de Lucena D, Paiva Pereira JM, Pinheiro e Silva RP, Lanza DCF. Characterization of microsatellite markers in the coding regions of the Penaeus vannamei genome. PLoS One 2024; 19:e0289351. [PMID: 38696386 PMCID: PMC11065258 DOI: 10.1371/journal.pone.0289351] [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: 12/11/2022] [Accepted: 07/18/2023] [Indexed: 05/04/2024] Open
Abstract
In this study, an extensive analysis of microsatellite markers (Single Tandem Repeats-STRs) in Penaeus vannamei was conducted at an advanced level. The markers were thoroughly examined, characterized, and specific markers located within coding regions were identified. Out of a total of 306 STRs, 117 were classified as perfect markers based on their single repeat motif. Among these perfect markers, 62 were found to be associated with predicted coding genes (mRNA), which were involved in various functions such as binding, catalytic activity, ATP-dependent activity, transcription, structural and molecular regulation. To validate the accuracy of the findings, a sample of nine markers was subjected to in vitro testing, which confirmed the presence of polymorphisms within the population. These results suggest the existence of different protein isoforms within the population, indicating the potential of these markers for application in both population and phenotype-genotype association studies. This innovative approach opens up new possibilities for investigating the impact of genomic plasticity in populations of P. vannamei.
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Affiliation(s)
- Iasmim Santos Mangabeira-Silva
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biotechnology, RENORBIO, Natal, RN, Brazil
| | - Paulo Eduardo Toscano Soares
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Yago Tomaz Vieira da Silva
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Beatriz Helena Dantas Rodrigues de Albuquerque
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Maryana Thalyta Ferreira Câmera de Oliveira
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | - Maria Fernanda Bezerra de Souza
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Danyllo Vieira de Lucena
- Postgraduate Program in Civil and Environmental Engineering, Federal University of Campina Grande, Campina Grande, PB, Brazil
| | | | | | - Daniel Carlos Ferreira Lanza
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biotechnology, RENORBIO, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
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13
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Wang XX, Ding MJ, Gao J, Zhao L, Cao R, Wang XW. Modulation of host lipid metabolism by virus infection leads to exoskeleton damage in shrimp. PLoS Pathog 2024; 20:e1012228. [PMID: 38739679 PMCID: PMC11115362 DOI: 10.1371/journal.ppat.1012228] [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: 12/06/2023] [Revised: 05/23/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
The arthropod exoskeleton provides protection and support and is vital for survival and adaption. The integrity and mechanical properties of the exoskeleton are often impaired after pathogenic infection; however, the detailed mechanism by which infection affects the exoskeleton remains largely unknown. Here, we report that the damage to the shrimp exoskeleton is caused by modulation of host lipid profiles after infection with white spot syndrome virus (WSSV). WSSV infection disrupts the mechanical performance of the exoskeleton by inducing the expression of a chitinase (Chi2) in the sub-cuticle epidermis and decreasing the cuticle chitin content. The induction of Chi2 expression is mediated by a nuclear receptor that can be activated by certain enriched long-chain saturated fatty acids after infection. The damage to the exoskeleton, an aftereffect of the induction of host lipogenesis by WSSV, significantly impairs the motor ability of shrimp. Blocking the WSSV-caused lipogenesis restored the mechanical performance of the cuticle and improved the motor ability of infected shrimp. Therefore, this study reveals a mechanism by which WSSV infection modulates shrimp internal metabolism resulting in phenotypic impairment, and provides new insights into the interactions between the arthropod host and virus.
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Affiliation(s)
- Xin-Xin Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ming-Jie Ding
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jie Gao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ling Zhao
- Department of Food Engineering and Nutrition, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Rong Cao
- Department of Food Engineering and Nutrition, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xian-Wei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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14
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Han Z, Wang Z, Rittschof D, Huang Z, Chen L, Hao H, Yao S, Su P, Huang M, Zhang YY, Ke C, Feng D. New genes helped acorn barnacles adapt to a sessile lifestyle. Nat Genet 2024; 56:970-981. [PMID: 38654131 DOI: 10.1038/s41588-024-01733-7] [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: 04/21/2023] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Barnacles are the only sessile lineages among crustaceans, and their sessile life begins with the settlement of swimming larvae (cyprids) and the formation of protective shells. These processes are crucial for adaptation to a sessile lifestyle, but the underlying molecular mechanisms remain poorly understood. While investigating these mechanisms in the acorn barnacle, Amphibalanus amphitrite, we discovered a new gene, bcs-6, which is involved in the energy metabolism of cyprid settlement and originated from a transposon by acquiring the promoter and cis-regulatory element. Unlike mollusks, the barnacle shell comprises alternate layers of chitin and calcite and requires another new gene, bsf, which generates silk-like fibers that efficiently bind chitin and aggregate calcite in the aquatic environment. Our findings highlight the importance of exploring new genes in unique adaptative scenarios, and the results will provide important insights into gene origin and material development.
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Affiliation(s)
- Zhaofang Han
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhixuan Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Daniel Rittschof
- Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC, USA
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Liying Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Huanhuan Hao
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, China
| | - Shanshan Yao
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, China
| | - Pei Su
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Miaoqin Huang
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China.
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
| | - Danqing Feng
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, China.
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15
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Alvanou MV, Feidantsis K, Lattos A, Stoforiadi A, Apostolidis AP, Michaelidis B, Giantsis IA. Influence of temperature on embryonic development of Pontastacus leptodactylus freshwater crayfish, and characterization of growth and osmoregulation related genes. BMC ZOOL 2024; 9:8. [PMID: 38679730 PMCID: PMC11057103 DOI: 10.1186/s40850-024-00198-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/10/2024] [Indexed: 05/01/2024] Open
Abstract
Narrow clawed crayfish, Pontastacus (Astacus) leptodactylus, represents an ecologically and economically valuable freshwater species. Despite the high importance of artificial breeding for conservation purpose and aquaculture potential, hatching protocols have not been developed so far in this species. Further, limited knowledge exists regarding the artificial egg incubation, the temperature effect on embryonic development, hatching synchronization and hatching rate. In the present study we investigated the temperature increase (from 17 oC to 22oC) effects in two different embryonic developmental stages of P. leptodactylus. Furthermore, two primer pairs for the Fibroblast Growth Factor Receptor 4 (FGFR4) gene cDNA amplification were successfully designed, characterising for the first time the FGFR4 gene in P. leptodactylus in relation to different developmental stages and temperatures. Apart from the FGFR4 gene, the Na+/K+-ATPase α-subunit expression was also explored. Both the FGFR4 and Na+/K+-ATPase α-subunit expression levels were higher in embryos closer to hatching. Egg incubation at 22oC for seven days led to significant increase of FGFR4 expression in embryos from earlier developmental stages. Nevertheless, temperature increase did not affect FGFR4 expression in eggs from latter developmental stages and Na+/K+-ATPase α-subunit expression in all developmental stages. Temperature increase represents therefore probably a promising strategy for accelerating hatching in freshwater crayfish particularly in early developmental stages. Specifically, our results indicate that FGFR4 expression increased in embryonic stages closer to hatching and that temperature influences significantly its expression in embryos from earlier developmental stages. Overall, these findings can provide a better understanding of artificial egg incubation of P. leptodactylus, and therefore can be employed for the effective management of this species, both for economic and biodiversity retention reasons.
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Affiliation(s)
- Maria V Alvanou
- Faculty of Agricultural Sciences, University of Western Macedonia, Florina, 53100, Greece
| | | | - Athanasios Lattos
- Faculty of Agricultural Sciences, University of Western Macedonia, Florina, 53100, Greece
| | - Anthi Stoforiadi
- Faculty of Agricultural Sciences, University of Western Macedonia, Florina, 53100, Greece
| | - Apostolos P Apostolidis
- Laboratory of Ichthyology & Fisheries, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Basile Michaelidis
- Laboratory of Animal Physiology, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Ioannis A Giantsis
- Faculty of Agricultural Sciences, University of Western Macedonia, Florina, 53100, Greece.
- Laboratory of Animal Physiology, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece.
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16
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Murphy EA, Kleiner FH, Helliwell KE, Wheeler GL. Channels of Evolution: Unveiling Evolutionary Patterns in Diatom Ca 2+ Signalling. PLANTS (BASEL, SWITZERLAND) 2024; 13:1207. [PMID: 38732422 PMCID: PMC11085791 DOI: 10.3390/plants13091207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024]
Abstract
Diatoms are important primary producers in marine and freshwater environments, but little is known about the signalling mechanisms they use to detect changes in their environment. All eukaryotic organisms use Ca2+ signalling to perceive and respond to environmental stimuli, employing a range of Ca2+-permeable ion channels to facilitate the movement of Ca2+ across cellular membranes. We investigated the distribution of different families of Ca2+ channels in diatom genomes, with comparison to other members of the stramenopile lineage. The four-domain voltage-gated Ca2+ channels (Cav) are present in some centric diatoms but almost completely absent in pennate diatoms, whereas single-domain voltage-gated EukCatA channels were found in all diatoms. Glutamate receptors (GLRs) and pentameric ligand-gated ion channels (pLGICs) also appear to have been lost in several pennate species. Transient receptor potential (TRP) channels are present in all diatoms, but have not undergone the significant expansion seen in brown algae. All diatom species analysed lacked the mitochondrial uniporter (MCU), a highly conserved channel type found in many eukaryotes, including several stramenopile lineages. These results highlight the unique Ca2+-signalling toolkit of diatoms and indicate that evolutionary gains or losses of different Ca2+ channels may contribute to differences in cellular-signalling mechanisms between species.
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Affiliation(s)
- Eleanor A. Murphy
- Marine Biological Association, Plymouth PL1 2PB, UK (K.E.H.)
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | | | - Katherine E. Helliwell
- Marine Biological Association, Plymouth PL1 2PB, UK (K.E.H.)
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Glen L. Wheeler
- Marine Biological Association, Plymouth PL1 2PB, UK (K.E.H.)
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17
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Du W, Li S, Li F. Different Immune Responses of Hemocytes from V. parahaemolyticus-Resistant and -Susceptible Shrimp at Early Infection Stage. BIOLOGY 2024; 13:300. [PMID: 38785782 PMCID: PMC11117703 DOI: 10.3390/biology13050300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/16/2024] [Accepted: 04/21/2024] [Indexed: 05/25/2024]
Abstract
Vibrio parahaemolyticus is one of the main causative agents leading to acute hepatopancreatic necrosis disease, the severe bacterial disease that occurs during shrimp aquaculture. Hemocytes play important roles during Vibrio infection. Previously, we found that there were few differentially expressed genes (DEGs) between hemocytes from V. parahaemolyticus-resistant and -susceptible shrimp before infection. We considered that there should be different immune responses between them after a pathogen infection. Here, the transcriptome data of hemocytes from V. parahaemolyticus-resistant and -susceptible shrimp before and after a pathogen infection were compared. The results showed that there were 157 DEGs responsive to infection in V. parahaemolyticus-resistant shrimp, while 33 DEGs in V. parahaemolyticus-susceptible shrimp. DEGs in V. parahaemolyticus-resistant shrimp were mainly related to immune and glycolytic processes, while those in V. parahaemolyticus-susceptible shrimp were mainly related to metabolism, with only two DEGs in common. A further analysis of genes involved in glucose metabolism revealed that GLUT2, HK, FBP, and PCK1 were lowly expressed while PC were highly expressed in hemocytes of the V. parahaemolyticus-resistant shrimp, indicating that glucose metabolism in shrimp hemocytes was related to a V. parahaemolyticus infection. After the knockdown of PC, the expression of genes in Toll and IMD signaling pathways were down-regulated, indicating that glucose metabolism might function through regulating host immunity during V. parahaemolyticus infection. The results suggest that the immune responses between V. parahaemolyticus-resistant and -susceptible shrimp were apparently different, which probably contribute to their different V. parahaemolyticus resistance abilities.
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Affiliation(s)
- Wenran Du
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China;
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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18
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Sha H, Lu J, Chen J, Xiong J. Rationally designed probiotics prevent shrimp white feces syndrome via the probiotics-gut microbiome-immunity axis. NPJ Biofilms Microbiomes 2024; 10:40. [PMID: 38605016 PMCID: PMC11009345 DOI: 10.1038/s41522-024-00509-5] [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: 10/03/2023] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Increasing evidence infers that some complex diseases are attributed to co-infection with multiple pathogens, such as shrimp white feces syndrome (WFS); however, there is a lack of experimental evidence to validate such causal link. This deficiency further impedes rational design of probiotics to elicit desired benefits to shrimp WFS resistance. Herein, we validated the causal roles of Vibrio fluvialis, V. coralliilyticus and V. tubiashii (in a ratio of 7:2:1) in shrimp WFS etiology, which fully satisfied Koch's postulates. Correspondingly, we precisely designed four antagonistic strains: Ruegeria lacuscaerulensis, Nioella nitratireducens, Bacillus subtilis and Streptomyces euryhalinus in a ratio of 4:3:2:1, which efficiently guarded against WFS. Dietary supplementation of the probiotics stimulated beneficial gut populations, streptomycin, short chain fatty acids, taurine metabolism potentials, network stability, tight junction, and host selection, while reducing turnover rate and average variation degree of gut microbiota, thereby facilitating ecological and mechanical barriers against pathogens. Additionally, shrimp immune pathways, such as Fcγ R-mediated phagocytosis, Toll-like receptor and RIG-I-like receptor signaling pathways conferring immune barrier, were activated by probiotics supplementation. Collectively, we establish an updated framework for precisely validating co-infection with multiple pathogens and rationally designing antagonistic probiotics. Furthermore, our findings uncover the underlying beneficial mechanisms of designed probiotics from the probiotics-gut microbiome-host immunity axis.
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Affiliation(s)
- Haonan Sha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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Si S, Zhang X, Yu Y, Zhong X, Zhang X, Yuan J, Li F. Structure and function analyses of the SRC gene in Pacific white shrimp Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2024; 147:109433. [PMID: 38336143 DOI: 10.1016/j.fsi.2024.109433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
SRC gene encodes scavenger receptor class C, a member of the scavenger receptor family, and has only been identified and investigated in invertebrates. Our previous studies have revealed that SRC is a novel candidate gene associated with body weight in Pacific white shrimp (Litopenaeus vannamei). In order to comprehend the underlying mechanism by which LvSRC affects shrimp growth, we analyzed the structure, phylogeny, expression profiles and RNA interference (RNAi) of this gene in L. vannamei. We found that LvSRC contains two CCP domains and one MAM domain, with the highest expression level in the heart and relatively low expression level in other tissues. Notably, LvSRC exhibited significantly higher expression levels in the fast-growing group among groups with different growth rates, suggesting its potential involvement as a gene contributing to the growth of L. vannamei. RNAi of LvSRC inhibited body length and body weight gain compared to the control groups. Moreover, through RNA-seq analysis, we identified 598 differentially expressed genes (DEGs), including genes associated with growth, immunity, protein processing and modification, signal transduction, lipid synthesis and metabolism. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed significant changes in the signaling pathways related to growth, lipid metabolism and immune response, suggesting that LvSRC exhibits the potential to participate in diverse physiological processes and immune regulation. These findings deepen our understanding of the structure and function of the SRC in shrimp and lay the foundation for further research into the regulatory mechanism of LvSRC. Additionally, they provide potential applications in shrimp genetics and breeding.
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Affiliation(s)
- Shuqing Si
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaoyun Zhong
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
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20
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Chen S, Shi C, Ye Y, Li R, Song W, Song C, Mu C, Ren Z, Wang C. Comparative Transcriptome Analysis Reveals the Light Spectra Affect the Growth and Molting of Scylla paramamosain by Changing the Chitin Metabolism. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:351-363. [PMID: 38498104 DOI: 10.1007/s10126-024-10301-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
Light is an essential ecological factor that has been demonstrated to affect aquatic animals' behavior, growth performance, and energy metabolism. Our previous study found that the full-spectrum light and cyan light could promote growth performance and molting frequency of Scylla paramamosain while it was suppressed by violet light. Hence, the purpose of this study is to investigate the underlying molecular mechanism that influences light spectral composition on the growth performance and molting of S. paramamosain. RNA-seq analysis and qPCR were employed to assess the differentially expressed genes (DEGs) of eyestalks from S. paramamosain reared under full-spectrum light (FL), violet light (VL), and cyan light (CL) conditions after 8 weeks trial. The results showed that there are 5024 DEGs in FL vs. VL, 3398 DEGs in FL vs. CL, and 3559 DEGs in VL vs. CL observed. GO analysis showed that the DEGs enriched in the molecular function category involved in chitin binding, structural molecular activity, and structural constituent of cuticle. In addition, the DEGs in FL vs. VL were mainly enriched in the ribosome, amino sugar and nucleotide sugar metabolism, lysosome, apoptosis, and antigen processing and presentation pathways by KEGG pathway analysis. Similarly, ribosome, lysosome, and antigen processing and presentation pathways were major terms that enriched in FL vs. CL group. However, only the ribosome pathway was significantly enriched in up-regulated DEGs in VL vs. CL group. Furthermore, five genes were randomly selected from DEGs for qPCR analysis to validate the RNA-seq data, and the result showed that there was high consistency between the RNA-seq and qPCR. Taken together, violet light exposure may affect the growth performance of S. paramamosain by reducing the ability of immunity and protein biosynthesis, and chitin metabolism.
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Affiliation(s)
- Shujian Chen
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, 818 Fenghua Road, Ningbo, 315211, China
- Marine Economic Research Center, Dong Hai Strategic Research Institute, Ningbo University, Ningbo University, 818 Fenghua Road, Ningbo, 315211, China
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, 818 Fenghua Road, Ningbo, 315211, China
| | - Ce Shi
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, 818 Fenghua Road, Ningbo, 315211, China.
- Marine Economic Research Center, Dong Hai Strategic Research Institute, Ningbo University, Ningbo University, 818 Fenghua Road, Ningbo, 315211, China.
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, 818 Fenghua Road, Ningbo, 315211, China.
| | - Yangfang Ye
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, 818 Fenghua Road, Ningbo, 315211, China
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, 818 Fenghua Road, Ningbo, 315211, China
| | - Ronghua Li
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, 818 Fenghua Road, Ningbo, 315211, China
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, 818 Fenghua Road, Ningbo, 315211, China
| | - Weiwei Song
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, 818 Fenghua Road, Ningbo, 315211, China
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, 818 Fenghua Road, Ningbo, 315211, China
| | - Changbin Song
- Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China
| | - Changkao Mu
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, 818 Fenghua Road, Ningbo, 315211, China
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, 818 Fenghua Road, Ningbo, 315211, China
| | - Zhiming Ren
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, 818 Fenghua Road, Ningbo, 315211, China
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, 818 Fenghua Road, Ningbo, 315211, China
| | - Chunlin Wang
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, 818 Fenghua Road, Ningbo, 315211, China
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, 818 Fenghua Road, Ningbo, 315211, China
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21
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Li Q, Liu X, Li L, Ge C, Jian L. A comprehensive analysis of hepatopancreas metabolomics and transcriptomics provides insights into the growth of three-year-old crabs (Eriocheir sinensis) under low temperature. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101182. [PMID: 38141371 DOI: 10.1016/j.cbd.2023.101182] [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: 10/05/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 12/25/2023]
Abstract
Low water temperature is a critical environmental factor limiting the size of cultivated aquatic individuals. However, it has found that a proportion of Eriocheir sinensis cultured in low water temperature with high-altitude can mature into three-year-old crabs, which present larger body size than conventional two-year-old crabs. Based on integrated transcriptomic and metabolomic analysis, the significantly difference focuses on metabolic pathways involving glycine, serine, and threonine metabolism, amino sugar and nucleotide sugar metabolism, cysteine and methionine metabolism, pantothenate and CoA biosynthesis, arginine and proline metabolism, and vitamin digestion and absorption. It revealed that the growth performance of three-year-old crabs is mainly regulated by improving its antioxidant defense to maintain physical fitness, while reducing protein consumption by intensifying energy supplement ability and enhancing the ability to digest and absorb nutrients at low temperature. This study provides new insights on the molecular and metabolic pathways that control E. sinensis growth at high-altitude and low water temperature, laying the theoretical basis for further artificial three-year-old crabs breeding.
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Affiliation(s)
- Qing Li
- Key Laboratory of Ecological Protection and Restoration of Typical Plateau Wetlands, Bijie 551700, Guizhou Province, China; College of Ecological Engineering, Guizhou University of Engineering Science, College Road, Bijie 551700, Guizhou Province, China; Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada.
| | - Xiangui Liu
- College of Ecological Engineering, Guizhou University of Engineering Science, College Road, Bijie 551700, Guizhou Province, China
| | - Lijuan Li
- Key Laboratory of Ecological Protection and Restoration of Typical Plateau Wetlands, Bijie 551700, Guizhou Province, China; College of Ecological Engineering, Guizhou University of Engineering Science, College Road, Bijie 551700, Guizhou Province, China
| | - Chuanlong Ge
- Key Laboratory of Ecological Protection and Restoration of Typical Plateau Wetlands, Bijie 551700, Guizhou Province, China; College of Ecological Engineering, Guizhou University of Engineering Science, College Road, Bijie 551700, Guizhou Province, China
| | - Li Jian
- Key Laboratory of Ecological Protection and Restoration of Typical Plateau Wetlands, Bijie 551700, Guizhou Province, China; College of Ecological Engineering, Guizhou University of Engineering Science, College Road, Bijie 551700, Guizhou Province, China
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22
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Liu LK, Jian JT, Jing SS, Gao RL, Chi XD, Tian G, Liu HP. The crustacean DNA virus tegument protein VP26 binds to SNAP29 to inhibit SNARE complex assembly and autophagic degradation. J Virol 2024; 98:e0140823. [PMID: 38189252 PMCID: PMC10878264 DOI: 10.1128/jvi.01408-23] [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: 09/09/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Autophagy generally functions as a cellular surveillance mechanism to combat invading viruses, but viruses have evolved various strategies to block autophagic degradation and even subvert it to promote viral propagation. White spot syndrome virus (WSSV) is the most highly pathogenic crustacean virus, but little is currently known about whether crustacean viruses such as WSSV can subvert autophagic degradation for escape. Here, we show that even though WSSV proliferation triggers the accumulation of autophagosomes, autophagic degradation is blocked in the crustacean species red claw crayfish. Interestingly, the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex including CqSNAP29, CqVAMP7, and the novel autophagosome SNARE protein CqSyx12 is required for autophagic flux to restrict WSSV replication, as revealed by gene silencing experiments. Simultaneously, the expressed WSSV tegument protein VP26, which likely localizes on autophagic membrane mediated by its transmembrane region, binds the Qb-SNARE domain of CqSNAP29 to competitively inhibit the binding of CqSyx12-Qa-SNARE with CqSNAP29-Qb-SNARE; this in turn disrupts the assembly of the CqSyx12-SNAP29-VAMP7 SNARE complex, which is indispensable for the proposed fusion of autophagosomes and lysosomes. Consequently, the autophagic degradation of WSSV is likely suppressed by the expressed VP26 protein in vivo in crayfish, thus probably protecting WSSV components from degradation via the autophagosome-lysosome pathway, resulting in evasion by WSSV. Collectively, these findings highlight how a DNA virus can subvert autophagic degradation by impairing the assembly of the SNARE complex to achieve evasion, paving the way for understanding host-DNA virus interactions from an evolutionary point of view, from crustaceans to mammals.IMPORTANCEWhite spot syndrome virus (WSSV) is one of the largest animal DNA viruses in terms of its genome size and has caused huge economic losses in the farming of crustaceans such as shrimp and crayfish. Detailed knowledge of WSSV-host interactions is still lacking, particularly regarding viral escape from host immune clearance. Intriguingly, we found that the presence of WSSV-VP26 might inhibit the autophagic degradation of WSSV in vivo in the crustacean species red claw crayfish. Importantly, this study is the first to show that viral protein VP26 functions as a core factor to benefit WSSV escape by disrupting the assembly of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex, which is necessary for the proposed fusion of autophagosomes with lysosomes for subsequent degradation. These findings highlight a novel mechanism of DNA virus evasion by blocking SNARE complex assembly and identify viral VP26 as a key candidate for anti-WSSV targeting.
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Affiliation(s)
- Ling-Ke Liu
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jiu-Ting Jian
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Shan-Shan Jing
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Rui-Lin Gao
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiao-Dong Chi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Geng Tian
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Hai-Peng Liu
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, China
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23
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Huo W, Qin L, Guo W, Zhang X, Du Q, Xia X. PvMR1, a novel C-type lectin plays a crucial role in the antibacterial immune response of Pacific white shrimp, Penaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2024; 145:109346. [PMID: 38163494 DOI: 10.1016/j.fsi.2023.109346] [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: 11/19/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
C-type lectins (CTLs) are important immune molecules in innate immune, which participate in non-self recognition and clearance of pathogens. Here, a new CTL with two distinct C-type lectin domains (CTLDs) from Pacific white shrimp Penaeus vannamei, designated as PvMR1 was identified. The obtained PvMR1 coding sequence (CDS) was 1044 bp long encoding a protein with 347 amino acids. PvMR1 had two CTLD, a conserved mannose-specific EPN motif and a galactose-specific QPD motif, clustering into the same branch as the crustacean CTLs. PvMR1 was widely distributed in shrimp tissues with the highest transcription level in the hepatopancreas, with significantly induced mRNA expression on the hepatopancreas and intestines after immune challenge with Vibrio anguillarum. In vitro assays with recombinant PvMR1 (rPvMR1) protein revealed that it exhibited a wide range of antimicrobial activity, bacterial binding ability, and bacterial agglutination activity in a Ca2+-independent manner. Moreover, PvMR1 promoted bacterial phagocytosis in hemocytes. Furthermore, rPvMR1 treatment could significantly enhance the bacterial clearance in hemolymph and greatly improved the survival of shrimp under V. anguillarum infection in vivo. These results collectively suggest that PvMR1 plays an important role in antibacterial immune response of P. vannamei.
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Affiliation(s)
- Weiran Huo
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Lu Qin
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Wanwan Guo
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Xiaowen Zhang
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Qiyan Du
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China.
| | - Xiaohua Xia
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China.
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24
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Hoyos-Gonzalez N, Ochoa-Leyva A, Benitez-Cardoza CG, Brieba LG, Lukaszewicz G, Trasviña-Arenas CH, Sotelo-Mundo RR. Identification of a cryptic functional apolipophorin-III domain within the Prominin-1 gene of Litopenaeus vannamei. Comp Biochem Physiol B Biochem Mol Biol 2024; 270:110928. [PMID: 38043730 DOI: 10.1016/j.cbpb.2023.110928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
The Apolipophorin-III (apoLp-III) is reported as an essential protein element in lipids transport and incorporation in lepidopterans. Structurally, apoLp-III has an α-helix bundle structure composed of five α-helices. Interestingly, classic studies proposed a structural switch triggered by its interaction with lipids, where the α-helix bundle opens. Currently, the study of the apoLp-III has been limited to insects, with no homologs identified in other arthropods. By implementing a structure-based search with the Phyre2 algorithm surveying the shrimp Litopenaeus vannamei's transcriptome, we identified a putative apoLp-III in this farmed penaeid (LvApoLp-III). Unlike canonical apoLp-III, the LvApoLp-III was identified as an internal domain within the transmembrane protein Prominin-1. Structural modeling using the template-based Phyre2 and template-free AlphaFold algorithms rendered two distinct structural topologies: the α-helix bundle and a coiled-coil structure. Notably, the secondary structure composition on both models was alike, with differences in the orientation and distribution of the α-helices and hydrophobic moieties. Both models provide insights into the classical structural switch induced by lipids in apoLp-III. To corroborate structure/function inferences, we cloned the synthetic LvApoLp-III domain, overexpressed, and purified the recombinant protein. Circular dichroism measurements with the recombinant LvApoLp-III agreed with the structural models. In vitro liposome interaction demonstrated that the apoLp-III domain within the PROM1 of L.vannamei associated similarly to exchangeable apolipoproteins. Altogether, this work reports the presence of an apolipophorin-III domain in crustaceans for the first time and opens questions regarding its function and importance in lipid metabolism or the immune system.
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Affiliation(s)
- Nallely Hoyos-Gonzalez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, Mexico. https://twitter.com/uga_langebio
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos 62210, Mexico. https://twitter.com/ibt_unam
| | - Claudia G Benitez-Cardoza
- Laboratorio de Bioquímica y Biofísica Computacional, ENMH, Instituto Politécnico Nacional, Mexico City, Mexico. https://twitter.com/IPN_mx
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, Mexico. https://twitter.com/uga_langebio
| | - German Lukaszewicz
- Instituto de Investigaciones Marinas y Costeras, IIMyC, FCEyN, UNMdP, CONICET, Mar del Plata B7608FBY, Argentina. https://twitter.com/fceyn_unmdp
| | - Carlos H Trasviña-Arenas
- Centro de Investigación sobre Envejecimiento, Centro de Investigación y de Estudios Avanzados (CINVESTAV) Unidad Sede Sur, Tlalpan, 14330 Mexico City, Mexico.
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C., Ejido La Victoria, Hermosillo, Sonora 83304, Mexico.
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25
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Li Y, Zhang X, Tong R, Xu Q, Zhang N, Liao Q, Pan L. Mechanisms of ammonotelism, epithelium damage, cellular apoptosis, and proliferation in gill of Litopenaeus vannamei under NH 4Cl exposure. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:15153-15171. [PMID: 38289553 DOI: 10.1007/s11356-024-32111-9] [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: 09/12/2023] [Accepted: 01/17/2024] [Indexed: 02/24/2024]
Abstract
Excessive ammonia-N in coastal environment and aquaculture threatens the health of marine organisms. To explore the mechanism of gill damage induced by ammonia-N, transcriptome of Litopenaeus vannamei 's gill was carried out under 20 mg/L NH4Cl for 0, 6, and 48 h. K-means clustering analysis suggested that ammonia excretion and metabolism-related genes were elevated. GO and KEGG enrichment analysis suggested that glycosyltransferase activity and amino acid metabolism were affected by ammonia. Moreover, histological observation via three staining methods gave clues on the changes of gill after ammonia-N exposure. Increased mucus, hemocyte infiltration, and lifting of the lamellar epithelium suggested that gill epithelium was suffering damage under ammonia-N stress. Meanwhile, the composition of extracellular matrix (ECM) in connective tissue changed. Based on the findings of transcriptomic and histological analysis, we further investigated the molecular mechanism of gill damage under multiple concentrations of NH4Cl (0, 2, 10, 20 mg/L) for multiple timepoints (0, 3, 6, 12, 24, 48, 72 h). First, ammonia excretion was elevated via ion channel, transporter, and exocytosis pathways, but hemolymph ammonia still kept at a high level under 20 mg/L NH4Cl exposure. Second, we focused on glycosaminoglycan metabolism which was related to the dynamics of ECM. It turned out that the degradation and biosynthesis of chondroitin sulfate (CS) were elevated, suggesting that the structure of CS might be destructed under ammonia-N stress and CS played an important role in maintaining gill structure. It was enlightening that the destructions occurred in extracellular regions were vital to gill damage. Third, ammonia-N stress induced a series of cellular responses including enhanced apoptosis, active inflammation, and inhibited proliferation which were closely linked and jointly led to the impairment of gill. Our results provided some insights into the physiological changes induced by ammonia-N and enriched the understandings of gill damage under environmental stress.
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Affiliation(s)
- Yaobing Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Xin Zhang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Ruixue Tong
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Qiuhong Xu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Ning Zhang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Qilong Liao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China.
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26
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Hyde CJ, Ventura T. CrustyBase v.2.0: new features and enhanced utilities to support open science. BMC Genomics 2024; 25:121. [PMID: 38281926 PMCID: PMC10823621 DOI: 10.1186/s12864-024-10033-7] [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: 10/24/2023] [Accepted: 01/20/2024] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Transcriptomes present a rich, multi-dimensional subset of genomics data. They provide broad insights into genetic sequence, and more significantly gene expression, across biological samples. This technology is frequently employed for describing the genetic response to experimental conditions and has created vast libraries of datasets which shed light on gene function across different tissues, diseases, diets and developmental stages in many species. However, public accessibility of these data is impeded by a lack of suitable software interfaces and databases with which to locate and analyse them. BODY: Here we present an update on the status of CrustyBase.org, an online resource for analysing and sharing crustacean transcriptome datasets. Since its release in October 2020, the resource has provided many thousands of transcriptome sequences and expression profiles to its users and received 19 new dataset imports from researchers across the globe. In this article we discuss user analytics which point towards the utilization of this resource. The architecture of the application has proven robust with over 99.5% uptime and effective reporting of bugs through both user engagement and the error logging mechanism. We also introduce several new features that have been developed as part of a new release of CrustyBase.org. Two significant features are described in detail, which allow users to navigate through transcripts directly by submission of transcript identifiers, and then more broadly by searching for encoded protein domains by keyword. The latter is a novel and experimental feature, and grants users the ability to curate gene families from any dataset hosted on CrustyBase in a matter of minutes. We present case studies to demonstrate the utility of these features. CONCLUSION Community engagement with this resource has been very positive, and we hope that improvements to the service will further enable the research of users of the platform. Web-based platforms such as CrustyBase have many potential applications across life science domains, including the health sector, which are yet to be realised. This leads to a wider discussion around the role of web-based resources in facilitating an open and collaborative research community.
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Affiliation(s)
- Cameron J Hyde
- Queensland Cyber Infrastructure Foundation, The University of Queensland, Level 5 Axon Building, St. Lucia, QLD, 4072, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Tomer Ventura
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.
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Kawato S, Nozaki R, Kondo H, Hirono I. Integrase-associated niche differentiation of endogenous large DNA viruses in crustaceans. Microbiol Spectr 2024; 12:e0055923. [PMID: 38063384 PMCID: PMC10871703 DOI: 10.1128/spectrum.00559-23] [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: 02/07/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Crustacean genomes harbor sequences originating from a family of large DNA viruses called nimaviruses, but it is unclear why they are present. We show that endogenous nimaviruses selectively insert into repetitive sequences within the host genome, and this insertion specificity was correlated with different types of integrases, which are DNA recombination enzymes encoded by the nimaviruses themselves. This suggests that endogenous nimaviruses have colonized various genomic niches through the acquisition of integrases with different insertion specificities. Our results point to a novel survival strategy of endogenous large DNA viruses colonizing the host genomes. These findings may clarify the evolution and spread of nimaviruses in crustaceans and lead to measures to control and prevent the spread of pathogenic nimaviruses in aquaculture settings.
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Affiliation(s)
- Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
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Miao M, Li S, Yu Y, Liu Y, Li F. Comparative transcriptome analysis of hepatopancreas reveals the potential mechanism of shrimp resistant to Vibrio parahaemolyticus infection. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109282. [PMID: 38081442 DOI: 10.1016/j.fsi.2023.109282] [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: 10/25/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
Vibrio parahaemolyticus carrying a pathogenic plasmid (VPAHPND) is one of the main causative agents of acute hepatopancreatic necrosis disease (AHPND) in shrimp aquaculture. Knowledge about the mechanism of shrimp resistant to VPAHPND is very helpful for developing efficient strategy for breeding AHPND resistant shrimp. In order to learn the mechanism of shrimp resistant to AHPND, comparative transcriptome was applied to analyze the different expressions of genes in the hepatopancreas of shrimp from different families with different resistance to VPAHPND. Through comparative analysis on the hepatopancreas of shrimp from VPAHPND resistant family and susceptible family, we found that differentially expressed genes (DEGs) were mainly involved in immune and metabolic processes. Most of the immune-related genes among DEGs were highly expressed in the hepatopancreas of shrimp from resistant family, involved in recognition of pathogen-associated molecular patterns, phagocytosis and elimination of pathogens, maintenance of reactive oxygen species homeostasis and other immune processes etc. However, most metabolic-related genes were highly expressed in the hepatopancreas of shrimp from susceptible family, involved in metabolism of lipid, vitamin, cofactors, glucose, carbohydrate and serine. Interestingly, when we analyzed the expression of above DEGs in the shrimp after VPAHPND infection, we found that the most of identified immune-related genes remained at high expression levels in the hepatopancreas of shrimp from the VPAHPND resistant family, and most of the identified metabolic-related genes were still at high expression levels in the hepatopancreas of shrimp from the VPAHPND susceptible family. The data suggested that the differential expression of these immune-related and metabolic-related genes in hepatopancreas might contribute to the resistance variations of shrimp to VPAHPND. These results provided valuable information for understanding the resistant mechanism of shrimp to VPAHPND.
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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, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yuan Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
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Hudson J, Egan S. Marine diseases and the Anthropocene: Understanding microbial pathogenesis in a rapidly changing world. Microb Biotechnol 2024; 17:e14397. [PMID: 38217393 PMCID: PMC10832532 DOI: 10.1111/1751-7915.14397] [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: 11/22/2023] [Accepted: 12/20/2023] [Indexed: 01/15/2024] Open
Abstract
Healthy marine ecosystems are paramount for Earth's biodiversity and are key to sustaining the global economy and human health. The effects of anthropogenic activity represent a pervasive threat to the productivity of marine ecosystems, with intensifying environmental stressors such as climate change and pollution driving the occurrence and severity of microbial diseases that can devastate marine ecosystems and jeopardise food security. Despite the potentially catastrophic outcomes of marine diseases, our understanding of host-pathogen interactions remains an understudied aspect of both microbiology and environmental research, especially when compared to the depth of information available for human and agricultural systems. Here, we identify three avenues of research in which we can advance our understanding of marine disease in the context of global change, and make positive steps towards safeguarding marine communities for future generations.
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Affiliation(s)
- Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyNew South WalesAustralia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyNew South WalesAustralia
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Wahl M, Levy T, Ventura T, Sagi A. Monosex Populations of the Giant Freshwater Prawn Macrobrachium rosenbergii-From a Pre-Molecular Start to the Next Generation Era. Int J Mol Sci 2023; 24:17433. [PMID: 38139271 PMCID: PMC10743721 DOI: 10.3390/ijms242417433] [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: 04/22/2023] [Revised: 10/27/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Sexual manipulation in the giant freshwater prawn Macrobrachium rosenbergii has proven successful in generating monosex (both all-male and all-female) populations for aquaculture using a crustacean-specific endocrine gland, the androgenic gland (AG), which serves as a key masculinizing factor by producing and secreting an insulin-like AG hormone (IAG). Here, we provide a summary of the advancements from the discovery of the AG and IAG in decapods through to the development of monosex populations in M. rosenbergii. We discuss the broader sexual development pathway, which is highly divergent across decapods, and provide our future perspective on the utility of novel genetic and genomic tools in promoting refined approaches towards monosex biotechnology. Finally, the future potential benefits of deploying monosex prawn populations for environmental management are discussed.
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Affiliation(s)
- Melody Wahl
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel;
| | - Tom Levy
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA;
- Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
| | - Tomer Ventura
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia;
- School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Amir Sagi
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel;
- 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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31
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Rahi ML, Mather PB, de Bello Cioffi M, Ezaz T, Hurwood DA. Genomic Basis of Freshwater Adaptation in the Palaemonid Prawn Genus Macrobrachium: Convergent Evolution Following Multiple Independent Colonization Events. J Mol Evol 2023; 91:976-989. [PMID: 38010517 DOI: 10.1007/s00239-023-10149-6] [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: 10/14/2022] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Adaptation to different salinity environments can enhance morphological and genomic divergence between related aquatic taxa. Species of prawns in the genus Macrobrachium naturally inhabit different osmotic niches and possess distinctive lifecycle traits associated with salinity tolerance. This study was conducted to investigate the patterns of adaptive genomic divergence during freshwater colonization in 34 Macrobrachium species collected from four continents; Australia, Asia, North and South America. Genotyping-by-sequencing (GBS) technique identified 5018 loci containing 82,636 single nucleotide polymorphisms (SNPs) that were used to reconstruct a phylogenomic tree. An additional phylogeny was reconstructed based on 43 candidate genes, previously identified as being potentially associated with freshwater adaptation. Comparison of the two phylogenetic trees revealed contrasting topologies. The GBS tree indicated multiple independent continent-specific invasions into freshwater by Macrobrachium lineages following common marine ancestry, as species with abbreviated larval development (ALD), i.e., species having a full freshwater life history, appeared reciprocally monophyletic within each continent. In contrast, the candidate gene tree showed convergent evolution for all ALD species worldwide, forming a single, well-supported clade. This latter pattern is likely the result of common evolutionary pressures selecting key mutations favored in continental freshwater habitats Results suggest that following multiple independent invasions into continental freshwaters at different evolutionary timescales, Macrobrachium taxa experienced adaptive genomic divergence, and in particular, convergence in the same genomic regions with parallel shifts in specific conserved phenotypic traits, such as evolution of larger eggs with abbreviated larval developmental.
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Affiliation(s)
- Md Lifat Rahi
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna, Bangladesh.
| | - Peter B Mather
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4001, Australia
| | - Marcelo de Bello Cioffi
- Department of Genetics and Evolution, Federal University of Sao Carlos, São Carlos, SP, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology (IAE), University of Canberra (UC), Canberra, ACT, 2617, Australia
| | - David A Hurwood
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4001, Australia
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Imaizumi K, Sano M, Kondo H, Hirono I. Insights Into a Chitin Synthase of Kuruma Shrimp Penaeus japonicus and Its Role in Peritrophic Membrane and Cuticle Formation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:837-845. [PMID: 37610536 DOI: 10.1007/s10126-023-10244-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023]
Abstract
Synthesis of chitin is a subject of great interest in the fields of physiology and immunology of crustaceans. Chitinous tissues include not only the carapace, but also an acellular membrane in the intestine called the peritrophic membrane (PM). Here, we describe the first report of chitin synthase (CHS) of a penaeid shrimp, kuruma shrimp Penaeus japonicus. Histological observations showed that fecal matter in the midgut of kuruma shrimp was wrapped with a PM, which physically separated it from the midgut epithelium. Subsequently, the chitin synthase transcript was amplified from the midgut of the shrimp. The chitin synthase gene of kuruma shrimp (MjCHS) encodes 1,523 amino acid residues. Structural prediction analysis showed that the N-terminal region of MjCHS protein included nine transmembrane helices, the middle region included the catalytic region with several conserved motifs which are found in CHSs from other arthropods, and the C-terminal region included seven transmembrane helices. Although insects have distinct exoskeletal and intestinal chitin synthases, the phylogenetic analysis suggested that crustaceans have a single CHS. MjCHS mRNA was constantly detected in the digestive tract, including the midgut and hepatopancreas of both juvenile and adult kuruma shrimp, suggesting a stable synthesis of chitin in those organs. In contrast, MjCHS mRNA was also detected in the hindgut and uropod of juvenile shrimp. After molting, the mRNA levels of MjCHS in the stomach and uropod were higher than other molting cycles. These results suggest that MjCHS contributes to chitin synthesis in both the digestive tract and the epidermis, providing fundamental insights into chitin synthesis of crustaceans.
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Affiliation(s)
- Kentaro Imaizumi
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Tokyo, Minato, 108-8477, Japan
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
| | - Motohiko Sano
- Laboratory of Fish Pathology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Tokyo, Minato, 108-8477, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Tokyo, Minato, 108-8477, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Tokyo, Minato, 108-8477, Japan.
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Wang H, Xiao B, Chen S, He J, Li C. Identification of an Ortholog of MALT1 from Shrimp That Induces NF-κB-Mediated Antiviral Immunity. Viruses 2023; 15:2361. [PMID: 38140602 PMCID: PMC10748089 DOI: 10.3390/v15122361] [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: 11/17/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
MALT1 (mucosa-associated lymphoid tissue lymphoma translocation protein 1) serves as a pivotal mediator for NF-κB activation in response to a wide spectrum of transmembrane receptor stimuli. In the present study, a homolog of MALT1, named LvMALT1, is cloned from the Pacific white shrimp (Litopenaeus vannamei) and its potential function in shrimp innate immunity is explored. The open reading frame of LvMALT1 is 2364 bp that encodes 787 amino acids. The predicted LvMALT1 protein structure comprises a death domain, three immunoglobulin domains, and a caspase-like domain, exhibiting remarkable similarity to other homologs. LvMALT1 is a cytoplasmic-localized protein and could interact with LvTRAF6. Overexpression of LvMALT1 induces the activation of promoter elements governing the expression of several key antimicrobial peptides (AMPs), including penaeidins (PENs) and crustins (CRUs). Conversely, silencing of LvMALT1 leads to a reduction in the phosphorylation levels of Dorsal and Relish, along with a concomitant decline in the in vivo expression levels of multiple AMPs. Furthermore, LvMALT1 is prominently upregulated in response to a challenge by the white spot syndrome virus (WSSV), facilitating the NF-κB-mediated expression of AMPs as a defense against viral infection. Taken together, we identified a MALT1 homolog from the shrimp L. vannamei, which plays a positive role in the TRAF6/NF-κB/AMPs axis-mediated innate immunity.
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Affiliation(s)
- Haiyang Wang
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Bang Xiao
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shihan Chen
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
- China-ASEAN Belt and Road Joint Laboratory on Marine Aquaculture Technology, Guangzhou 510275, China
| | - Chaozheng Li
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
- China-ASEAN Belt and Road Joint Laboratory on Marine Aquaculture Technology, Guangzhou 510275, China
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Li S, Chu KH, Wai CYY. Genomics of Shrimp Allergens and Beyond. Genes (Basel) 2023; 14:2145. [PMID: 38136967 PMCID: PMC10742822 DOI: 10.3390/genes14122145] [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: 10/25/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Allergy to shellfishes, including mollusks and crustaceans, is a growing health concern worldwide. Crustacean shellfish is one of the "Big Eight" allergens designated by the U.S. Food and Drug Administration and is the major cause of food-induced anaphylaxis. Shrimp is one of the most consumed crustaceans triggering immunoglobulin E (IgE)-mediated allergic reactions. Over the past decades, the allergen repertoire of shrimp has been unveiled based on conventional immunodetection methods. With the availability of genomic data for penaeid shrimp and other technological advancements like transcriptomic approaches, new shrimp allergens have been identified and directed new insights into their expression levels, cross-reactivity, and functional impact. In this review paper, we summarize the current knowledge on shrimp allergens, as well as allergens from other crustaceans and mollusks. Specific emphasis is put on the genomic information of the shrimp allergens, their protein characteristics, and cross-reactivity among shrimp and other organisms.
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Affiliation(s)
- Shanshan Li
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (S.L.); (K.H.C.)
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (S.L.); (K.H.C.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510000, China
| | - Christine Yee Yan Wai
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
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Zhang J, Liu K, Gong X, Zhang N, Zeng Y, Ren W, Huang A, Long H, Xie Z. Transcriptome analysis of the hepatopancreas from the Litopenaeus vannamei infected with different flagellum types of Vibrio alginolyticus strains. Front Cell Infect Microbiol 2023; 13:1265917. [PMID: 38076457 PMCID: PMC10703188 DOI: 10.3389/fcimb.2023.1265917] [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: 07/24/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Vibrio alginolyticus, one of the prevalently harmful Vibrio species found in the ocean, causes significant economic damage in the shrimp farming industry. Its flagellum serves as a crucial virulence factor in the invasion of host organisms. However, the processes of bacteria flagella recognition and activation of the downstream immune system in shrimp remain unclear. To enhance comprehension of this, a ΔflhG strain was created by in-frame deletion of the flhG gene in V. alginolyticus strain HN08155. Then we utilized the transcriptome analysis to examine the different immune responses in Litopenaeus vannamei hepatopancreas after being infected with the wild type and the mutant strains. The results showed that the ΔflhG strain, unlike the wild type, lost its ability to regulate flagella numbers negatively and displayed multiple flagella. When infected with the hyperflagella-type strain, the RNA-seq revealed the upregulation of several immune-related genes in the shrimp hepatopancreas. Notably, two C-type lectins (CTLs), namely galactose-specific lectin nattectin and macrophage mannose receptor 1, and the TNF receptor-associated factor (TRAF) 6 gene were upregulated significantly. These findings suggested that C-type lectins were potentially involved in flagella recognition in shrimp and the immune system was activated through the TRAF6 pathway after flagella detection by CTLs.
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Affiliation(s)
- Jingwen Zhang
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, China
- Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, China
| | - Kaifang Liu
- School of Fisheries, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Xiaoxiao Gong
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, China
- Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, China
| | - Na Zhang
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, China
- Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, China
| | - Yanhua Zeng
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, China
- Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou, China
| | - Wei Ren
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, China
- Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou, China
| | - Aiyou Huang
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, China
- Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou, China
| | - Hao Long
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, China
- Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou, China
| | - Zhenyu Xie
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, China
- Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou, China
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Zhang X, Xiang J, Yuan J, Li F. Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era. Genes (Basel) 2023; 14:2050. [PMID: 38002993 PMCID: PMC10671375 DOI: 10.3390/genes14112050] [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: 10/09/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Chromosome studies provide the foundation for comprehending inheritance, variation, systematics, and evolution. Penaeid shrimps are a group of crustaceans with great economic importance. Basic cytogenetic information obtained from these shrimps can be used to study their genome structure, chromosome relationships, chromosome variation, polyploidy manipulation, and breeding. The study of shrimp chromosomes experienced significant growth in the 1990s and has been closely linked to the progress of genome research since the application of next-generation sequencing technology. To date, the genome sequences of five penaeid shrimp species have been published. The availability of these genomes has ushered the study of shrimp chromosomes into the post-genomic era. Currently, research on shrimp cytogenetics not only involves chromosome counting and karyotyping, but also extends to investigating submicroscopic changes; exploring genome structure and regulation during various cell divisions; and contributing to the understanding of mechanisms related to growth, sexual control, stress resistance, and genome evolution. In this article, we provide an overview of the progress made in chromosome research on penaeid shrimp. We emphasize the mutual promotion between studies on chromosome structure and genome research and highlight the impact of chromosome-level assembly on studies of genome structure and function. Additionally, we summarize the emerging trends in post-genomic-era shrimp chromosome research.
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Affiliation(s)
- Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Yang L, Wang ZA, Gan Y, Zuo H, Deng H, Weng S, He J, Xu X. Basigin binds bacteria and activates Dorsal signaling to promote antibacterial defense in Penaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109123. [PMID: 37813154 DOI: 10.1016/j.fsi.2023.109123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
The NF-κB pathway plays an important role in immune regulation. Basigin, an immunoglobulin superfamily membrane protein, is involved in the activation of NF-κB. However, its role in NF-κB signaling in response to pathogen infection remains unclear. In this study, we identified the Basigin gene from Pacific white shrimp, Penaeus vannamei, a representative species for studying the innate immune system of invertebrates. Basigin promoted the degradation of the IκB homolog Cactus, facilitated the nuclear translocation of the NF-κB family member Dorsal, and positively regulated the expression of Dorsal pathway downstream antimicrobial peptide genes. Interestingly, recombinant Basigin protein could bind a variety of Gram-positive and Gram-negative bacteria. Silencing of Basigin inhibited the Dorsal signaling activated by V. parahaemolyticus infection and significantly decreased the survival rate of V. parahaemolyticus-infected shrimp. The expression levels of the antimicrobial peptides ALF1 and ALF2 were downregulated, and the phagocytosis of hemocytes was attenuated in Basigin-silenced shrimp. Similar results were observed in shrimp treated with a recombinant extracellular region of the Basigin protein that was able to compete with endogenous Basigin. Therefore, to the best of our knowledge, this study is the first to demonstrate the function of Basigin as a pathogen recognition receptor that activates NF-κB signaling for antibacterial immunity in shrimp.
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Affiliation(s)
- Linwei Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Zi-Ang Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Yushi Gan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Hongliang Zuo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Hengwei Deng
- School of Marine Biology and Fisheries, Hainan University, Haikou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Jianguo He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China.
| | - Xiaopeng Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China.
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Bai Y, Liu S, Hu Y, Yu H, Kong L, Xu C, Li Q. Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters. BMC Biol 2023; 21:204. [PMID: 37775818 PMCID: PMC10543319 DOI: 10.1186/s12915-023-01706-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Molluscan shell, composed of a diverse range of architectures and microstructures, is a classic model system to study the relationships between molecular evolution and biomineralized structure formation. The shells of oysters differ from those of other molluscs by possessing a novel microstructure, chalky calcite, which facilitates adaptation to the sessile lifestyle. However, the genetic basis and evolutionary origin of this adaptive innovation remain largely unexplored. RESULTS We report the first whole-genome assembly and shell proteomes of the Iwagaki oyster Crassostrea nippona. Multi-omic integrative analyses revealed that independently expanded and co-opted tyrosinase, peroxidase, TIMP genes may contribute to the chalky layer formation in oysters. Comparisons with other molluscan shell proteomes imply that von Willebrand factor type A and chitin-binding domains are basic members of molluscan biomineralization toolkit. Genome-wide identification and analyses of these two domains in 19 metazoans enabled us to propose that the well-known Pif may share a common origin in the last common ancestor of Bilateria. Furthermore, Pif and LamG3 genes acquire new genetic function for shell mineralization in bivalves and the chalky calcite formation in oysters likely through a combination of gene duplication and domain reorganization. CONCLUSIONS The spatial expression of SMP genes in the mantle and molecular evolution of Pif are potentially involved in regulation of the chalky calcite deposition, thereby shaping the high plasticity of the oyster shell to adapt to a sessile lifestyle. This study further highlights neo-functionalization as a crucial mechanism for the diversification of shell mineralization and microstructures in molluscs, which may be applied more widely for studies on the evolution of metazoan biomineralization.
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Affiliation(s)
- Yitian Bai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yiming Hu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Ye Y, Zhu B, Zhang J, Yang Y, Tian J, Xu W, Du X, Huang Y, Li Y, Zhao Y. Comparison of Growth Performance and Biochemical Components between Low-Salinity-Tolerant Hybrid and Normal Variety of Pacific White Shrimp ( Penaeus vannamei). Animals (Basel) 2023; 13:2837. [PMID: 37760237 PMCID: PMC10525212 DOI: 10.3390/ani13182837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Penaeus vannamei, a high-yield economical shrimp, is confronting germplasm degradation in the culture environments found in China, which results in a sharp drop in production. Genetic improvement by hybridization is an effective way to solve this problem. In this study, we selected the hybrid species adapted to low-salinity culture obtained by intraspecific crossing as the experimental group. The control group consisted of normal variety from the Hainan Lutai Company. The two groups of shrimps were cultured for three months under salinities of 1 PSU, 5 PSU, and 15 PSU. Growth-performance-related indicators, biochemical composition, and molting-related gene expression were examined. The results showed that at salinities of 1 PSU and 5 PSU, the survival rate and growth performance of the low-salt breeding group were better than those of the normal variety population. The digestive enzyme activity in the low-salt breeding group was higher, which was consistent with its better growth performance, and was also associated with higher triglyceride, total cholesterol, and glycogen content. Lower levels of lactic acid indicated less anaerobic metabolism and better adaptability to the environment. The amino acid and fatty acids analysis showed that levels of essential amino acids and high unsaturated fatty acids were both higher in the low-salt breeding group than in the normal variety shrimp cultured in a low-salinity environment. The expression levels of genes associated with molting (CHS, CaMKI, RXR, EcR, HSP60, and HSP70) were also higher in the low-salt breeding group than in the control group. The results indicated that the hybrid shrimp showed better growth performance and nutritional advantages compared with the normal shrimp under salinities of 1 PSU and 5 PSU. This research provides a valuable reference for subsequent genetic breeding and shrimp culture.
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Affiliation(s)
- Yucong Ye
- School of Life Science, East China Normal University, Shanghai 200241, China; (Y.Y.); (B.Z.); (J.Z.); (Y.Y.); (J.T.); (W.X.); (X.D.); (Y.H.)
| | - Bihong Zhu
- School of Life Science, East China Normal University, Shanghai 200241, China; (Y.Y.); (B.Z.); (J.Z.); (Y.Y.); (J.T.); (W.X.); (X.D.); (Y.H.)
| | - Junya Zhang
- School of Life Science, East China Normal University, Shanghai 200241, China; (Y.Y.); (B.Z.); (J.Z.); (Y.Y.); (J.T.); (W.X.); (X.D.); (Y.H.)
| | - Ying Yang
- School of Life Science, East China Normal University, Shanghai 200241, China; (Y.Y.); (B.Z.); (J.Z.); (Y.Y.); (J.T.); (W.X.); (X.D.); (Y.H.)
| | - Jiangtao Tian
- School of Life Science, East China Normal University, Shanghai 200241, China; (Y.Y.); (B.Z.); (J.Z.); (Y.Y.); (J.T.); (W.X.); (X.D.); (Y.H.)
| | - Wenyue Xu
- School of Life Science, East China Normal University, Shanghai 200241, China; (Y.Y.); (B.Z.); (J.Z.); (Y.Y.); (J.T.); (W.X.); (X.D.); (Y.H.)
| | - Xinglin Du
- School of Life Science, East China Normal University, Shanghai 200241, China; (Y.Y.); (B.Z.); (J.Z.); (Y.Y.); (J.T.); (W.X.); (X.D.); (Y.H.)
| | - Yizhou Huang
- School of Life Science, East China Normal University, Shanghai 200241, China; (Y.Y.); (B.Z.); (J.Z.); (Y.Y.); (J.T.); (W.X.); (X.D.); (Y.H.)
| | - Yiming Li
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fisheries Sciences, Shanghai 200092, China
| | - Yunlong Zhao
- School of Life Science, East China Normal University, Shanghai 200241, China; (Y.Y.); (B.Z.); (J.Z.); (Y.Y.); (J.T.); (W.X.); (X.D.); (Y.H.)
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
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Sun M, Yu Y, Li S, Liu Y, Zhang X, Li F. Integrated application of transcriptomics and metabolomics provides insights into acute hepatopancreatic necrosis disease resistance of Pacific white shrimp Litopenaeus vannamei. mSystems 2023; 8:e0006723. [PMID: 37358285 PMCID: PMC10469596 DOI: 10.1128/msystems.00067-23] [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: 01/19/2023] [Accepted: 05/04/2023] [Indexed: 06/27/2023] Open
Abstract
Acute hepatopancreatic necrosis disease (AHPND) has caused a huge economic loss to shrimp aquaculture. Vibrio parahaemolyticus (VpAHPND) is regarded as a major causative agent of AHPND in the Pacific white shrimp Litopenaeus vannamei. However, knowledge about how shrimp resist to AHPND is very limited. In order to learn the molecular mechanisms underlying AHPND resistance of shrimp, comparison between disease-resistant family and susceptible family of L. vannamei were performed at transcriptional and metabolic levels. Integrated analysis of transcriptomics and metabolomics on hepatopancreas of shrimp, the target tissue of VpAHPND, showed that significant differences existed between resistant family and susceptible family of shrimp. The susceptible family showed higher level of glycolysis, serine-glycine metabolism, purine and pyrimidine metabolism, but lower level of betaine-homocysteine metabolism in the hepatopancreas in comparison with the resistant family without VpAHPND infection. Curiously, VpAHPND infection induced up-regulation of glycolysis, serine-glycine metabolism, purine metabolism, pyrimidine metabolism, and pentose phosphate pathway, and down-regulation of betaine-homocysteine metabolism in resistant family. In addition, arachidonic acid metabolism and some immune pathways, like NF-κB and cAMP pathways, were up-regulated in the resistant family after VpAHPND infection. In contrast, amino acid catabolism boosted via PEPCK-mediated TCA cycle flux was activated in the susceptible family after VpAHPND infection. These differences in transcriptome and metabolome between resistant family and susceptible family might contribute to the resistance of shrimp to bacteria. IMPORTANCE Vibrio parahaemolyticus (VpAHPND) is a major aquatic pathogen causing acute hepatopancreatic necrosis disease (AHPND) and leads to a huge economic loss to shrimp aquaculture. Despite the recent development of controlling culture environment, disease resistant broodstock breeding is still a sustainable approach for aquatic disease control. Metabolic changes occurred during VpAHPND infection, but knowledge about the metabolism in resistance to AHPND is very limited. Integrated analysis of transcriptome and metabolome revealed the basal metabolic differences exhibited between disease-resistant and susceptible shrimp. Amino acid catabolism might contribute to the pathogenesis of VpAHPND and arachidonic acid metabolism might be responsible for the resistance phenotype. This study will help to enlighten the metabolic and molecular mechanisms underlying shrimp resistance to AHPND. Also, the key genes and metabolites of amino acid and arachidonic acid pathway identified in this study will be applied for disease resistance improvement in the shrimp culture industry.
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Affiliation(s)
- Mingzhe Sun
- 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
| | - Yang Yu
- 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
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 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
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yuan Liu
- 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
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 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
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 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
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, China
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Rutz C, Bonassin L, Kress A, Francesconi C, Boštjančić LL, Merlat D, Theissinger K, Lecompte O. Abundance and Diversification of Repetitive Elements in Decapoda Genomes. Genes (Basel) 2023; 14:1627. [PMID: 37628678 PMCID: PMC10454600 DOI: 10.3390/genes14081627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.
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Affiliation(s)
- Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Lena Bonassin
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Arnaud Kress
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Caterina Francesconi
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Ljudevit Luka Boštjančić
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Dorine Merlat
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
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Zhang X, Zhang X, Yuan J, Li F. The Responses of Alternative Splicing during Heat Stress in the Pacific White Shrimp Litopenaeus vannamei. Genes (Basel) 2023; 14:1473. [PMID: 37510377 PMCID: PMC10379218 DOI: 10.3390/genes14071473] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Heat tolerance is increasingly becoming a crucial trait for aquaculture species in the face of rapidly changing climate conditions. Alternative splicing (AS) is a vital mechanism within cells that modulates gene abundance and functional diversity, enabling organisms to effectively respond to diverse stressful conditions, including thermal stress. However, it is still uncertain whether AS contributes to heat tolerance in shrimp. In this study, we conducted an extensive transcriptome analysis on the Pacific white shrimp, Litopenaeus vannamei, revealing a total of 1267, 987, and 130 differential AS events (DAS) in the gill, hepatopancreas, and muscle, respectively, following exposure to heat stress. Among all of the DAS events, exon skipping (ES) was the predominant form of splicing modification observed. Interestingly, a minor portion of DAS genes exhibited overlap across the three tissues, implying that heat stress exerts unique effects on various tissue types. Moreover, the functional enrichment analysis demonstrated that commonly identified DAS genes were primarily associated with the "spliceosome" pathway, indicating that the AS of splicing-related genes played a crucial role in the response to heat stress. Our findings also revealed that heat stress tended to induce longer mRNA isoforms through differential alternative 3' splice site (A3SS) events. Notably, A3SS events exhibited the highest proportion of maintained open reading frames (ORFs) under heat stress. Interestingly, we observed a limited overlap between the genes exhibiting DAS and those showing differential gene expression (DEG), indicating that AS may function as a distinct regulatory mechanism independent of transcriptional regulation in response to heat stress. This is the first comprehensive study on AS in crustacea species under heat stress, which broadens our understanding of the regulatory mechanisms governing the crustaceans' response to environmental stress, providing valuable insights for the aquaculture breeding of shrimp and other aquatic animals.
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Affiliation(s)
- Xiaoxi Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, 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 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, 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 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, 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 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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Yu Y, Hu L, Tian D, Yu Y, Lu L, Zhang J, Huang X, Yan M, Chen L, Wu Z, Shi W, Liu G. Toxicities of polystyrene microplastics (MPs) and hexabromocyclododecane (HBCD), alone or in combination, to the hepatopancreas of the whiteleg shrimp, Litopenaeus vannamei. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121646. [PMID: 37105466 DOI: 10.1016/j.envpol.2023.121646] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/21/2023]
Abstract
The hepatopancreas is one of the largest organs playing crucial roles in metabolism and detoxification in crustacean invertebrates. Although toxicities have been increasingly documented for the two ubiquitous pollutants, hexabromocyclododecane (HBCD) and microplastics (MPs), in model animals, little is known about their impacts on the hepatopancreas of crustaceans. To fill this knowledge gap, the effects of MPs and HBCD, alone or in combination, on the hepatopancreas were evaluated in a commercially important crustacean species (the whiteleg shrimp) by histological observation as well as quantification of hepatic lesion-, metabolism-, and detoxification-related parameters. In addition, to reveal potential mechanisms underlying the hepatoxicity observed, the accumulation of HBCD in the shrimp and the status of oxidative stress were also investigated. Our results demonstrated that exposure of the whiteleg shrimp to MPs and HBCD for 4 weeks resulted in evident histological injury in the hepatopancreas and marked elevation in hepatic lesion markers (alanine aminotransferase and aspartate aminotransferase) in the hemolymph. Moreover, both metabolism (activity of phosphofructokinase, contents of lactic acid and adenosine triphosphate, and expression of metabolism-related genes) and detoxification (contents of cytochrome P450, UDP-glucuronosyltransferase, and glutathione, activity of glutathione S-transferase, and expression of detoxification-related genes) were found to be disrupted by the pollutants tested. In addition, exposure to MPs and HBCD also led to alterations in the contents and/or activities of antioxidant enzymes and resulted in oxidative damage to the hepatopancreas (indicated by marked elevation in malondialdehyde content). Furthermore, a significant amount of HBCD accumulated in shrimp treated with HBCD-containing seawater. The data also illustrated that HBCD-MP coexposure was more toxic than single exposure to these pollutants. These findings suggest that MPs and HBCD may exert hepatotoxic impacts on whiteleg shrimp by accumulating in vivo and inducing oxidative stress, which could pose a severe threat to the health of this important crustacean species.
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Affiliation(s)
- Yihan Yu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Lihua Hu
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou, 325005, China; Wenzhou Key Laboratory of Marine Biological Genetics and Breeding, Zhejiang Mariculture Research Institute, Wenzhou, 325005, China
| | - Dandan Tian
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Yingying Yu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Lingzheng Lu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Jiongming Zhang
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou, 325005, China; Wenzhou Key Laboratory of Marine Biological Genetics and Breeding, Zhejiang Mariculture Research Institute, Wenzhou, 325005, China
| | - Xianke Huang
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou, 325005, China; Wenzhou Key Laboratory of Marine Biological Genetics and Breeding, Zhejiang Mariculture Research Institute, Wenzhou, 325005, China
| | - Maocang Yan
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou, 325005, China; Wenzhou Key Laboratory of Marine Biological Genetics and Breeding, Zhejiang Mariculture Research Institute, Wenzhou, 325005, China
| | - Liangbiao Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhichao Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Wei Shi
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Guangxu Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China.
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Si S, Zhang X, Yu Y, Zhang X, Zhong X, Yuan J, Yang S, Li F. Structure and function analyses of the Mmd2 gene in pacific white shrimp Litopenaeus vannamei. Front Genet 2023; 14:1151193. [PMID: 37485334 PMCID: PMC10361620 DOI: 10.3389/fgene.2023.1151193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/15/2023] [Indexed: 07/25/2023] Open
Abstract
Monocyte to macrophage differentiation factor 2 gene (Mmd2) encodes a member of the progestin and adipoQ receptor (PAQR) family, and plays a key role in growth and development. Our previous studies had found Mmd2 (Monocyte to macrophage differentiation factor 2) is a new candidate gene for growth traits in Pacific white shrimp (Litopenaeus vannamei). For the purpose of understanding the underlying mechanism of LvMmd2 affecting the growth of shrimp, we analyzed the gene structure, phylogeny, expression profiles and RNA interference of this gene in L. vannamei. We found the LvMmd2 gene sequence was highly conserved in transmembrane regions, it was widely expressed in different tissues, with the highest expression level in the eye stalk. Knockdown LvMmd2 could significantly promote body length and body weight gain, suggesting it is a growth suppressor. Through transcriptome analysis we identified 422 differentially expressed genes (DEGs) between the dsMmd2 group and control group, among which 337 genes were upregulated in the dsMmd2 group, including numerous muscle-related genes and protein synthesis genes. Further bioinformatics analysis showed that growth, metabolism, and immune-related signal pathway had changed significantly. The above results greatly increase our understanding on the conservative structure and function of LvMmd2 gene, and provide potential application prospects in genetics and breeding.
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Affiliation(s)
- Shuqing Si
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- School of Life and Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- School of Life and Sciences, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xiaoyun Zhong
- 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
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Song Yang
- School of Life and Sciences, Qingdao Agricultural University, Qingdao, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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45
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Zuo B, Nneji LM, Sun YB. Comparative genomics reveals insights into anuran genome size evolution. BMC Genomics 2023; 24:379. [PMID: 37415107 DOI: 10.1186/s12864-023-09499-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/30/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types. RESULTS Our results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats. CONCLUSIONS Overall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.
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Affiliation(s)
- Bin Zuo
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China
| | - Lotanna Micah Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Yan-Bo Sun
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China.
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, 650091, China.
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Yang L, Han D, Wang ZA, Chen N, Zuo H, Guo Z, Xu M, Weng S, He J, Xu X. The Hippo-Yki pathway downstream transcription factor Scalloped negatively regulates immune defense against Vibrio parahaemolyticus infection in shrimp. FISH & SHELLFISH IMMUNOLOGY 2023:108917. [PMID: 37355218 DOI: 10.1016/j.fsi.2023.108917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 06/26/2023]
Abstract
The Hippo-Yki signaling pathway plays a crucial role in numerous biological processes. Previous studies have demonstrated the significance of signal transduction components of the Hippo pathway in the immune response of shrimp. In this study, the downstream transcription factor of the Hippo signaling pathway, Scalloped, was analyzed in the context of Vibrio parahaemolyticus infection in Pacific white shrimp, Penaeus vannamei. Upon bacterial and fungal infections, the expression of Scalloped was upregulated in hemocytes. Scalloped was found to localize in the nucleus and interact with the Hippo pathway downstream transcriptional co-activator Yki. With the assistance of Yki, Scalloped activated the promoter of Cactus, which is a cytoplasmic inhibitor of the NF-κB pathway, leading to the inhibition of the nuclear translocation of the NF-κB family member Dorsal in shrimp. By inhibiting the Dorsal pathway, Scalloped reduced the expression of immune functional proteins and negatively regulated the immune response against bacterial infection in shrimp. RNAi-mediated silencing of Scalloped significantly enhanced the survival rate of V. parahaemolyticus-infected shrimp and reduced the bacterial load in tissues. These findings demonstrate the potential of Scalloped as a therapeutic target for vibriosis in crustaceans and contribute to our understanding of the shrimp's antibacterial defense and the functional roles of Hippo signaling in animal immunity.
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Affiliation(s)
- Linwei Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Deyu Han
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Zi-Ang Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Nuo Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Hongliang Zuo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Zhixun Guo
- South China Sea Fisheries Research Institute (CAFS), Guangzhou, 510300, PR China
| | - Menghuang Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China
| | - Jianguo He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Xiaopeng Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China.
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47
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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: 5] [Impact Index Per Article: 5.0] [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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48
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Chen Y, Luo K, Zhang B, Lu Z, Wang F. Shrimp MANF maintains hemocyte viability via interaction with a tyrosine kinase Abl. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 143:104675. [PMID: 36863646 DOI: 10.1016/j.dci.2023.104675] [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: 11/03/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a highly conserved cell protective protein. In this study, we explored its functions in shrimp hemocytes. Our results indicated that LvMANF knockdown could cause a decrease in total hemocyte count (THC) and an increase in caspase3/7 activity. To further explore its working mechanism, transcriptomic analyses were performed with wild-type and LvMANF-knockdown hemocytes. Three upregulated genes from transcriptomic data, including FAS-associated factor 2, rho-associated protein kinase 1, and serine/threonine-protein kinase WNK4 were validated with qPCR. Further experiments showed that LvMANF knockdown and tyrosine kinase LvAbl knockdown could decrease tyrosine phosphorylation in shrimp hemocytes. In addition, the interaction between LvMANF and LvAbl was validated with immunoprecipitation. The knockdown of LvMANF would decrease ERK phosphorylation and increase LvAbl expression. Our results suggest intracellular LvMANF may maintain shrimp hemocyte viability by interacting with LvAbl.
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Affiliation(s)
- Yaohui Chen
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China
| | - Kaiwen Luo
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China
| | - Baoyuan Zhang
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China
| | - Zhiyao Lu
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China
| | - Fan Wang
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China; Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
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49
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Zhang Q, Chen HJ, Xie CZ, Qiu GF. Potential role for the germ cell-specific Rad21 in early meiosis of oocyte and spermatocyte in the Chinese mitten crab Eriocheir sinensis. Gene 2023; 862:147262. [PMID: 36764338 DOI: 10.1016/j.gene.2023.147262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Rad21/Rec8 family proteins are vital for sister chromatid segregation in mitosis and homologous recombination in meiosis, but no molecular data are available in crustacean species. In this study, a germ cell-specific Rad21 named EsRad21 was identified in the crab Eriocheir sinensis. EsRad21 mRNA has an open reading frame of 2310 base pairs (bp) encoding a 769 amino acids (aa) protein. RT-PCR showed that EsRad21 mRNA was particularly expressed in testis and ovary. The RT-qPCR results further revealed that the EsRad21 mRNA exhibited similar expression pattern in gonads at various developmental stages. EsRad21 mRNA expression level was the highest in testis at early spermatogenesis stage and ovaries at previtellogenesis stage, thereafter decreased significantly at middle spermatogenesis and vitellogenesis, and finally reach the lowest level at late spermatogenesis and vitellogenesis. In situ hybridization (ISH) analysis showed that EsRad21 mRNA was exclusively expressed in germline cells, but not in gonadal somatic cells. Notably, hybridized signal was detected on chromosomes of metaphase spermatocytes. EsRad21 is thus an underlying helpful indicator of the early phases of germ cell development. RNAi knockdown of EsRad21 downregulated the expression of other meiosis-related genes like Smc5-Smc6 and SPO11 and resulted in high mortality of individuals after 24 h post injection of EsRad21 dsRNA. Taken together, our results showed a potential role for EsRad21 in early meiosis of oocytes and spermatocytes in E. sinensis. This is the first report on the molecular characterization of the Rad21 transcript in a crustacean species.
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Affiliation(s)
- Qin Zhang
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Hong-Jun Chen
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Chi-Zhen Xie
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Gao-Feng Qiu
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
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50
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Zhang X, Zhang X, Yuan J, Li F. ACD-containing chaperones reveal the divergent thermo-tolerance in penaeid shrimp. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163239. [PMID: 37023801 DOI: 10.1016/j.scitotenv.2023.163239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/14/2023]
Abstract
The α-crystallin domain-containing (ACD-containing) gene family, which includes typical small heat shock proteins (sHSPs), is the most ubiquitous and diverse family of putative chaperones in all organisms, including eukaryotes and prokaryotes. In the present study, approximately 54-117 ACD-containing genes were identified in five penaeid shrimp species, yielding a significant expansion in comparison with other crustaceans (generally 6-20 ACD-containing genes). Unlike typical sHSPs, which contain a single ACD domain, the ACD-containing genes of penaeid shrimp contain additional ACD domains (3-7 domains, in general), thus having a larger molecular weight and a more complex 3D structure. As indicated by the RNA-seq and qRT-PCR results, the ACD-containing genes of penaeid shrimp showed a strong response to high temperatures. Furthermore, heterologous expression and citrate synthase assays of three representative ACD-containing genes confirmed that their chaperone activity could enhance the thermo-tolerance of E. coli and prevent the aggregation of substrate proteins at high temperatures. Compared with penaeid shrimp species with a relatively low thermo-tolerance (Fenneropenaeus chinensis and Marsupenaeus japonicus), the species with high thermo-tolerance (Litopenaeus vannamei and Fenneropenaeus indicus) contained more ACD-containing genes due to tandem duplication and exhibited biased expression levels under high temperatures. This can explain the divergent thermo-tolerance of different penaeid shrimp species. In conclusion, the ACD-containing genes in penaeid shrimp could be assigned as new chaperones and contribute to their divergent thermo-tolerance phenotypes and adaptations to the ecological environment.
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Affiliation(s)
- Xiaoxi Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, 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 266071, China; 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
| | - Jianbo Yuan
- Chinese Academy of Sciences (CAS) and Shandong Province 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 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, 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 266071, China; 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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