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Zhang E, Li Z, Dong L, Feng Y, Sun G, Xu X, Wang Z, Cui C, Wang W, Yang J. Exploration of Molecular Mechanisms of Immunity in the Pacific Oyster ( Crassostrea gigas) in Response to Vibrio alginolyticus Invasion. Animals (Basel) 2024; 14:1707. [PMID: 38891754 PMCID: PMC11171025 DOI: 10.3390/ani14111707] [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: 04/26/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Over the years, oysters have faced recurring mass mortality issues during the summer breeding season, with Vibrio infection emerging as a significant contributing factor. Tubules of gill filaments were confirmed to be in the hematopoietic position in Crassostrea gigas, which produce hemocytes with immune defense capabilities. Additionally, the epithelial cells of oyster gills produce immune effectors to defend against pathogens. In light of this, we performed a transcriptome analysis of gill tissues obtained from C. gigas infected with Vibrio alginolyticus for 12 h and 48 h. Through this analysis, we identified 1024 differentially expressed genes (DEGs) at 12 h post-injection and 1079 DEGs at 48 h post-injection. Enrichment analysis of these DEGs revealed a significant association with immune-related Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. To further investigate the immune response, we constructed a protein-protein interaction (PPI) network using the DEGs enriched in immune-associated KEGG pathways. This network provided insights into the interactions and relationships among these genes, shedding light on the underlying mechanisms of the innate immune defense mechanism in oyster gills. To ensure the accuracy of our findings, we validated 16 key genes using quantitative RT-PCR. Overall, this study represents the first exploration of the innate immune defense mechanism in oyster gills using a PPI network approach. The findings provide valuable insights for future research on oyster pathogen control and the development of oysters with enhanced antimicrobial resistance.
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Affiliation(s)
- Enshuo Zhang
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
| | - Zan Li
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
- Yantai Haiyu Marine Technology Co., Ltd., Yantai 264000, China
| | - Luyao Dong
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Yanwei Feng
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
- Yantai Haiyu Marine Technology Co., Ltd., Yantai 264000, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
- Yantai Haiyu Marine Technology Co., Ltd., Yantai 264000, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
- Yantai Haiyu Marine Technology Co., Ltd., Yantai 264000, China
| | - Zhongping Wang
- Yantai Kongtong Island Industrial Co., Ltd., Yantai 264000, China
| | - Cuiju Cui
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
- Yantai Haiyu Marine Technology Co., Ltd., Yantai 264000, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
- Yantai Kongtong Island Industrial Co., Ltd., Yantai 264000, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
- Yantai Haiyu Marine Technology Co., Ltd., Yantai 264000, China
- Yantai Kongtong Island Industrial Co., Ltd., Yantai 264000, China
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Zhang E, Li Z, Lv T, Fu J, Dong L, Feng Y, Sun G, Xu X, Cui C, Wang W, Yang J. Transcriptome profiling explores the immune defence mechanism of triploid Pacific oyster (Crassostrea gigas) blood against Vibrio alginolyticus based on protein interaction networks. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 143:104677. [PMID: 36870582 DOI: 10.1016/j.dci.2023.104677] [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: 12/20/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Triploid oysters have provided the oyster industry with many benefits, such as fast growth rates, meat quality improvement, and increased oyster production and economic benefits, since the first report on triploid oysters was published. The development of polyploid technology has remarkably increased the output of triploid oysters to meet the increasing demand of consumers for Crassostrea gigas in the past decades. At present, research on triploid oyster has mainly focused on breeding and growth, but studies on the immunity of triploid oysters are limited. According to recent reports, Vibrio alginolyticus is a highly virulent strain that can cause disease and death in shellfish, shrimp, as well as serious economic losses. V. alginolyticus may be a reason why oysters die during summer. Therefore, using V. alginolyticus to explore the resistance and immune defense mechanisms of triploid oysters against pathogens presents practical significance. Transcriptome analysis of gene expression was performed in triploid C. gigas at 12 and 48 h after infection with V. alginolyticus, and the respective 2257 and 191 differentially expressed genes (DEGs) were identified. The results of GO and KEGG enrichment analyses showed that multiple significantly enriched GO terms and KEGG signaling pathways are associated with immunity. A protein-protein interaction network was constructed to investigate the interaction relationship of immune-related genes. Finally, we verified the expression situation of 16 key genes using quantitative RT-PCR. This study is the first to use the PPI network in exploring the immune defense mechanism of triploid C. gigas blood to fill the gap in the immune mechanism of triploid oysters and other mollusks, and provide valuable reference for future triploid farming and pathogen prevention and control.
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Affiliation(s)
- Enshuo Zhang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Zan Li
- School of Agriculture, Ludong University, Yantai, 264025, China.
| | - Tingjin Lv
- Yantai Institute of Marine Economy, Yantai, 264003, China
| | - Jingjing Fu
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Luyao Dong
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Yanwei Feng
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Cuiju Cui
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai, 264025, China.
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, 264025, China
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Erofeeva TV, Grigorenko AP, Gusev FE, Kosevich IA, Rogaev EI. Studying of Molecular Regulation of Developmental Processes of Lower Metazoans Exemplified by Cnidaria Using High-Throughput Sequencing. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:269-293. [PMID: 35526848 DOI: 10.1134/s0006297922030075] [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: 10/28/2021] [Revised: 12/13/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
A unique set of features and characteristics of species of the Cnidaria phylum is the one reason that makes them a model for a various studies. The plasticity of a life cycle and the processes of cell differentiation and development of an integral multicellular organism associated with it are of a specific scientific interest. A new stage of development of molecular genetic methods, including methods for high-throughput genome, transcriptome, and epigenome sequencing, both at the level of the whole organism and at the level of individual cells, makes it possible to obtain a detailed picture of the development of these animals. This review examines some modern approaches and advances in the reconstruction of the processes of ontogenesis of cnidarians by studying the regulatory signal transduction pathways and their interactions.
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Affiliation(s)
- Taisia V Erofeeva
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anastasia P Grigorenko
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Fedor E Gusev
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Igor A Kosevich
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Evgeny I Rogaev
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
- Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
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A comparative genomics study of neuropeptide genes in the cnidarian subclasses Hexacorallia and Ceriantharia. BMC Genomics 2020; 21:666. [PMID: 32993486 PMCID: PMC7523074 DOI: 10.1186/s12864-020-06945-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/24/2020] [Indexed: 12/24/2022] Open
Abstract
Background Nervous systems originated before the split of Proto- and Deuterostomia, more than 600 million years ago. Four animal phyla (Cnidaria, Placozoa, Ctenophora, Porifera) diverged before this split and studying these phyla could give us important information on the evolution of the nervous system. Here, we have annotated the neuropeptide preprohormone genes of twenty species belonging to the subclass Hexacorallia or Ceriantharia (Anthozoa: Cnidaria), using thirty-seven publicly accessible genome or transcriptome databases. Studying hexacorals is important, because they are versatile laboratory models for development (e.g., Nematostella vectensis) and symbiosis (e.g., Exaiptasia diaphana) and also are prominent reef-builders. Results We found that each hexacoral or ceriantharian species contains five to ten neuropeptide preprohormone genes. Many of these preprohormones contain multiple copies of immature neuropeptides, which can be up to 50 copies of identical or similar neuropeptide sequences. We also discovered preprohormones that only contained one neuropeptide sequence positioned directly after the signal sequence. Examples of them are neuropeptides that terminate with the sequence RWamide (the Antho-RWamides). Most neuropeptide sequences are N-terminally protected by pyroglutamyl (pQ) or one or more prolyl residues, while they are C-terminally protected by an amide group. Previously, we isolated and sequenced small neuropeptides from hexacorals that were N-terminally protected by an unusual L-3-phenyllactyl group. In our current analysis, we found that these N-phenyllactyl-peptides are derived from N-phenylalanyl-peptides located directly after the signal sequence of the preprohormone. The N-phenyllactyl- peptides appear to be confined to the hexacorallian order Actiniaria and do not occur in other cnidarians. On the other hand, (1) the neuropeptide Antho-RFamide (pQGRFamide); (2) peptides with the C-terminal sequence GLWamide; and (3) tetrapeptides with the X1PRX2amide consensus sequence (most frequently GPRGamide) are ubiquitous in Hexacorallia. Conclusions We found GRFamide, GLWamide, and X1PRX2amide peptides in all tested Hexacorallia. Previously, we discovered these three neuropeptide classes also in Cubozoa, Scyphozoa, and Staurozoa, indicating that these neuropeptides originated in the common cnidarian ancestor and are evolutionarily ancient. In addition to these ubiquitous neuropeptides, other neuropeptides appear to be confined to specific cnidarian orders or subclasses.
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Ohdera A, Ames CL, Dikow RB, Kayal E, Chiodin M, Busby B, La S, Pirro S, Collins AG, Medina M, Ryan JF. Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa). Gigascience 2019; 8:giz069. [PMID: 31257419 PMCID: PMC6599738 DOI: 10.1093/gigascience/giz069] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 03/27/2019] [Accepted: 05/21/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Anthozoa, Endocnidozoa, and Medusozoa are the 3 major clades of Cnidaria. Medusozoa is further divided into 4 clades, Hydrozoa, Staurozoa, Cubozoa, and Scyphozoa-the latter 3 lineages make up the clade Acraspeda. Acraspeda encompasses extraordinary diversity in terms of life history, numerous nuisance species, taxa with complex eyes rivaling other animals, and some of the most venomous organisms on the planet. Genomes have recently become available within Scyphozoa and Cubozoa, but there are currently no published genomes within Staurozoa and Cubozoa. FINDINGS Here we present 3 new draft genomes of Calvadosia cruxmelitensis (Staurozoa), Alatina alata (Cubozoa), and Cassiopea xamachana (Scyphozoa) for which we provide a preliminary orthology analysis that includes an inventory of their respective venom-related genes. Additionally, we identify synteny between POU and Hox genes that had previously been reported in a hydrozoan, suggesting this linkage is highly conserved, possibly dating back to at least the last common ancestor of Medusozoa, yet likely independent of vertebrate POU-Hox linkages. CONCLUSIONS These draft genomes provide a valuable resource for studying the evolutionary history and biology of these extraordinary animals, and for identifying genomic features underlying venom, vision, and life history traits in Acraspeda.
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Affiliation(s)
- Aki Ohdera
- Department of Biology, Pennsylvania State University, 326 Mueller, University Park, PA, 16801, USA
| | - Cheryl L Ames
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th Street & Constitution Avenue NW, Washington DC, 20560, USA
- National Center for Biotechnology Information, 8600 Rockville Pike MSC 3830, Bethesda, MD, 20894, USA
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 10th Street & Constitution Avenue NW, Washington DC, 20560, USA
| | - Ehsan Kayal
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th Street & Constitution Avenue NW, Washington DC, 20560, USA
- UPMC, CNRS, FR2424, ABiMS, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Marta Chiodin
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Ben Busby
- National Center for Biotechnology Information, 8600 Rockville Pike MSC 3830, Bethesda, MD, 20894, USA
| | - Sean La
- National Center for Biotechnology Information, 8600 Rockville Pike MSC 3830, Bethesda, MD, 20894, USA
- Department of Mathematics, Simon Fraser University, 8888 University Drive, Barnaby, British Columbia, BC, V5A 1S6, Canada
| | - Stacy Pirro
- Iridian Genomes, Inc., 6213 Swords Way, Bethesda, MD, 20817, USA
| | - Allen G Collins
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th Street & Constitution Avenue NW, Washington DC, 20560, USA
- National Systematics Laboratory of NOAA's Fisheries Service, 1315 East-West Highway, Silver Spring, MD, 20910, USA
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, 326 Mueller, University Park, PA, 16801, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
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Koch TL, Grimmelikhuijzen CJP. Global Neuropeptide Annotations From the Genomes and Transcriptomes of Cubozoa, Scyphozoa, Staurozoa (Cnidaria: Medusozoa), and Octocorallia (Cnidaria: Anthozoa). Front Endocrinol (Lausanne) 2019; 10:831. [PMID: 31866941 PMCID: PMC6909153 DOI: 10.3389/fendo.2019.00831] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/13/2019] [Indexed: 12/05/2022] Open
Abstract
During animal evolution, ancestral Cnidaria and Bilateria diverged more than 600 million years ago. The nervous systems of extant cnidarians are strongly peptidergic. Neuropeptides have been isolated and sequenced from a few model cnidarians, but a global investigation of the presence of neuropeptides in all cnidarian classes has been lacking. Here, we have used a recently developed software program to annotate neuropeptides in the publicly available genomes and transcriptomes from members of the classes Cubozoa, Scyphozoa, and Staurozoa (which all belong to the subphylum Medusozoa) and contrasted these results with neuropeptides present in the subclass Octocorallia (belonging to the class Anthozoa). We found three to six neuropeptide preprohormone genes in members of the above-mentioned cnidarian classes or subclasses, each coding for several (up to thirty-two) similar or identical neuropeptide copies. Two of these neuropeptide preprohormone genes are present in all cnidarian classes/subclasses investigated, so they are good candidates for being among the first neuropeptide genes evolved in cnidarians. One of these primordial neuropeptide genes codes for neuropeptides having the C-terminal sequence GRFamide (pQGRFamide in Octocorallia; pQWLRGRFamide in Cubozoa and Scyphozoa; pQFLRGRFamide in Staurozoa). The other primordial neuropeptide gene codes for peptides having RPRSamide or closely resembling amino acid sequences. In addition to these two primordial neuropeptide sequences, cnidarians have their own class- or subclass-specific neuropeptides, which probably evolved to serve class/subclass-specific needs. When we carried out phylogenetic tree analyses of the GRFamide or RPRSamide preprohormones from cubozoans, scyphozoans, staurozoans, and octocorallia, we found that their phylogenetic relationships perfectly agreed with current models of the phylogeny of the studied cnidarian classes and subclasses. These results support the early origins of the GRFamide and RPRSamide preprohormone genes.
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