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Kron NS, Fieber LA, Baker L, Campbell C, Schmale MC. Host response to Aplysia Abyssovirus 1 in nervous system and gill. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 159:105211. [PMID: 38885747 PMCID: PMC11378725 DOI: 10.1016/j.dci.2024.105211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
The California sea hare (Aplysia californica) is a model for age associated cognitive decline. Recent researched identified a novel nidovirus, Aplysia Abyssovirus 1, with broad tropism enriched in the Aplysia nervous system. This virus is ubiquitous in wild and maricultured, young and old animals without obvious pathology. Here we re-evaluated gene expression data from several previous studies to investigate differential expression in the nervous system and gill in response to virus and aging as well as the mutational spectrum observed in the viral sequences obtained from these datasets. Viral load and age were highly correlated, indicating persistent infection. Upregulated genes in response to virus were enriched for immune genes and signatures of ER and proteostatic stress, while downregulated genes were enriched for mitochondrial metabolism. Differential expression with respect to age suggested increased iron accumulation and decreased glycolysis, fatty acid metabolism, and proteasome function. Interaction of gene expression trends associated with viral infection and aging suggest that viral infection likely plays a role in aging in the Aplysia nervous system. Mutation analysis of viral RNA identified signatures suggesting ADAR and AID/APOBEC like deaminase act as part of Aplysia anti-viral defense.
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Affiliation(s)
- Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA.
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
| | - Lydia Baker
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
| | | | - Michael C Schmale
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
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Li YN, Zhang X, Huang BW, Xin LS, Wang CM, Bai CM. Localization and Tissue Tropism of Ostreid Herpesvirus 1 in Blood Clam Anadara broughtonii. BIOLOGY 2024; 13:720. [PMID: 39336147 PMCID: PMC11429395 DOI: 10.3390/biology13090720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Revised: 09/08/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024]
Abstract
OsHV-1 caused detrimental infections in a variety of bivalve species of major importance to aquaculture worldwide. Since 2012, there has been a notable increase in the frequency of mass mortality events of the blood clam associated with OsHV-1 infection. The pathological characteristics, tissue and cellular tropisms of OsHV-1 in A. broughtonii remain unknown. In this study, we sought to investigate the distribution of OsHV-1 in five different organs (mantle, hepatopancreas, gill, foot, and adductor muscle) of A. broughtonii by quantitative PCR, histopathology and in situ hybridization (ISH), to obtain insight into the progression of the viral infection. Our results indicated a continuous increase in viral loads with the progression of OsHV-1 infection, reaching a peak at 48 h or 72 h post-infection according to different tissues. Tissue damage and necrosis, as well as colocalized OsHV-1 ISH signals, were observed primarily in the connective tissues of various organs and gills. Additionally, minor tissue damage accompanied by relatively weak ISH signals was detected in the foot and adductor muscle, which were filled with muscle tissue. The predominant cell types labeled by ISH signals were infiltrated hemocytes, fibroblastic-like cells, and flat cells in the gill filaments. These results collectively illustrated the progressive alterations in pathological confusion and OsHV-1 distribution in A. broughtonii, which represent most of the possible responses of cells and tissues to the virus.
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Affiliation(s)
- Ya-Nan Li
- College of Ocean and Biology Engineering, Yancheng Teachers University, Yancheng 224007, China;
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.Z.); (B.-W.H.); (L.-S.X.); (C.-M.W.)
| | - Xiang Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.Z.); (B.-W.H.); (L.-S.X.); (C.-M.W.)
| | - Bo-Wen Huang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.Z.); (B.-W.H.); (L.-S.X.); (C.-M.W.)
| | - Lu-Sheng Xin
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.Z.); (B.-W.H.); (L.-S.X.); (C.-M.W.)
| | - Chong-Ming Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.Z.); (B.-W.H.); (L.-S.X.); (C.-M.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Chang-Ming Bai
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.Z.); (B.-W.H.); (L.-S.X.); (C.-M.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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ADAR-Editing during Ostreid Herpesvirus 1 Infection in Crassostrea gigas: Facts and Limitations. mSphere 2022; 7:e0001122. [PMID: 35379005 PMCID: PMC9044936 DOI: 10.1128/msphere.00011-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ostreid herpesvirus-1 (OsHV-1) RNAs are enzymatically modified by A-to-I conversions during the infection of Crassostrea gigas. The increase of ADAR1 expression and hyper-editing activity parallel to OsHV-1 RNAs suggests a functional connection between dsRNA editing and antiviral responses. We analyzed 87 RNA-seq data sets from immuno-primed, resistant, and susceptible oysters exposed to OsHV-1 to compare the ADAR hyper-editing levels on host and viral transcripts and trace hyper-editing on the oyster genes. Host RNAs were more hyper-edited than viral RNAs, despite the increased editing of viral RNAs in late infection phases. A set of genes, representing ∼0.5% of the oyster transcriptome and including several tripartite motif-containing sequences, were constantly hyper-edited. Conversely, we identified genes involved in antiviral response, miRNA maturation, and epigenetic regulation that were hyper-edited in specific conditions only. Despite technical and biological bottlenecks that hamper the understanding of the bivalve “RNA editome,” available tools and technologies can be adapted to bivalve mollusks. IMPORTANCE Ostreid herpesvirus-1 (OsHV-1) is a harmful pathogen of bivalve species, such as oysters. However, knowledge is lacking about host–virus interactions at the molecular level, hampering the possibility of a correct management of viral outbreaks and related massive mortalities. Notably, OsHV-1 transcripts are massively modified by host RNA editing enzyme during infection, resulting in multiple A-to-I variations along RNAs assuming double-strand conformations. The impact of these modifications on host transcripts is, however, not completely clear. Analyzing RNA-seq data of oysters infected with OsHV-1, we revealed that ∼0.5% of the oyster transcriptome is always enzymatically modified by ADAR, whereas genes involved in antiviral response, miRNA maturation, and epigenetic regulation were hyper-edited in specific conditions only. Despite our results, relevant technical bottlenecks impair an accurate quantification of RNA editing events, making necessary an approach specifically dedicated to the progressive understanding of oyster “RNA editome.”
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Bai CM, Rosani U, Zhang X, Xin LS, Bortoletto E, Wegner KM, Wang CM. Viral Decoys: The Only Two Herpesviruses Infecting Invertebrates Evolved Different Transcriptional Strategies to Deflect Post-Transcriptional Editing. Viruses 2021; 13:v13101971. [PMID: 34696401 PMCID: PMC8537636 DOI: 10.3390/v13101971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/29/2021] [Indexed: 12/26/2022] Open
Abstract
The highly versatile group of Herpesviruses cause disease in a wide range of hosts. In invertebrates, only two herpesviruses are known: the malacoherpesviruses HaHV-1 and OsHV-1 infecting gastropods and bivalves, respectively. To understand viral transcript architecture and diversity we first reconstructed full-length viral genomes of HaHV-1 infecting Haliotis diversicolor supertexta and OsHV-1 infecting Scapharca broughtonii by DNA-seq. We then used RNA-seq over the time-course of experimental infections to establish viral transcriptional dynamics, followed by PacBio long-read sequencing of full-length transcripts to untangle viral transcript architectures at two selected time points. Despite similarities in genome structure, in the number of genes and in the diverse transcriptomic architectures, we measured a ten-fold higher transcript variability in HaHV-1, with more extended antisense gene transcription. Transcriptional dynamics also appeared different, both in timing and expression trends. Both viruses were heavily affected by post-transcriptional modifications performed by ADAR1 affecting sense-antisense gene pairs forming dsRNAs. However, OsHV-1 concentrated these modifications in a few genomic hotspots, whereas HaHV-1 diluted ADAR1 impact by elongated and polycistronic transcripts distributed over its whole genome. These transcriptional strategies might thus provide alternative potential roles for sense-antisense transcription in viral transcriptomes to evade the host's immune response in different virus-host combinations.
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Affiliation(s)
- Chang-Ming Bai
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, China; (C.-M.B.); (X.Z.); (L.-S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Umberto Rosani
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Warden Sea Station, 25992 List auf Sylt, Germany; (U.R.); (K.M.W.)
- Department of Biology, University of Padova, 35121 Padova, Italy;
| | - Xiang Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, China; (C.-M.B.); (X.Z.); (L.-S.X.)
- College of Fisheries, Tianjin Agricultural University, Tianjin 300380, China
| | - Lu-Sheng Xin
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, China; (C.-M.B.); (X.Z.); (L.-S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | | | - K. Mathias Wegner
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Warden Sea Station, 25992 List auf Sylt, Germany; (U.R.); (K.M.W.)
| | - Chong-Ming Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, China; (C.-M.B.); (X.Z.); (L.-S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence:
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Morga B, Jacquot M, Pelletier C, Chevignon G, Dégremont L, Biétry A, Pepin JF, Heurtebise S, Escoubas JM, Bean TP, Rosani U, Bai CM, Renault T, Lamy JB. Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species. Front Microbiol 2021; 12:711377. [PMID: 34326830 PMCID: PMC8313985 DOI: 10.3389/fmicb.2021.711377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/21/2021] [Indexed: 11/15/2022] Open
Abstract
The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. This is particularly true for pathogens with low per-site mutation rates, such as DNA viruses, that do not exhibit a large amount of evolutionary change among genetic sequences sampled at different time points. However, whole-genome sequencing can reveal the accumulation of novel genetic variation between samples, promising to render most, if not all, microbial pathogens measurably evolving and suitable for analytical techniques derived from population genetic theory. Here, we aim to assess the measurability of evolution on epidemiological time scales of the Ostreid herpesvirus 1 (OsHV-1), a double stranded DNA virus of which a new variant, OsHV-1 μVar, emerged in France in 2008, spreading across Europe and causing dramatic economic and ecological damage. We performed phylogenetic analyses of heterochronous (n = 21) OsHV-1 genomes sampled worldwide. Results show sufficient temporal signal in the viral sequences to proceed with phylogenetic molecular clock analyses and they indicate that the genetic diversity seen in these OsHV-1 isolates has arisen within the past three decades. OsHV-1 samples from France and New Zealand did not cluster together suggesting a spatial structuration of the viral populations. The genome-wide study of simple and complex polymorphisms shows that specific genomic regions are deleted in several isolates or accumulate a high number of substitutions. These contrasting and non-random patterns of polymorphism suggest that some genomic regions are affected by strong selective pressures. Interestingly, we also found variant genotypes within all infected individuals. Altogether, these results provide baseline evidence that whole genome sequencing could be used to study population dynamic processes of OsHV-1, and more broadly herpesviruses.
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Affiliation(s)
| | | | | | | | | | | | - Jean-François Pepin
- Ifremer, ODE-Littoral-Laboratoire Environnement Ressources des Pertuis Charentais (LER-PC), La Tremblade, France
| | | | - Jean-Michel Escoubas
- IHPE, CNRS, Ifremer, Université de Montpellier - Université de Perpignan Via Domitia, Montpellier, France
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom
| | - Umberto Rosani
- Department of Biology, University of Padua, Padua, Italy
| | - Chang-Ming Bai
- Yellow Sea Fisheries Research Institute, CAFS, Qingdao, China
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Friedman CS, Reece KS, Wippel BJT, Agnew MV, Dégremont L, Dhar AK, Kirkland P, MacIntyre A, Morga B, Robison C, Burge CA. Unraveling concordant and varying responses of oyster species to Ostreid Herpesvirus 1 variants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 739:139752. [PMID: 32846506 DOI: 10.1016/j.scitotenv.2020.139752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/12/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
The Ostreid herpesvirus 1 (OsHV-1) and variants, particularly the microvariants (μVars), are virulent and economically devastating viruses impacting oysters. Since 2008 OsHV-1 μVars have emerged rapidly having particularly damaging effects on aquaculture industries in Europe, Australia and New Zealand. We conducted field trials in Tomales Bay (TB), California where a non-μVar strain of OsHV-1 is established and demonstrated differential mortality of naturally exposed seed of three stocks of Pacific oyster, Crassostrea gigas, and one stock of Kumamoto oyster, C. sikamea. Oysters exposed in the field experienced differential mortality that ranged from 64 to 99% in Pacific oysters (Tasmania>Midori = Willapa stocks), which was much higher than that of Kumamoto oysters (25%). Injection trials were done using French (FRA) and Australian (AUS) μVars with the same oyster stocks as planted in the field and, in addition, two stocks of the Eastern oyster, C. virginica. No mortality was observed in control oysters. One C. virginica stock suffered ~10% mortality when challenged with both μVars tested. Two Pacific oyster stocks suffered 75 to 90% mortality, while one C. gigas stock had relatively low mortality when challenged with the AUS μVar (~22%) and higher mortality when challenged with the French μVar (~72%). Conversely, C. sikamea suffered lower mortality when challenged with the French μVar (~22%) and higher mortality with the AUS μVar (~44%). All dead oysters had higher viral loads (~1000×) as measured by quantitative PCR relative to those that survived. However, some survivors had high levels of virus, including those from species with lower mortality. Field mortality in TB correlated with laboratory mortality of the FRA μVar (69% correlation) but not with that of the AUS μVar, which also lacked correlation with the FRA μVar. The variation in response to OsHV-1 variant challenges by oyster species and stocks demonstrates the need for empirical assessment of multiple OsHV-1 variants.
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Affiliation(s)
- Carolyn S Friedman
- School of Aquatic & Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98105, USA
| | - Kimberly S Reece
- Virginia Institute of Marine Sciences, William & Mary, P.O. Box 1346, Gloucester Point, Virginia 23062, USA
| | - Bryanda J T Wippel
- School of Aquatic & Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98105, USA
| | - M Victoria Agnew
- Institute of Marine and Environmental Technology, University of Maryland Baltimore County, 701 E Pratt Street, Baltimore, MD 21202, USA
| | - Lionel Dégremont
- Ifremer, SG2M-LGPMM, Station La Tremblade, 17390 La Tremblade, France
| | - Arun K Dhar
- Aquaculture Pathology Laboratory, Animal and Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell Road, Tucson, AZ 85721, USA
| | - Peter Kirkland
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
| | - Alanna MacIntyre
- Virginia Institute of Marine Sciences, William & Mary, P.O. Box 1346, Gloucester Point, Virginia 23062, USA
| | - Benjamin Morga
- Ifremer, SG2M-LGPMM, Station La Tremblade, 17390 La Tremblade, France
| | - Clara Robison
- Virginia Institute of Marine Sciences, William & Mary, P.O. Box 1346, Gloucester Point, Virginia 23062, USA
| | - Colleen A Burge
- Institute of Marine and Environmental Technology, University of Maryland Baltimore County, 701 E Pratt Street, Baltimore, MD 21202, USA.
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Rosani U, Abbadi M, Green T, Bai CM, Turolla E, Arcangeli G, Wegner KM, Venier P. Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1. BMC Genomics 2020; 21:620. [PMID: 32912133 PMCID: PMC7488030 DOI: 10.1186/s12864-020-07026-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
Background Since 2008, the aquaculture production of Crassostrea gigas was heavily affected by mass mortalities associated to Ostreid herpesvirus 1 (OsHV-1) microvariants worldwide. Transcriptomic studies revealed the major antiviral pathways of the oyster immune response while other findings suggested that also small non-coding RNAs (sncRNA) such as microRNAs might act as key regulators of the oyster response against OsHV-1. To explore the explicit connection between small non-coding and protein-coding transcripts, we performed paired whole transcriptome analysis of sncRNA and messenger RNA (mRNA) in six oysters selected for different intensities of OsHV-1 infection. Results The mRNA profiles of the naturally infected oysters were mostly governed by the transcriptional activity of OsHV-1, with several differentially expressed genes mapping to the interferon, toll, apoptosis, and pro-PO pathways. In contrast, miRNA profiles suggested more complex regulatory mechanisms, with 15 differentially expressed miRNAs (DE-miRNA) pointing to a possible modulation of the host response during OsHV-1 infection. We predicted 68 interactions between DE-miRNAs and oyster 3′-UTRs, but only few of them involved antiviral genes. The sncRNA reads assigned to OsHV-1 rather resembled mRNA degradation products, suggesting the absence of genuine viral miRNAs. Conclusions We provided data describing the miRNAome during OsHV-1 infection in C. gigas. This information can be used to understand the role of miRNAs in healthy and diseased oysters, to identify new targets for functional studies and, eventually to disentangle cause and effect relationships during viral infections in marine mollusks.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, 35121, Padova, Italy. .,Coastal Ecology Section, AWI - Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, 25992, List, Germany.
| | - Miriam Abbadi
- Istituto Zooprofilattico delle Venezie, Legnaro, Italy
| | - Timothy Green
- Centre for Shellfish Research & Department of Fisheries and Aquaculture, Vancouver Island University, Nanaimo, BC, V9R 5S5, Canada
| | - Chang-Ming Bai
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | | | | | - K Mathias Wegner
- Coastal Ecology Section, AWI - Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, 25992, List, Germany
| | - Paola Venier
- Department of Biology, University of Padova, 35121, Padova, Italy.
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Leprêtre M, Palos-Ladeiro M, Faugere J, Almunia C, Lemoine J, Armengaud J, Geffard A, Salvador A. From shotgun to targeted proteomics: rapid Scout-MRM assay development for monitoring potential immunomarkers in Dreissena polymorpha. Anal Bioanal Chem 2020; 412:7333-7347. [DOI: 10.1007/s00216-020-02868-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/27/2020] [Accepted: 08/06/2020] [Indexed: 12/17/2022]
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Neave MJ, Corbeil S, McColl KA, Crane MSJ. Investigating the natural resistance of blackfoot p-a%%KERN_ERR%%ua Haliotis iris to abalone viral ganglioneuritis using whole transcriptome analysis. DISEASES OF AQUATIC ORGANISMS 2019; 135:107-119. [PMID: 31342912 DOI: 10.3354/dao03390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The natural resistance of New Zealand blackfoot p-a%%%%%%%%%%%%%%KERN_ERR%%KERN_ERR%%KERN_ERR%%KERN_ERR%%KERN_ERR%%KERN_ERR%%KERN_ERR%%ua Haliotis iris to infection by haliotid herpesvirus-1 (HaHV-1) and to the disease abalone viral ganglioneuritis was investigated in experimentally challenged p-aua using high throughput RNA-sequencing. HaHV-1-challenged p-aua up-regulated broad classes of genes that contained chitin-binding peritrophin-A domains, which seem to play diverse roles in the p-aua immune response. The p-aua also up-regulated vascular adhesion protein-1 (VAP-1), an important adhesion molecule for lymphocytes, and chitotriosidase-1 (CHIT-1), an immunologically important gene in mammalian immune systems. Moreover, several blood coagulation pathways were dysregulated in the p-aua, possibly indicating viral modulation. We also saw several indications that neurological tissues were specifically affected by HaHV-1, including the dysregulation of beta-1,4-N-acetylgalactosaminyltransferase (B4GALNT), GM2 ganglioside, neuroligin-4 and the Notch signalling pathway. This research may support the development of molecular therapeutics useful to control and/or manage viral outbreaks in abalone culture.
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Affiliation(s)
- Matthew J Neave
- Australian Animal Health Laboratory, Private Bag 24, Geelong, VIC 3220, Australia
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Bai CM, Xin LS, Rosani U, Wu B, Wang QC, Duan XK, Liu ZH, Wang CM. Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C. Gigascience 2019; 8:giz067. [PMID: 31289832 PMCID: PMC6615981 DOI: 10.1093/gigascience/giz067] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/23/2019] [Accepted: 05/14/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The blood clam, Scapharca (Anadara) broughtonii, is an economically and ecologically important marine bivalve of the family Arcidae. Efforts to study their population genetics, breeding, cultivation, and stock enrichment have been somewhat hindered by the lack of a reference genome. Herein, we report the complete genome sequence of S. broughtonii, a first reference genome of the family Arcidae. FINDINGS A total of 75.79 Gb clean data were generated with the Pacific Biosciences and Oxford Nanopore platforms, which represented approximately 86× coverage of the S. broughtonii genome. De novo assembly of these long reads resulted in an 884.5-Mb genome, with a contig N50 of 1.80 Mb and scaffold N50 of 45.00 Mb. Genome Hi-C scaffolding resulted in 19 chromosomes containing 99.35% of bases in the assembled genome. Genome annotation revealed that nearly half of the genome (46.1%) is composed of repeated sequences, while 24,045 protein-coding genes were predicted and 84.7% of them were annotated. CONCLUSIONS We report here a chromosomal-level assembly of the S. broughtonii genome based on long-read sequencing and Hi-C scaffolding. The genomic data can serve as a reference for the family Arcidae and will provide a valuable resource for the scientific community and aquaculture sector.
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Affiliation(s)
- Chang-Ming Bai
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China
| | - Lu-Sheng Xin
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China
| | - Umberto Rosani
- Department of Biology, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy
- Alfred Wegener Institute – Helmholtz Centre for Polar and Marine Research, Wadden Sea Station, Hafenstraße 43, List/Sylt 25992, Germany
| | - Biao Wu
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China
| | - Qing-Chen Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China
| | - Xiao-Ke Duan
- Biomarker Technologies Corporation, 12 Fuqian Street, Beijing 101200, China
| | - Zhi-Hong Liu
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China
| | - Chong-Ming Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China
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Dual Transcriptomic Analysis Reveals a Delayed Antiviral Response of Haliotis diversicolor supertexta against Haliotid Herpesvirus-1. Viruses 2019; 11:v11040383. [PMID: 31022987 PMCID: PMC6520846 DOI: 10.3390/v11040383] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 12/29/2022] Open
Abstract
Haliotid herpesvirus-1 (HaHV-1) is the first identified gastropod herpesvirus, causing a highly lethal neurologic disease of abalone species. The genome of HaHV-1 has been sequenced, but the functions of the putative genes and their roles during infection are still poorly understood. In the present study, transcriptomic profiles of Haliotis diversicolor supertexta at 0, 24 and 60 h post injection (hpi) with HaHV-1 were characterized through high-throughput RNA sequencing. A total of 448 M raw reads were obtained and assembled into 2.08 × 105 unigenes with a mean length of 1486 bp and an N50 of 2455 bp. Although we detected increased HaHV-1 DNA loads and active viral expression at 24 hpi, this evidence was not linked to significant changes of host transcriptomic profiles between 0 and 24 hpi, whereas a rich immune-related gene set was over-expressed at 60 hpi. These results indicate that, at least at the beginning of HaHV-1 infection, the virus can replicate with no activation of the host immune response. We propose that HaHV-1 may evolve more effective strategies to modulate the host immune response and hide during replication, so that it could evade the immune surveillance at the early stage of infection.
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12
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Rosani U, Young T, Bai CM, Alfaro AC, Venier P. Dual Analysis of Virus-Host Interactions: The Case of Ostreid herpesvirus 1 and the Cupped Oyster Crassostrea gigas. Evol Bioinform Online 2019; 15:1176934319831305. [PMID: 30828244 PMCID: PMC6388457 DOI: 10.1177/1176934319831305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022] Open
Abstract
Dual analyses of the interactions between Ostreid herpesvirus 1 (OsHV-1) and the bivalve Crassostrea gigas during infection can unveil events critical to the onset and progression of this viral disease and can provide novel strategies for mitigating and preventing oyster mortality. Among the currently used “omics” technologies, dual transcriptomics (dual RNA-seq) coupled with the analysis of viral DNA in the host tissues has greatly advanced the knowledge of genes and pathways mostly contributing to host defense responses, expression profiles of annotated and unknown OsHV-1 open reading frames (ORFs), and viral genome variability. In addition to dual RNA-seq, proteomics and metabolomics analyses have the potential to add complementary information, needed to understand how a malacoherpesvirus can redirect and exploit the vital processes of its host. This review explores our current knowledge of “omics” technologies in the study of host-pathogen interactions and highlights relevant applications of these fields of expertise to the complex case of C gigas infections by OsHV-1, which currently threaten the mollusk production sector worldwide.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, Padova, Italy
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Chang-Ming Bai
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Paola Venier
- Department of Biology, University of Padova, Padova, Italy
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