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Li X, Bai Y, Dong Z, Xu C, Liu S, Yu H, Kong L, Li Q. Chromosome-level genome assembly of the European flat oyster (Ostrea edulis) provides insights into its evolution and adaptation. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101045. [PMID: 36470107 DOI: 10.1016/j.cbd.2022.101045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
The European flat oyster (Ostrea edulis) is an endangered and economically important marine bivalve species that plays a critical role in the coastal ecosystem. Here, we report a high-quality chromosome-level genome assembly of O. edulis, generated using PacBio HiFi-CCS long reads and annotated with Nanopore full-length transcriptome. The O. edulis genome covers 946.06 Mb (scaffold N50 94.82 Mb) containing 34,495 protein-coding genes and a high proportion of repeat sequences (58.49 %). The reconstructed demographic histories show that O. edulis population might be shaped by breeding habit (embryo brooding) and historical climatic change. Comparative genomic analysis indicates that transposable elements may drive lineage-specific evolution in oysters. Notably, the O. edulis genome has a Hox gene cluster rearrangement that has never been reported in bivalves, making this species valuable for evolutionary studies of molluscan diversification. Moreover, genome expansion of O. edulis is probably central to its adaptation to filter-feeding and sessile lifestyles, as well as embryo brooding and pathogen resistance, in coastal ecosystems. This chromosome-level genome assembly provides new insights into the genome feature of oysters, and presents an important resource for genetic research, evolutionary studies, and biological conservation of O. edulis.
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Affiliation(s)
- Xinchun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yitian Bai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Zhen Dong
- 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
| | - Shikai Liu
- 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
| | - 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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Proestou DA, Sullivan ME, Lundgren KM, Ben-Horin T, Witkop EM, Hart KM. Understanding Crassostrea virginica tolerance of Perkinsus marinus through global gene expression analysis. Front Genet 2023; 14:1054558. [PMID: 36741318 PMCID: PMC9892467 DOI: 10.3389/fgene.2023.1054558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
Disease tolerance, a host's ability to limit damage from a given parasite burden, is quantified by the relationship between pathogen load and host survival or reproduction. Dermo disease, caused by the protozoan parasite P. marinus, negatively impacts survival in both wild and cultured eastern oyster (C. virginica) populations. Resistance to P. marinus has been the focus of previous studies, but tolerance also has important consequences for disease management in cultured and wild populations. In this study we measured dermo tolerance and evaluated global expression patterns of two sensitive and two tolerant eastern oyster families experimentally challenged with distinct doses of P. marinus (0, 106, 107, and 108 parasite spores per gram wet weight, n = 3-5 individuals per family per dose). Weighted Gene Correlation Network Analysis (WGCNA) identified several modules correlated with increasing parasite dose/infection intensity, as well as phenotype. Modules positively correlated with dose included transcripts and enriched GO terms related to hemocyte activation and cell cycle activity. Additionally, these modules included G-protein coupled receptor, toll-like receptor, and tumor necrosis factor pathways, which are important for immune effector molecule and apoptosis activation. Increased metabolic activity was also positively correlated with treatment. The module negatively correlated with infection intensity was enriched with GO terms associated with normal cellular activity and growth, indicating a trade-off with increased immune response. The module positively correlated with the tolerant phenotype was enriched for transcripts associated with "programmed cell death" and contained a large number of tripartite motif-containing proteins. Differential expression analysis was also performed on the 108 dosed group using the most sensitive family as the comparison reference. Results were consistent with the network analysis, but signals for "programmed cell death" and serine protease inhibitors were stronger in one tolerant family than the other, suggesting that there are multiple avenues for disease tolerance. These results provide new insight for defining dermo response traits and have important implications for applying selective breeding for disease management.
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Affiliation(s)
- Dina A. Proestou
- National Cold Water Marine Aquaculture Center, USDA Agricultural Research Service, Kingston, RI, United States,*Correspondence: Dina A. Proestou,
| | - Mary E. Sullivan
- National Cold Water Marine Aquaculture Center, USDA Agricultural Research Service, Kingston, RI, United States
| | - Kathryn Markey Lundgren
- National Cold Water Marine Aquaculture Center, USDA Agricultural Research Service, Kingston, RI, United States
| | - Tal Ben-Horin
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, Kingston, RI, United States
| | - Erin M. Witkop
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, Kingston, RI, United States
| | - Keegan M. Hart
- National Cold Water Marine Aquaculture Center, USDA Agricultural Research Service, Kingston, RI, United States
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Gundappa MK, Peñaloza C, Regan T, Boutet I, Tanguy A, Houston RD, Bean TP, Macqueen DJ. Chromosome level reference genome for European flat oyster (
Ostrea edulis
L.). Evol Appl 2022; 15:1713-1729. [DOI: 10.1111/eva.13460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/07/2022] [Accepted: 07/13/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Campus
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Campus
| | - Tim Regan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Campus
| | - Isabelle Boutet
- Station Biologique de Roscoff, Laboratoire Adaptation et Diversité en Milieu Marin (UMR 7144 AD2M CNRS‐Sorbonne Université), Place Georges Tessier, 29680 Roscoff France
| | - Arnaud Tanguy
- Station Biologique de Roscoff, Laboratoire Adaptation et Diversité en Milieu Marin (UMR 7144 AD2M CNRS‐Sorbonne Université), Place Georges Tessier, 29680 Roscoff France
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Campus
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Campus
| | - Daniel J. Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Campus
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Sambade IM, Casanova A, Blanco A, Gundappa MK, Bean TP, Macqueen DJ, Houston RD, Villalba A, Vera M, Kamermans P, Martínez P. A single genomic region involving a putative chromosome rearrangement in flat oyster (
Ostrea edulis
) is associated with differential host resilience to the parasite
Bonamia ostreae. Evol Appl 2022; 15:1408-1422. [PMID: 36187184 PMCID: PMC9488685 DOI: 10.1111/eva.13446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/17/2022] [Accepted: 06/21/2022] [Indexed: 01/31/2023] Open
Abstract
European flat oyster (Ostrea edulis) is an ecologically and economically important marine bivalve, that has been severely affected by the intracellular parasite Bonamia ostreae. In this study, a flat oyster SNP array (~14,000 SNPs) was used to validate previously reported outlier loci for divergent selection associated with B. ostreae exposure in the Northeast Atlantic Area. A total of 134 wild and hatchery individuals from the North Sea, collected in naïve (NV) and long‐term affected (LTA) areas, were analysed. Genetic diversity and differentiation were related to the sampling origin (wild vs. hatchery) when using neutral markers, and to bonamiosis status (NV vs. LTA) when using outlier loci for divergent selection. Two genetic clusters appeared intermingled in all sampling locations when using outlier loci, and their frequency was associated with their bonamiosis status. When both clusters were compared, outlier data sets showed high genetic divergence (FST > 0.25) unlike neutral loci (FST not ≠ 0). Moreover, the cluster associated with LTA samples showed much higher genetic diversity and significant heterozygote excess with outlier loci, but not with neutral data. Most outliers mapped on chromosome 8 (OE‐C8) of the flat oyster genome, supporting a main genomic region underlying resilience to bonamiosis. Furthermore, differentially expressed genes previously reported between NV and LTA strains showed higher mapping density on OE‐C8. A range of relevant immune functions were specifically enriched among genes annotated on OE‐C8, providing hypotheses for resilience mechanisms to an intracellular parasite. The results suggest that marker‐assisted selection could be applied to breed resilient strains of O. edulis to bonamiosis, if lower parasite load and/or higher viability of the LTA genetic cluster following B. ostreae infection is demonstrated.
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Affiliation(s)
- Inés Martínez Sambade
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary Universidade de Santiago de Compostela Lugo Spain
| | - Adrian Casanova
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary Universidade de Santiago de Compostela Lugo Spain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary Universidade de Santiago de Compostela Lugo Spain
| | - Manu K. Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies Midlothian UK
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies Midlothian UK
| | - Daniel J. Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies Midlothian UK
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies Midlothian UK
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA) Vilanova de Arousa Spain
- Departamento de Ciencias de la Vida Universidad de Alcalá Alcalá de Henares Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE) University of the Basque Country (UPV/EHU) Plentzia Spain
| | - Manuel Vera
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary Universidade de Santiago de Compostela Lugo Spain
| | - Pauline Kamermans
- Wageningen Marine Research Yerseke The Netherlands
- Marine Animal Ecology Group Wageningen University Wageningen The Netherlands
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary Universidade de Santiago de Compostela Lugo Spain
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de la Ballina NR, Villalba A, Cao A. Shotgun analysis to identify differences in protein expression between granulocytes and hyalinocytes of the European flat oyster Ostrea edulis. FISH & SHELLFISH IMMUNOLOGY 2021; 119:678-691. [PMID: 34748932 DOI: 10.1016/j.fsi.2021.10.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 10/19/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
Recovery of wild populations of the European flat oyster Ostrea edulis is important for ecosystem health and conservation of this species, because native oyster populations have dramatically declined or disappeared in most European waters. Diseases have contributed to oyster decline and are important constrains for oyster recovery. Understanding oyster immune system should contribute to design effective strategies to fight oyster diseases. Haemocytes play a pivotal role in mollusc immune responses protecting from infection. Two main types of haemocytes, granulocytes and hyalinocytes, are distinguished in O. edulis. A study aiming to explore differential functions between both haemocyte types and, thus, to enrich the knowledge of Ostrea edulis immune system, was performed by comparing the proteome of the two haemolymph cell types, using a shotgun approach through liquid chromatography (LC) coupled to mass spectrometry (MS). Cells from oyster haemolymph were differentially separated by Percoll density gradient centrifugation. Shotgun LC-MS/MS performance allowed the identification of 145 proteins in hyalinocytes and 138 in the proteome of granulocytes. After a comparative analysis, 55 proteins with main roles in defence were identified, from which 28 were representative of granulocytes and 27 of hyalinocytes, plus 11 proteins shared by both cell types. Different proteins involved in signal transduction, apoptosis, oxidative response, processes related with the cytoskeleton and structure, recognition and wound healing were identified as representatives of each haemocyte type. Important signalling pathways in the immune response such as MAPK, Ras and NF-κβ seemed to be more relevant for granulocytes, while the Wnt signalling pathway, particularly relevant for wound healing, more relevant in hyalinocytes. The differences in proteins involved in recognition and in cytoskeleton and structure suggest differential specialisation in processes of phagocytosis and internalisation of pathogens between haemocyte types. Apoptosis seemed more active in granulocytes. The differences in proteins involved in oxidative response also suggest different redox processes in each cell type.
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Affiliation(s)
- Nuria R de la Ballina
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620, Vilanova de Arousa, Spain
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620, Vilanova de Arousa, Spain; Departamento de Ciencias de la Vida, Universidad de Alcalá, 28871, Alcalá de Henares, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620, Plentzia, Spain.
| | - Asunción Cao
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620, Vilanova de Arousa, Spain
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6
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Egerton S, Lynch SA, Prado-Alvarez M, Flannery G, Brennan E, Hugh-Jones T, Hugh-Jones D, Culloty SC. A Naïve Population of European Oyster Ostrea edulis with Reduced Susceptibility to the Pathogen Bonamia ostreae: Are S-Strategy Life Traits Providing Protection? Integr Comp Biol 2021; 60:249-260. [PMID: 32533837 DOI: 10.1093/icb/icaa071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
European populations of the native flat oyster, Ostrea edulis, have been heavily depleted by two protozoan parasites, Marteila refringens and Bonamia ostreae, with mortalities of up to 90% reported in naïve populations. However, in studies carried out over a 10-year period, researching the parasite-host relationship of B. ostreae and O. edulis in several age cohorts within a naïve O. edulis population from Loch Ryan (LR), Scotland, 1364 specimens were challenged and only 64 (5%), across multiple testing protocols, screened positive for B. ostreae. This article presents a case for the development of S-strategy life traits in the LR population that coincide with enhanced immune function and survival. Oysters are considered typical r-strategists (small in size with fast development and high fecundity) while S-strategists, as outlined in Grime's (1977) competitor-stress tolerant-ruderal (C-S-R) triangle theory, are characterized by slow growth and investment in the durability of individuals. This study hypothesizes that slower growth and reduced reproductive output in LR oysters has resulted in the investment of an enhanced immune function and reduced susceptibility to B. ostreae that is, r-strategists with S-strategy life traits equates to protection from significant pathogens. The findings presented here within provide a strong case study for local adaptation of energy allocation and provides empirical support for the C-S-R triangle theory in a marine organism.
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Affiliation(s)
- Sian Egerton
- Aquaculture and Fisheries Development Centre, School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Sharon A Lynch
- Aquaculture and Fisheries Development Centre, School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Maria Prado-Alvarez
- Marine Molecular Pathobiology Research Group, Institute of Marine Research, Spanish National Research Council (CSIC), Vigo, Pontevedra, Spain
| | | | - Elaine Brennan
- Aquaculture and Fisheries Development Centre, School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Tristan Hugh-Jones
- Atlantic Shellfish Ltd, Rossmore, Carrigtwohill, Co. Cork, Ireland.,Loch Ryan Oysters, Loch Ryan, Scotland, UK
| | - David Hugh-Jones
- Atlantic Shellfish Ltd, Rossmore, Carrigtwohill, Co. Cork, Ireland.,Loch Ryan Oysters, Loch Ryan, Scotland, UK
| | - Sarah C Culloty
- Aquaculture and Fisheries Development Centre, School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,MaREI centre, Environmental Research Institute, University College Cork, Cork, Ireland
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7
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Holbrook Z, Bean TP, Lynch SA, Hauton C. What do the terms resistance, tolerance, and resilience mean in the case of Ostrea edulis infected by the haplosporidian parasite Bonamia ostreae. J Invertebr Pathol 2021; 182:107579. [PMID: 33811850 DOI: 10.1016/j.jip.2021.107579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 01/21/2021] [Accepted: 02/25/2021] [Indexed: 12/29/2022]
Abstract
The decline of the European flat oyster Ostrea edulis represents a loss to European coastal economies both in terms of food security and by affecting the Good Environmental Status of the marine environment as set out by the European Council's Marine Strategy Framework Directive (2008/56/EC). Restoration of O. edulis habitat is being widely discussed across Europe, addressing key challenges such as the devastating impact of the haplosporidian parasite Bonamia ostreae. The use of resistant, tolerant, or resilient oysters as restoration broodstock has been proposed by restoration practitioners, but the definitions and implications of these superficially familiar terms have yet to be defined and agreed by all stakeholders. This opinion piece considers the challenges of differentiating Bonamia resistance, tolerance, and resilience; challenges which impede the adoption of robust definitions. We argue that, disease-resistance is reduced susceptibility to infection by the parasite, or active suppression of the parasites ability to multiply and proliferate. Disease-tolerance is the retention of fitness and an ability to neutralise the virulence of the parasite. Disease-resilience is the ability to recover from illness and, at population level, tolerance could be interpreted as resilience. We concede that further work is required to resolve practical uncertainty in applying these definitions, and argue for a collaboration of experts to achieve consensus. Failure to act now might result in the future dispersal of this disease into new locations and populations, because robust definitions are important components of regulatory mechanisms that underpin marine management.
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Affiliation(s)
- Zoë Holbrook
- Ocean and Earth Science, University of Southampton Waterfront Campus, National Oceanography Centre Southampton, UK
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Sharon A Lynch
- School of Biological, Earth and Environmental Sciences, Aquaculture and Fisheries Development Centre, and Environmental Research Institute, University College Cork, Ireland
| | - Chris Hauton
- Ocean and Earth Science, University of Southampton Waterfront Campus, National Oceanography Centre Southampton, UK.
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8
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de la Ballina NR, Villalba A, Cao A. Differences in proteomic profile between two haemocyte types, granulocytes and hyalinocytes, of the flat oyster Ostrea edulis. FISH & SHELLFISH IMMUNOLOGY 2020; 100:456-466. [PMID: 32205190 DOI: 10.1016/j.fsi.2020.03.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/05/2020] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
Haemocytes play a dominant role in shellfish immunity, being considered the main defence effector cells in molluscs. These cells are known to be responsible for many functions, including chemotaxis, cellular recognition, attachment, aggregation, shell repair and nutrient transport and digestion. There are two basic cell types of bivalve haemocytes morphologically distinguishable, hyalinocytes and granulocytes; however, functional differences and specific abilities are poorly understood: granulocytes are believed to be more efficient in killing microorganisms, while hyalinocytes are thought to be more specialised in clotting and wound healing. A proteomic approach was implemented to find qualitative differences in the protein profile between granulocytes and hyalinocytes of the European flat oyster, Ostrea edulis, as a way to evaluate functional differences. Oyster haemolymph cells were differentially separated by Percoll® density gradient centrifugation. Granulocyte and hyalinocyte proteins were separated by 2D-PAGE and their protein profiles were analysed and compared with PD Quest software; the protein spots exclusive for each haemocyte type were excised from gels and analysed by MALDI-TOF/TOF with a combination of mass spectrometry (MS) and MS/MS for sequencing and protein identification. A total of 34 proteins were identified, 20 unique to granulocytes and 14 to hyalinocytes. The results suggested differences between the haemocyte types in signal transduction, apoptosis, oxidation reduction processes, cytoskeleton, phagocytosis and pathogen recognition. These results contribute to identify differential roles of each haemocyte type and to better understand the oyster immunity mechanisms, which should help to fight oyster diseases.
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Affiliation(s)
- Nuria R de la Ballina
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620, Vilanova de Arousa, Spain
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620, Vilanova de Arousa, Spain; Departamento de Ciencias de la Vida, Universidad de Alcalá, 28871, Alcalá de Henares, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620, Plentzia, Spain.
| | - Asunción Cao
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620, Vilanova de Arousa, Spain
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Satheeswaran T, Yuvaraj P, Damotharan P, Karthikeyan V, Jha DK, Dharani G, Balasubramanian T, Kirubagaran R. Assessment of trace metal contamination in the marine sediment, seawater, and bivalves of Parangipettai, southeast coast of India. MARINE POLLUTION BULLETIN 2019; 149:110499. [PMID: 31430667 DOI: 10.1016/j.marpolbul.2019.110499] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/13/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
Industrial and domestic discharge into the coastal environment has driven us to propose an integrated approach to delineate stations contaminated with metals on the Parangipettai coast by collecting sediment and seawater samples monthly at 18 stations from 2015 to 2017. Descriptive statistics revealed that the concentrations of some metals in the sediment and seawater samples were beyond the permissible level. Further, factor analysis showed a sampling adequacy of 0.90 with high positive loading for Ni (0.94), Cd (0.91), Co (0.90), Pb (0.89), and Zn (0.87) in sediment samples. The degree of contamination by metals was evaluated using pollution indices. The results of the contamination index revealed that some stations in the study area were moderately polluted, and those of the ecological index showed that open sea was under low risk while other stations were in the moderate-to-high-risk category. The results obtained are essential to establish the reference condition for a comparative study in similar environments in the tropical regions.
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Affiliation(s)
- Thangaraj Satheeswaran
- Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences (Govt. of India), Chennai 600100, India.
| | - Purushothaman Yuvaraj
- Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences (Govt. of India), Chennai 600100, India
| | - Palani Damotharan
- Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences (Govt. of India), Chennai 600100, India
| | - Velmurugan Karthikeyan
- Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences (Govt. of India), Chennai 600100, India
| | - Dilip Kumar Jha
- Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences (Govt. of India), Chennai 600100, India
| | - Gopal Dharani
- Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences (Govt. of India), Chennai 600100, India.
| | - Thangavel Balasubramanian
- Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences (Govt. of India), Chennai 600100, India
| | - Ramalingam Kirubagaran
- Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences (Govt. of India), Chennai 600100, India
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10
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Vera M, Pardo BG, Cao A, Vilas R, Fernández C, Blanco A, Gutierrez AP, Bean TP, Houston RD, Villalba A, Martínez P. Signatures of selection for bonamiosis resistance in European flat oyster ( Ostrea edulis): New genomic tools for breeding programs and management of natural resources. Evol Appl 2019; 12:1781-1796. [PMID: 31548857 PMCID: PMC6752124 DOI: 10.1111/eva.12832] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/18/2019] [Accepted: 06/09/2019] [Indexed: 12/18/2022] Open
Abstract
The European flat oyster (Ostrea edulis) is a highly appreciated mollusk with an important aquaculture production throughout the 20th century, in addition to playing an important role on coastal ecosystems. Overexploitation of natural beds, habitat degradation, introduction of non-native species, and epidemic outbreaks have severely affected this important resource, particularly, the protozoan parasite Bonamia ostreae, which is the main concern affecting its production and conservation. In order to identify genomic regions and markers potentially associated with bonamiosis resistance, six oyster beds distributed throughout the European Atlantic coast were sampled. Three of them have been exposed to this parasite since the early 1980s and showed some degree of innate resistance (long-term affected group, LTA), while the other three were free of B. ostreae at least until sampling date (naïve group, NV). A total of 14,065 SNPs were analyzed, including 37 markers from candidate genes and 14,028 from a medium-density SNP array. Gene diversity was similar between LTA and NV groups suggesting no genetic erosion due to long-term exposure to the parasite, and three population clusters were detected using the whole dataset. Tests for divergent selection between NV and LTA groups detected the presence of a very consistent set of 22 markers, located within a putative single genomic region, which suggests the presence of a major quantitative trait locus associated with B. ostreae resistance. Moreover, 324 outlier loci associated with factors other than bonamiosis were identified allowing fully discrimination of all the oyster beds. A practical tool which included the 84 highest discriminative markers for tracing O. edulis populations was developed and tested with empirical data. Results reported herein could assist the production of stocks with improved resistance to bonamiosis and facilitate the management of oyster beds for recovery production and ecosystem services provided by this species.
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Affiliation(s)
- Manuel Vera
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
- Instituto de AcuiculturaUniversidade de Santiago de CompostelaLugoSpain
| | - Belén G. Pardo
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
- Instituto de AcuiculturaUniversidade de Santiago de CompostelaLugoSpain
| | - Asunción Cao
- Centro de Investigacións Mariñas (CIMA)Consellería do Mar, Xunta de GaliciaPontevedraSpain
| | - Román Vilas
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
- Instituto de AcuiculturaUniversidade de Santiago de CompostelaLugoSpain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
- Instituto de AcuiculturaUniversidade de Santiago de CompostelaLugoSpain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
- Instituto de AcuiculturaUniversidade de Santiago de CompostelaLugoSpain
| | - Alejandro P. Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA)Consellería do Mar, Xunta de GaliciaPontevedraSpain
- Departamento de Ciencias de la VidaUniversidad de AlcaláMadridSpain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE)University of the Basque Country (UPV/EHU)Basque CountrySpain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
- Instituto de AcuiculturaUniversidade de Santiago de CompostelaLugoSpain
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de la Ballina NR, Villalba A, Cao A. Proteomic profile of Ostrea edulis haemolymph in response to bonamiosis and identification of candidate proteins as resistance markers. DISEASES OF AQUATIC ORGANISMS 2018; 128:127-145. [PMID: 29733027 DOI: 10.3354/dao03220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
European flat oyster Ostrea edulis populations have suffered extensive mortalities caused by bonamiosis. The protozoan parasite Bonamia ostreae is largely responsible for this disease in Europe, while its congener B. exitiosa has been detected more recently in various European countries. Both of these intracellular parasites are able to survive and proliferate within haemocytes, the main cellular effectors of the immune system in molluscs. Two-dimensional electrophoresis was used to compare the haemolymph protein profile between Bonamia spp.-infected and non-infected oysters within 3 different stocks, a Galician stock of oysters selected for resistance against bonamiosis, a non-selected Galician stock and a selected Irish stock. Thirty-four proteins with a presumably relevant role in the oyster-Bonamia spp. interaction were identified; they were involved in major metabolic pathways, such as energy production, respiratory chain, oxidative stress, signal transduction, transcription, translation, protein degradation and cell defence. Furthermore, the haemolymph proteomic profiles of the non-infected oysters of the 2 Galician stocks were compared. As a result, 7 proteins representative of the non-infected Galician oysters selected for resistance against bonamiosis were identified; these 7 proteins could be considered as candidate markers of resistance to bonamiosis, which should be further assessed.
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Affiliation(s)
- Nuria R de la Ballina
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain
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Long-term affected flat oyster (Ostrea edulis) haemocytes show differential gene expression profiles from naïve oysters in response to Bonamia ostreae. Genomics 2018; 110:390-398. [PMID: 29678683 DOI: 10.1016/j.ygeno.2018.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/15/2018] [Accepted: 04/06/2018] [Indexed: 02/06/2023]
Abstract
European flat oyster (Ostrea edulis) production has suffered a severe decline due to bonamiosis. The responsible parasite enters in oyster haemocytes, causing an acute inflammatory response frequently leading to death. We used an immune-enriched oligo-microarray to understand the haemocyte response to Bonamia ostreae by comparing expression profiles between naïve (NS) and long-term affected (AS) populations along a time series (1 d, 30 d, 90 d). AS showed a much higher response just after challenge, which might be indicative of selection for resistance. No regulated genes were detected at 30 d in both populations while a notable reactivation was observed at 90 d, suggesting parasite latency during infection. Genes related to extracellular matrix and protease inhibitors, up-regulated in AS, and those related to histones, down-regulated in NS, might play an important role along the infection. Twenty-four candidate genes related to resistance should be further validated for selection programs aimed to control bonamiosis.
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13
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Gutierrez AP, Turner F, Gharbi K, Talbot R, Lowe NR, Peñaloza C, McCullough M, Prodöhl PA, Bean TP, Houston RD. Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters ( Crassostrea gigas and Ostrea edulis). G3 (BETHESDA, MD.) 2017; 7:2209-2218. [PMID: 28533337 PMCID: PMC5499128 DOI: 10.1534/g3.117.041780] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/06/2017] [Indexed: 01/01/2023]
Abstract
SNP arrays are enabling tools for high-resolution studies of the genetic basis of complex traits in farmed and wild animals. Oysters are of critical importance in many regions from both an ecological and economic perspective, and oyster aquaculture forms a key component of global food security. The aim of our study was to design a combined-species, medium density SNP array for Pacific oyster (Crassostrea gigas) and European flat oyster (Ostrea edulis), and to test the performance of this array on farmed and wild populations from multiple locations, with a focus on European populations. SNP discovery was carried out by whole-genome sequencing (WGS) of pooled genomic DNA samples from eight C. gigas populations, and restriction site-associated DNA sequencing (RAD-Seq) of 11 geographically diverse O. edulis populations. Nearly 12 million candidate SNPs were discovered and filtered based on several criteria, including preference for SNPs segregating in multiple populations and SNPs with monomorphic flanking regions. An Affymetrix Axiom Custom Array was created and tested on a diverse set of samples (n = 219) showing ∼27 K high quality SNPs for C. gigas and ∼11 K high quality SNPs for O. edulis segregating in these populations. A high proportion of SNPs were segregating in each of the populations, and the array was used to detect population structure and levels of linkage disequilibrium (LD). Further testing of the array on three C. gigas nuclear families (n = 165) revealed that the array can be used to clearly distinguish between both families based on identity-by-state (IBS) clustering parental assignment software. This medium density, combined-species array will be publicly available through Affymetrix, and will be applied for genome-wide association and evolutionary genetic studies, and for genomic selection in oyster breeding programs.
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Affiliation(s)
- Alejandro P Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Frances Turner
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, EH9 3FL, United Kingdom
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, EH9 3FL, United Kingdom
| | - Richard Talbot
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, EH9 3FL, United Kingdom
| | - Natalie R Lowe
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Mark McCullough
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, BT7 1NN, United Kingdom
| | - Paulo A Prodöhl
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, BT7 1NN, United Kingdom
| | - Tim P Bean
- Centre for Environment Fisheries and Aquaculture Science, Cefas Weymouth Laboratory, Dorset DT4 8UB, United Kingdom
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
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