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Villalba A, Coimbra RM, Pampín M, Iglesias D, Costas D, Mariño C, Blanco A, Vera M, Domínguez M, Cacabelos E, Abella E, Incera M, Otero RF, Martínez P. A common garden experiment supports a genetic component underlying the increased resilience of common cockle ( Cerastoderma edule) to the parasite Marteilia cochillia. Evol Appl 2023; 16:1789-1804. [PMID: 38029062 PMCID: PMC10681494 DOI: 10.1111/eva.13601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/27/2023] [Accepted: 09/15/2023] [Indexed: 12/01/2023] Open
Abstract
The common cockle is a valuable bivalve species inhabiting the Atlantic European coasts. The parasite Marteilia cochillia has devastated cockle beds in the southern Galician (NW Spain) rias since 2012. Previous data suggested that cockles from Ría de Arousa acquired some resilience to this parasite through natural selection after consecutive annual marteiliosis outbreaks and candidate markers associated with marteiliosis resilience were identified using population genomics and transcriptomics approaches. Here, a common garden experiment was performed using a naïve stock (from Ría de Muros-Noia) and an affected stock (from Ría de Arousa) to test this hypothesis. Breeders from both stocks were used to produce seed cohorts at hatchery, which were pre-grown in a raft (outdoor nursery stage) and deployed in two shellfish beds affected by marteiliosis in Ría de Arousa (growing-out stage). In both beds, the naïve stock showed high marteiliosis prevalence and was fully depleted in a short period, while the affected stock barely showed evidence of marteiliosis. A set of 45 SNPs putatively associated with marteiliosis resilience were fitted for MassARRAY genotyping to check their role in the differential resilience detected between both stocks. Though no significant differentiation was found between the naïve and the affected stocks with neutral markers, 28 SNPs showed significant divergence between them, suggesting that these SNPs were involved in directional selection during eight generations (to the most) of marteiliosis pressure (long-term selection). Furthermore, signals of selection were also detected in the naïve stock along the marteiliosis outbreak in the growing-out stage (short-term selection) and six SNPs, all shared with the long-term evaluation, showed consistent signals of differentiation according to the infection severity. Some of these SNPs were located within immune genes pertaining to families such as proteasome, ubiquitin, tumor necrosis factor, and glutathione S-transferase. These resilience-associated markers will be useful to recover cockle production in Galicia.
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Affiliation(s)
- Antonio Villalba
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de GaliciaVilanova de ArousaSpain
- Departamento de Ciencias de la VidaUniversidad de AlcaláAlcalá de HenaresSpain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE)University of the Basque Country (UPV/EHU)PlentziaSpain
| | - Raquel M. Coimbra
- Departamento de Pesca e AquiculturaUniversidade Federal Rural de PernambucoRecifeBrazil
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus TerraUniversidade de Santiago de CompostelaLugoSpain
| | - Marina Pampín
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus TerraUniversidade de Santiago de CompostelaLugoSpain
| | - David Iglesias
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de GaliciaVilanova de ArousaSpain
| | - Damián Costas
- Centro de Investigación MariñaUniversidade de Vigo, ECIMATVigoSpain
| | | | - Andrés Blanco
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus TerraUniversidade de Santiago de CompostelaLugoSpain
| | - Manuel Vera
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus TerraUniversidade de Santiago de CompostelaLugoSpain
| | | | - Eva Cacabelos
- Hydrosphere S. L.VigoSpain
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones CientíficasIIM‐CSICVigoSpain
| | - Emilio Abella
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de GaliciaVilanova de ArousaSpain
- Confraría de Pescadores A PastorizaVilanova de ArousaSpain
| | - Mónica Incera
- Centro Tecnolóxico do Mar ‐ Fundación CETMARVigoSpain
| | | | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus TerraUniversidade de Santiago de CompostelaLugoSpain
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Correia S, Fernández-Boo S, Magalhães L, de Montaudouin X, Daffe G, Poulin R, Vera M. Trematode genetic patterns at host individual and population scales provide insights about infection mechanisms. Parasitology 2023; 150:1207-1220. [PMID: 38084628 PMCID: PMC10941227 DOI: 10.1017/s0031182023000987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/02/2023] [Accepted: 10/07/2023] [Indexed: 01/10/2024]
Abstract
Multiple parasites can infect a single host, creating a dynamic environment where each parasite must compete over host resources. Such interactions can cause greater harm to the host than single infections and can also have negative consequences for the parasites themselves. In their first intermediate hosts, trematodes multiply asexually and can eventually reach up to 20% of the host's biomass. In most species, it is unclear whether this biomass results from a single infection or co-infection by 2 or more infective stages (miracidia), the latter being more likely a priori in areas where prevalence of infection is high. Using as model system the trematode Bucephalus minimus and its first intermediate host cockles, we examined the genetic diversity of the cytochrome c oxidase subunit I region in B. minimus from 3 distinct geographical areas and performed a phylogeographic study of B. minimus populations along the Northeast Atlantic coast. Within localities, the high genetic variability found across trematodes infecting different individual cockles, compared to the absence of variability within the same host, suggests that infections could be generally originating from a single miracidium. On a large spatial scale, we uncovered significant population structure of B. minimus, specifically between the north and south of Bay of Biscay. Although other explanations are possible, we suggest this pattern may be driven by the population structure of the final host.
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Affiliation(s)
- Simão Correia
- Department of Biology, CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
- Aquatic and Animal Health Group, CIIMAR, University of Porto, 4450-208 Matosinhos, Portugal
- Department of Zoology, Genetics and Physical Anthropology, Campus Terra, University of Santiago de Compostela, 27002 Lugo, Spain
- Department of Zoology, University of Otago, 9054 Dunedin, New Zealand
| | - Sergio Fernández-Boo
- Aquatic and Animal Health Group, CIIMAR, University of Porto, 4450-208 Matosinhos, Portugal
| | - Luísa Magalhães
- Department of Biology, CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | | | - Guillemine Daffe
- Université de Bordeaux, CNRS, Observatoire Aquitain des Sciences de l'Univers, F-33615 Pessac, France
| | - Robert Poulin
- Department of Zoology, University of Otago, 9054 Dunedin, New Zealand
| | - Manuel Vera
- Department of Zoology, Genetics and Physical Anthropology, Campus Terra, University of Santiago de Compostela, 27002 Lugo, Spain
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Vera M, Wilmes SB, Maroso F, Hermida M, Blanco A, Casanova A, Iglesias D, Cao A, Culloty SC, Mahony K, Orvain F, Bouza C, Robins PE, Malham SK, Lynch S, Villalba A, Martínez P. Heterogeneous microgeographic genetic structure of the common cockle (Cerastoderma edule) in the Northeast Atlantic Ocean: biogeographic barriers and environmental factors. Heredity (Edinb) 2023; 131:292-305. [PMID: 37596415 PMCID: PMC10539317 DOI: 10.1038/s41437-023-00646-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023] Open
Abstract
Knowledge of genetic structure at the finest level is essential for the conservation of genetic resources. Despite no visible barriers limiting gene flow, significant genetic structure has been shown in marine species. The common cockle (Cerastoderma edule) is a bivalve of great commercial and ecological value inhabiting the Northeast Atlantic Ocean. Previous population genomics studies demonstrated significant structure both across the Northeast Atlantic, but also within small geographic areas, highlighting the need to investigate fine-scale structuring. Here, we analysed two geographic areas that could represent opposite models of structure for the species: (1) the SW British Isles region, highly fragmented due to biogeographic barriers, and (2) Galicia (NW Spain), a putative homogeneous region. A total of 9250 SNPs genotyped by 2b-RAD on 599 individuals from 22 natural beds were used for the analysis. The entire SNP dataset mostly confirmed previous observations related to genetic diversity and differentiation; however, neutral and divergent SNP outlier datasets enabled disentangling physical barriers from abiotic environmental factors structuring both regions. While Galicia showed a homogeneous structure, the SW British Isles region was split into four reliable genetic regions related to oceanographic features and abiotic factors, such as sea surface salinity and temperature. The information gathered supports specific management policies of cockle resources in SW British and Galician regions also considering their particular socio-economic characteristics; further, these new data will be added to those recently reported in the Northeast Atlantic to define sustainable management actions across the whole distribution range of the species.
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Affiliation(s)
- Manuel Vera
- Department of Zoology, Genetics and Physics Anthropology, ACUIGEN Group, Faculty of Veterinary, Campus Terra, University of Santiago de Compostela, 27002, Lugo, Spain.
| | - Sophie B Wilmes
- School of Ocean Sciences, Marine Centre Wales, Bangor University, Menai Bridge, UK
| | - Francesco Maroso
- Department of Zoology, Genetics and Physics Anthropology, ACUIGEN Group, Faculty of Veterinary, Campus Terra, University of Santiago de Compostela, 27002, Lugo, Spain
| | - Miguel Hermida
- Department of Zoology, Genetics and Physics Anthropology, ACUIGEN Group, Faculty of Veterinary, Campus Terra, University of Santiago de Compostela, 27002, Lugo, Spain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physics Anthropology, ACUIGEN Group, Faculty of Veterinary, Campus Terra, University of Santiago de Compostela, 27002, Lugo, Spain
| | - Adrián Casanova
- Department of Zoology, Genetics and Physics Anthropology, ACUIGEN Group, Faculty of Veterinary, Campus Terra, University of Santiago de Compostela, 27002, Lugo, Spain
| | - David Iglesias
- Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, 36620, Vilanova de Arousa, Spain
| | - Asunción Cao
- Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, 36620, Vilanova de Arousa, Spain
| | - Sarah C Culloty
- School of Biological, Earth and Environmental Sciences/Aquaculture and Fisheries Development Centre, University College Cork, North Mall, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
- MaREI Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Kate Mahony
- School of Biological, Earth and Environmental Sciences/Aquaculture and Fisheries Development Centre, University College Cork, North Mall, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Francis Orvain
- UNICAEN - UMR BOREA "Biologie des ORganismes et Ecosystèmes Aquatiques" MNHN, UPMC, UCBN, CNRS-7208, IRD-207, University of Caen, Caen, France
| | - Carmen Bouza
- Department of Zoology, Genetics and Physics Anthropology, ACUIGEN Group, Faculty of Veterinary, Campus Terra, University of Santiago de Compostela, 27002, Lugo, Spain
| | - Peter E Robins
- School of Ocean Sciences, Marine Centre Wales, Bangor University, Menai Bridge, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Marine Centre Wales, Bangor University, Menai Bridge, UK
| | - Sharon Lynch
- School of Biological, Earth and Environmental Sciences/Aquaculture and Fisheries Development Centre, University College Cork, North Mall, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Antonio Villalba
- Centro de Investigacións Mariñas, 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, Basque Country, Spain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physics Anthropology, ACUIGEN Group, Faculty of Veterinary, Campus Terra, University of Santiago de Compostela, 27002, Lugo, Spain.
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Hermida M, Robledo D, Díaz S, Costas D, Bruzos AL, Blanco A, Pardo BG, Martínez P. The first high-density genetic map of common cockle (Cerastoderma edule) reveals a major QTL controlling shell color variation. Sci Rep 2022; 12:16971. [PMID: 36216849 PMCID: PMC9551087 DOI: 10.1038/s41598-022-21214-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/23/2022] [Indexed: 12/29/2022] Open
Abstract
Shell color shows broad variation within mollusc species and despite information on the genetic pathways involved in shell construction and color has recently increased, more studies are needed to understand its genetic architecture. The common cockle (Cerastoderma edule) is a valuable species from ecological and commercial perspectives which shows important variation in shell color across Northeast Atlantic. In this study, we constructed a high-density genetic map, as a tool for screening common cockle genome, which was applied to ascertain the genetic basis of color variation in the species. The consensus genetic map comprised 19 linkage groups (LGs) in accordance with the cockle karyotype (2n = 38) and spanned 1073 cM, including 730 markers per LG and an inter-marker distance of 0.13 cM. Five full-sib families showing segregation for several color-associated traits were used for a genome-wide association study and a major QTL on chromosome 13 associated to different color-traits was detected. Mining on this genomic region revealed several candidate genes related to shell construction and color. A genomic region previously reported associated with divergent selection in cockle distribution overlapped with this QTL suggesting its putative role on adaptation.
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Affiliation(s)
- Miguel Hermida
- Department of Zoology, Genetics and Physical Anthropology, Acuigen Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Seila Díaz
- Genomes and Disease Group, Department of Zoology, Genetics and Physical Anthropology, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
- ECOMARE, CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Santiago University Campus, 3810-193, Aveiro, Portugal
| | - Damián Costas
- Centro de Investigación Mariña, Universidade de Vigo, ECIMAT, 36331, Vigo, Spain
| | - Alicia L Bruzos
- Genomes and Disease Group, Department of Zoology, Genetics and Physical Anthropology, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
- Mosaicism and Precision Medicine Group, Department of Genetics and Genomic Medicine, The Francis Crick Institute, University College of London, London, UK
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical Anthropology, Acuigen Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain
| | - Belén G Pardo
- Department of Zoology, Genetics and Physical Anthropology, Acuigen Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, Acuigen Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain.
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5
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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] [Key Words] [Grants] [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 (F ST > 0.25) unlike neutral loci (F ST 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 VeterinaryUniversidade de Santiago de CompostelaLugoSpain
| | - Adrian Casanova
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
| | - Manu K. Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesMidlothianUK
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesMidlothianUK
| | - Daniel J. Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesMidlothianUK
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesMidlothianUK
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA)Vilanova de ArousaSpain
- Departamento de Ciencias de la VidaUniversidad de AlcaláAlcalá de HenaresSpain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE)University of the Basque Country (UPV/EHU)PlentziaSpain
| | - Manuel Vera
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
| | - Pauline Kamermans
- Wageningen Marine ResearchYersekeThe Netherlands
- Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
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