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Regan T, Hori TS, Bean TP. A chromosome-scale Mytilus edulis genome assembly for aquaculture, marine ecology, and evolution. G3 (BETHESDA, MD.) 2024; 14:jkae138. [PMID: 38935082 PMCID: PMC11304980 DOI: 10.1093/g3journal/jkae138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
The smooth-shelled blue mussel, Mytilus edulis is part of the Mytilus species complex, encompassing at least three putative species: M. edulis, Mytilus galloprovincialis, and Mytilus trossulus. These three species occur on both sides of the Atlantic and hybridize in nature, and both M. edulis and M. galloprovincialis are important aquaculture species. They are also invasive species in many parts of the world. Here, we present a chromosome-level assembly of M. edulis. We used a combination of PacBio sequencing and Dovetail's Omni-C technology to generate an assembly with 14 long scaffolds containing 94% of the predicted length of the M. edulis genome (1.6 out of 1.7 Gb). Assembly statistics were as follows: total length = 1.65 Gb, N50 = 116 Mb, L50 = 7, and L90 = 13. BUSCO analysis showed 92.55% eukaryote BUSCOs identified. AB-Initio annotation using RNA-seq from mantle, gills, muscle, and foot predicted 47,128 genes. These gene models were combined with IsoSeq validation resulting in 45,379 full CDS protein sequences and 129,708 isoforms. Using GBS and shotgun sequencing, we also sequenced several eastern Canadian populations of Mytilus to characterize single-nucleotide as well as structural variance. This high-quality genome for M. edulis provides a platform to develop tools that can be used in breeding, molecular ecology and evolution to address questions of both commercial and environmental perspectives.
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Affiliation(s)
- Tim Regan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Tiago S Hori
- Atlantic Aqua Farms Ltd., Charlottetown, Prince Edward Island, PE C1A 4A2, Canada
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
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2
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van der Pouw Kraan D, Graham CT, Kavanagh F, Mirimin L. Development and validation of a DNA-based multi-species biomonitoring toolkit using a high-throughput qPCR platform: A case study of Irish shellfish species. Mol Ecol Resour 2024; 24:e13945. [PMID: 38429942 DOI: 10.1111/1755-0998.13945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 03/03/2024]
Abstract
Biomonitoring of marine life has been enhanced in recent years by the integration of innovative DNA-based approaches, which offer advantages over more laborious techniques (e.g. microscopy). However, trade-offs between throughput, sensitivity and quantitative measurements must be made when choosing between the prevailing molecular methodologies (i.e. metabarcoding or qPCR/dPCR). Thus, the aim of the present study was to demonstrate the utility of a microfluidic-enabled high-throughput quantitative PCR platform (HTqPCR) for the rapid and cost-effective development and validation of a DNA-based multi-species biomonitoring toolkit, using larvae of 23 commercially targeted bivalve and crustacean species as a case study. The workflow was divided into three main phases: definition of (off-) target taxa and establishment of reference databases (PHASE 1); selection/development and assessment of molecular assays (PHASE 2); and protocol optimization and field validation (PHASE 3). 42 assays were eventually chosen and validated. Genetic signal not only showed good correlation with direct visual counts by microscopy but also showed the ability to provide quantitative data at the highest taxonomic resolution (species level) in a time- and cost-effective fashion. This study developed a biomonitoring toolkit, demonstrating the considerable advantages of this state-of-the-art technology in boosting the developmental testing and application of panels of molecular assays for the monitoring and management of natural resources. Once developed, this approach provides a cost and time-effective alternative compared to other multi-species approaches (e.g. metabarcoding). In addition, it is transferable to a wide range of species and will aid future monitoring programmes.
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Affiliation(s)
- Dennis van der Pouw Kraan
- Marine and Freshwater Research Centre, Department of Natural Resources and the Environment, Atlantic Technological University (ATU), Galway, Ireland
| | - Conor T Graham
- Marine and Freshwater Research Centre, Department of Natural Resources and the Environment, Atlantic Technological University (ATU), Galway, Ireland
| | - Fiona Kavanagh
- Marine and Freshwater Research Centre, Department of Natural Resources and the Environment, Atlantic Technological University (ATU), Galway, Ireland
| | - Luca Mirimin
- Marine and Freshwater Research Centre, Department of Natural Resources and the Environment, Atlantic Technological University (ATU), Galway, Ireland
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3
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Corrochano-Fraile A, Carboni S, Green DM, Taggart JB, Adams TP, Aleynik D, Bekaert M. Estimating blue mussel (Mytilus edulis) connectivity and settlement capacity in mid-latitude fjord regions. Commun Biol 2024; 7:166. [PMID: 38337015 PMCID: PMC10858254 DOI: 10.1038/s42003-023-05498-3] [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: 05/11/2023] [Accepted: 10/24/2023] [Indexed: 02/12/2024] Open
Abstract
The mussel industry faces challenges such as low and inconsistent levels of larvae settlement and poor-quality spat, leading to variable production. However, mussel farming remains a vital sustainable and environmentally responsible method for producing protein, fostering ecological responsibility in the aquaculture sector. We investigate the population connectivity and larval dispersion of blue mussels (Mytilus edulis) in Scottish waters, as a case study, using a multidisciplinary approach that combined genetic data and particle modelling. This research allows us to develop a thorough understanding of blue mussel population dynamics in mid-latitude fjord regions, to infer gene-flow patterns, and to estimate population divergence. Our findings reveal a primary south-to-north particle transport direction and the presence of five genetic clusters. We discover a significant and continuous genetic material exchange among populations within the study area, with our biophysical model's outcomes aligning with our genetic observations. Additionally, our model reveals a robust connection between the southwest coast and the rest of the west coast. This study will guide the preservation of mussel farming regions, ensuring sustainable populations that contribute to marine ecosystem health and resilience.
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Affiliation(s)
- Ana Corrochano-Fraile
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Stefano Carboni
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
- Fondazione IMC, Torre Grande, Oristano, Italy
| | - Darren M Green
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - John B Taggart
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Thomas P Adams
- Scottish Sea Farms Limited, Barcaldine Hatchery, Argyll, UK
| | | | - Michaël Bekaert
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK.
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Jilberto F, Zbawicka M, Wenne R, Larraín MA, Araneda C. SNP genotyping revealed a hybrid zone between Mytilus chilensis and M. platensis in southern South America (the Strait of Magellan, Isla Grande de Tierra del Fuego and the Falkland Islands). Mol Ecol 2024; 33:e17211. [PMID: 37996993 DOI: 10.1111/mec.17211] [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: 06/23/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
Hybrid zones among mussel species have been extensively studied in the northern hemisphere. In South America, it has only recently become possible to study the natural hybrid zones, due to the clarification of the taxonomy of native mussels of the Mytilus genus. Analysing 54 SNP markers, we show the genetic species composition and admixture in the hybrid zone between M. chilensis and M. platensis in the southern end of South America. Bayesian, non-Bayesian clustering and re-assignment algorithms showed that the natural hybrid zone between M. chilensis and M. platensis in the Strait of Magellan, Isla Grande de Tierra del Fuego and the Falkland Islands shows clinal architecture. The hybrid zone can be divided into three different areas: the first one is on the Atlantic coast where only pure M. platensis and hybrid were found. In the second one, inside the Strait of Magellan, pure individuals of both species and mussels with variable degrees of hybridisation coexist. In the last area at the Strait in front of Punta Arenas City, fjords on the Isla Grande de Tierra del Fuego, and at the Beagle Channel, only M. chilensis and a low number of hybrids were found. According to the proportion of hybrids, bays with protected conditions away from strong currents would give better conditions for hybridisation. We do not find evidence of any other mussel species such as M. edulis, M. galloprovincialis, M. planulatus or M. trossulus in the zone.
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Affiliation(s)
- Felipe Jilberto
- Food Quality Research Center, Universidad de Chile, Santiago, Chile
| | | | - Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - María Angélica Larraín
- Food Quality Research Center, Universidad de Chile, Santiago, Chile
- Departamento de Ciencia de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Cristián Araneda
- Food Quality Research Center, Universidad de Chile, Santiago, Chile
- Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
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Guo F, Ye Y, Zhu K, Lin S, Wang Y, Dong Z, Yao R, Li H, Wang W, Liao Z, Guo B, Yan X. Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel Mytilus coruscus Revealed by Whole-Genome Sequencing. Int J Mol Sci 2023; 24:13641. [PMID: 37686445 PMCID: PMC10488143 DOI: 10.3390/ijms241713641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The hard-shell mussel (Mytilus coruscus) is widespread in the temperate coastal areas of the northwest Pacific and holds a significant position in the shellfish aquaculture market in China. However, the natural resources of this species have been declining, and population genetic studies of M. coruscus are also lacking. In this study, we conducted whole-genome resequencing (WGR) of M. coruscus from eight different latitudes along the Chinese coast and identified a total of 25,859,986 single nucleotide polymorphism (SNP) markers. Our findings indicated that the genetic diversity of M. coruscus from the Zhoushan region was lower compared with populations from other regions. Furthermore, we observed that the evolutionary tree clustered into two primary branches, and the Zhangzhou (ZZ) population was in a separate branch. The ZZ population was partly isolated from populations in other regions, but the distribution of branches was not geographically homogeneous, and a nested pattern emerged, consistent with the population differentiation index (FST) results. To investigate the selection characteristics, we utilized the northern M. coruscus populations (Dalian and Qingdao) and the central populations (Zhoushan and Xiangshan) as reference populations and the southern ZZ population as the target population. Our selection scan analysis identified several genes associated with thermal responses, including Hsp70 and CYP450. These genes may play important roles in the adaptation of M. coruscus to different living environments. Overall, our study provides a comprehensive understanding of the genomic diversity of coastal M. coruscus in China and is a valuable resource for future studies on genetic breeding and the evolutionary adaptation of this species.
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Affiliation(s)
- Feng Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Kecheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China;
| | - Shuangrui Lin
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Yuxia Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Zhenyu Dong
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Ronghui Yao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Hongfei Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Weifeng Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Zhi Liao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Xiaojun Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
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Chatelain P, Elias M, Fontaine C, Villemant C, Dajoz I, Perrard A. Müllerian mimicry among bees and wasps: a review of current knowledge and future avenues of research. Biol Rev Camb Philos Soc 2023; 98:1310-1328. [PMID: 36994698 DOI: 10.1111/brv.12955] [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: 05/23/2022] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023]
Abstract
Many bees and stinging wasps, or aculeates, exhibit striking colour patterns or conspicuous coloration, such as black and yellow stripes. Such coloration is often interpreted as an aposematic signal advertising aculeate defences: the venomous sting. Aposematism can lead to Müllerian mimicry, the convergence of signals among different species unpalatable to predators. Müllerian mimicry has been extensively studied, notably on Neotropical butterflies and poison frogs. However, although a very high number of aculeate species harbour putative aposematic signals, aculeates are under-represented in mimicry studies. Here, we review the literature on mimicry rings that include bee and stinging wasp species. We report over a hundred described mimicry rings, involving a thousand species that belong to 19 aculeate families. These mimicry rings are found all throughout the world. Most importantly, we identify remaining knowledge gaps and unanswered questions related to the study of Müllerian mimicry in aculeates. Some of these questions are specific to aculeate models, such as the impact of sociality and of sexual dimorphism in defence levels on mimicry dynamics. Our review shows that aculeates may be one of the most diverse groups of organisms engaging in Müllerian mimicry and that the diversity of aculeate Müllerian mimetic interactions is currently under-explored. Thus, aculeates represent a new and major model system to study the evolution of Müllerian mimicry. Finally, aculeates are important pollinators and the global decline of pollinating insects raises considerable concern. In this context, a better understanding of the impact of Müllerian mimicry on aculeate communities may help design strategies for pollinator conservation, thereby providing future directions for evolutionary research.
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Affiliation(s)
- Paul Chatelain
- Institute of Ecology and Environmental Sciences-Paris (iEES-Paris), Sorbonne Université, CNRS, IRD, INRAE, Université Paris Cité, UPEC, 4 Place Jussieu, Paris, 75005, France
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 50, 57 rue Cuvier, Paris, 75005, France
| | - Marianne Elias
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 50, 57 rue Cuvier, Paris, 75005, France
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Colin Fontaine
- Centre d'Ecologie et des Sciences de la conservation, CESCO UMR 7204, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, 43 rue Cuvier, Paris, 75005, France
| | - Claire Villemant
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 50, 57 rue Cuvier, Paris, 75005, France
| | - Isabelle Dajoz
- Institute of Ecology and Environmental Sciences-Paris (iEES-Paris), Sorbonne Université, CNRS, IRD, INRAE, Université Paris Cité, UPEC, 4 Place Jussieu, Paris, 75005, France
- Université Paris Cité, 45 Rue des Saints-Pères, Paris, F-75006, France
| | - Adrien Perrard
- Institute of Ecology and Environmental Sciences-Paris (iEES-Paris), Sorbonne Université, CNRS, IRD, INRAE, Université Paris Cité, UPEC, 4 Place Jussieu, Paris, 75005, France
- Université Paris Cité, 45 Rue des Saints-Pères, Paris, F-75006, France
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DeHart HM, Gasser MT, Dixon J, Thielen P. An aquatic environmental DNA filtration system to maximize recovery potential and promote filtration approach standardization. PeerJ 2023; 11:e15360. [PMID: 37456865 PMCID: PMC10349554 DOI: 10.7717/peerj.15360] [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: 01/25/2023] [Accepted: 04/16/2023] [Indexed: 07/18/2023] Open
Abstract
Background Aquatic environmental DNA (eDNA) has emerged as a promising approach to identify organisms in freshwater and marine environments. While the recovery of eDNA from water most commonly involves capture of biological debris on a filter matrix, practitioners are yet to converge on standardized approaches for filtration, particularly in the field. This lack of standardization has resulted in inconsistent handling of samples following collection, limiting interpretation of results across studies and burdening groups with inconvenient storage and transport logistics that may compromise eDNA integrity. Methods A simple to assemble and low-cost ($350 USD) water filtration system is demonstrated that can be used in field and laboratory settings to reduce time between sample acquisition and eDNA filtration, maximizing eDNA sample recovery. Quantitative PCR is used to show the utility of the platform for laboratory and marine eDNA analysis. Results The resulting eDNA collection system is easily transported in a rugged water-resistant case, operates for more than eight hours on a 12-volt lead-acid battery, and has an unobstructed filtration rate of 150.05 ± 7.01 mL/min and 151.70 ± 6.72 mL/min with 0.22 µm and 0.45 µm Sterivex filters, respectively. We show that immediate sample filtration increases eDNA recovery in the laboratory, and demonstrate collections in aquaria and marine environments. We anticipate that providing easy to obtain, open hardware designs for eDNA sample collection will increase standardization of aquatic eDNA collection methods and improve cross-study comparisons.
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Affiliation(s)
- Hayley M. DeHart
- Research and Exploratory Development Department, The Johns Hopkins University, Laurel, MD, United States of America
| | - Mark T. Gasser
- Research and Exploratory Development Department, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States of America
| | - Jarret Dixon
- Force Projection Sector, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States of America
| | - Peter Thielen
- Research and Exploratory Development Department, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States of America
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Nascimento‐Schulze JC, Bean TP, Peñaloza C, Paris JR, Whiting JR, Simon A, Fraser BA, Houston RD, Bierne N, Ellis RP. SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array. Evol Appl 2023; 16:1044-1060. [PMID: 37216031 PMCID: PMC10197230 DOI: 10.1111/eva.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/15/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium-density 60 K SNP-array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole-genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change.
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Affiliation(s)
- Jennifer C. Nascimento‐Schulze
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Environment, Fisheries and Aquaculture ScienceWeymouth LaboratoryWeymouthUK
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Josephine R. Paris
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - James R. Whiting
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - Alexis Simon
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Bonnie A. Fraser
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | | | - Nicolas Bierne
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Robert P. Ellis
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Sustainable Aquaculture FuturesUniversity of ExeterExeterUK
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Blin M, Dametto S, Agniwo P, Webster BL, Angora E, Dabo A, Boissier J. A duplex tetra-primer ARMS-PCR assay to discriminate three species of the Schistosoma haematobium group: Schistosoma curassoni, S. bovis, S. haematobium and their hybrids. Parasit Vectors 2023; 16:121. [PMID: 37029440 PMCID: PMC10082484 DOI: 10.1186/s13071-023-05754-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
BACKGROUND The use of applications involving single nucleotide polymorphisms (SNPs) has greatly increased since the beginning of the 2000s, with the number of associated techniques expanding rapidly in the field of molecular research. Tetra-primer amplification refractory mutation system-PCR (T-ARMS-PCR) is one such technique involving SNP genotyping. It has the advantage of amplifying multiple alleles in a single reaction with the inclusion of an internal molecular control. We report here the development of a rapid, reliable and cost-effective duplex T-ARMS-PCR assay to distinguish between three Schistosoma species, namely Schistosoma haematobium (human parasite), Schistosoma bovis and Schistosoma curassoni (animal parasites), and their hybrids. This technique will facilitate studies of population genetics and the evolution of introgression events. METHODS During the development of the technique we focused on one of the five inter-species internal transcribed spacer (ITS) SNPs and one of the inter-species 18S SNPs which, when combined, discriminate between all three Schistosoma species and their hybrid forms. We designed T-ARMS-PCR primers to amplify amplicons of specific lengths for each species, which in turn can then be visualized on an electrophoresis gel. This was further tested using laboratory and field-collected adult worms and field-collected larval stages (miracidia) from Spain, Egypt, Mali, Senegal and Ivory Coast. The combined duplex T-ARMS-PCR and ITS + 18S primer set was then used to differentiate the three species in a single reaction. RESULTS The T-ARMS-PCR assay was able to detect DNA from both species being analysed at the maximum and minimum levels in the DNA ratios (95/5) tested. The duplex T-ARMS-PCR assay was also able to detect all hybrids tested and was validated by sequencing the ITS and the 18S amplicons of 148 of the field samples included in the study. CONCLUSIONS The duplex tetra-primer ARMS-PCR assay described here can be applied to differentiate between Schistosoma species and their hybrid forms that infect humans and animals, thereby providing a method to investigate the epidemiology of these species in endemic areas. The addition of several markers in a single reaction saves considerable time and is of long-standing interest for investigating genetic populations.
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Affiliation(s)
- Manon Blin
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan Via Domitia, Perpignan, 66860, France
- SAS ParaDev®, 66860, Perpignan, France
| | - Sarah Dametto
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan Via Domitia, Perpignan, 66860, France
| | - Privat Agniwo
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan Via Domitia, Perpignan, 66860, France
- Department of Epidemiology of Infectious Diseases, Faculty of Pharmacy, IRL 3189, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Bonnie L Webster
- Wolfson Wellcome Biomedical Laboratories, Department of Science, Natural History Museum, London, SW7 5BD, UK
- London Centre for Neglected Tropical Disease Research, Imperial College London School of Public Health, London, W2 1PG, UK
| | - Etienne Angora
- Swiss Tropical and Public Health Institute, P.O. Box, 4002, Basel, Switzerland
- University of Basel, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- Unité de Formation et de Recherche Sciences Pharmaceutiques et Biologiques, Université Félix Houphouët-Boigny, BPV 34, Abidjan, Côte d'Ivoire
| | - Abdoulaye Dabo
- Department of Epidemiology of Infectious Diseases, Faculty of Pharmacy, IRL 3189, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Jérôme Boissier
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan Via Domitia, Perpignan, 66860, France.
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Development of a diagnostic single nucleotide polymorphism (SNP) panel for identifying geographic origins of Cochliomyia hominivorax, the New World screwworm. Vet Parasitol 2023; 315:109884. [PMID: 36701943 DOI: 10.1016/j.vetpar.2023.109884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/21/2022] [Accepted: 01/16/2023] [Indexed: 01/20/2023]
Abstract
The New World screwworm, Cochliomyia hominivorax, causes myiasis in livestock, humans, and other warm-blooded animals in much of South America and the Caribbean. It has been eradicated from North and Central America using the sterile insect technique and a biological barrier is currently maintained at the Panama - Colombian border. However, C. hominivorax is still a threat to eradicated areas as outbreaks can and do occur. In order to identify the origin of a fly involved in an outbreak scenario, diagnostic tools would be beneficial. Recently, the geographic population structure of this species was identified using single nucleotide polymorphisms (SNPs). Here we characterize the three major regional clusters: South America, the Inner Caribbean, and the Outer Caribbean. The objective of this study was to develop a SNP (single nucleotide polymorphism) panel to distinguish between these three clusters. A panel was developed using two unique SNPs per region for a total of six SNPs. This diagnostic SNP assay will allow for rapid source determination of flies from future incursions in order to intercept introductory pathways and aid in the control of New World screwworm.
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11
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Pillet M, Evensen KG, Marengo M, Lejeune P, Poynton HC, Thomas H. First insight into the development of a new transcriptomic tool in French Corsica harbors. MARINE POLLUTION BULLETIN 2022; 184:114173. [PMID: 36191473 DOI: 10.1016/j.marpolbul.2022.114173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Coastal harbor areas are subjected to a myriad of contamination sources with largely unknown effects. Such complex chemical mixtures are difficult to monitor but transcriptomics is a promising approach for such biomonitoring. The present study was designed to verify the use of the Coastal Biosensor for Endocrine Disruption (C-BED) assay, previously developed to detect emerging contaminants and their effects on Mytilus edulis, on another mussel species, Mytilus galloprovincialis. Mussels were caged on St-Florent harbor (contaminated) and on Revellata Bay (reference) for three months. A classical multibiomarkers approach was coupled to the C-BED assay. The results of both approaches were analysed using the Integrated Biomarkers Responses (IBR) and compared to each other. Both approaches demonstrated a higher contamination and probable endocrine disruption of mussels in St-Florent, compared to the reference station. These results confirm that the C-BED assay provides an innovative method to expand our ability to detect emerging contaminants.
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Affiliation(s)
- Marion Pillet
- STAtion de REcherches Sous-marines et Océanographiques, Punta Revellata, 20260 Calvi, France; LIttoral ENvironnement et Sociétés (UMR7266 CNRS), La Rochelle Université, 2 rue Olympe de Gouges, 17000 La Rochelle, France.
| | - K Garrett Evensen
- School for the Environment, University of Massachusetts, 100 William T. Morrissey Blvd., Boston, MA 02125, United States
| | - Michel Marengo
- STAtion de REcherches Sous-marines et Océanographiques, Punta Revellata, 20260 Calvi, France
| | - Pierre Lejeune
- STAtion de REcherches Sous-marines et Océanographiques, Punta Revellata, 20260 Calvi, France
| | - Helen C Poynton
- School for the Environment, University of Massachusetts, 100 William T. Morrissey Blvd., Boston, MA 02125, United States
| | - Hélène Thomas
- LIttoral ENvironnement et Sociétés (UMR7266 CNRS), La Rochelle Université, 2 rue Olympe de Gouges, 17000 La Rochelle, France
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12
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Vargas-Peralta CE, Araneda C, Galindo-Sánchez CE, Larraín MA, Del Río-Portilla MA, Lafarga-De la Cruz F. Species identification in Haliotis genus from the northeastern Pacific Ocean using genome-wide RAD-SNPs. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Corrochano-Fraile A, Davie A, Carboni S, Bekaert M. Evidence of multiple genome duplication events in Mytilus evolution. BMC Genomics 2022; 23:340. [PMID: 35501689 PMCID: PMC9063065 DOI: 10.1186/s12864-022-08575-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
Background Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia. Results Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences. Conclusions The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multi-disciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08575-9.
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Affiliation(s)
- Ana Corrochano-Fraile
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Andrew Davie
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Stefano Carboni
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK. .,International Marine Centre, Loc. Sa Mardini snc, 09170, Torre Grande, OR, Italy.
| | - Michaël Bekaert
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
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14
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Khaitov V, Marchenko J, Katolikova M, Väinölä R, Kingston SE, Carlon DB, Gantsevich M, Strelkov P. Species identification based on a semi-diagnostic marker: Evaluation of a simple conchological test for distinguishing blue mussels Mytilus edulis L. and M. trossulus Gould. PLoS One 2021; 16:e0249587. [PMID: 34297723 PMCID: PMC8301678 DOI: 10.1371/journal.pone.0249587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 03/22/2021] [Indexed: 11/19/2022] Open
Abstract
Cryptic and hybridizing species may lack diagnostic taxonomic characters leaving researchers with semi-diagnostic ones. Identification based on such characters is probabilistic, the probability of correct identification depending on the species composition in a mixed population. Here we test the possibilities of applying a semi-diagnostic conchological character for distinguishing two cryptic species of blue mussels, Mytilus edulis and M. trossulus. These ecologically, stratigraphically and economically important molluscs co-occur and hybridize in many areas of the North Atlantic and the neighboring Arctic. Any cues for distinguishing them in sympatry without genotyping would save much research effort. Recently these species have been shown to statistically differ in the White Sea, where a simple character of the shell was used to distinguish two mussel morphotypes. In this paper, we analyzed the associations between morphotypes and species-specific genotypes based on an abundant material from the waters of the Kola Peninsula (White Sea, Barents Sea) and a more limited material from Norway, the Baltic Sea, Scotland and the Gulf of Maine. The performance of the "morphotype test" for species identification was formally evaluated using approaches from evidence-based medicine. Interspecific differences in the morphotype frequencies were ubiquitous and unidirectional, but their scale varied geographically (from 75% in the White Sea to 15% in the Baltic Sea). In addition, salinity-related variation of this character within M. edulis was revealed in the Arctic Barents Sea. For every studied region, we established relationships between the proportions of the morphotypes in the populations as well as between the proportions of the morphotypes in samples and the probabilities of mussels of different morphotypes being M. trossulus and M. edulis. We provide recommendations for the application of the morphotype test to mussels from unstudied contact zones and note that they may apply equally well to other taxa identified by semi-diagnostic traits.
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Affiliation(s)
- Vadim Khaitov
- St. Petersburg State University, St. Petersburg, Russia
- Kandalaksha State Nature Reserve, Kandalaksha, Murmansk Region, Russia
| | | | - Marina Katolikova
- St. Petersburg State University, St. Petersburg, Russia
- Murmansk Marine Biological Institute, Murmansk, Russia
| | - Risto Väinölä
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Sarah E. Kingston
- Department of Biology & Schiller Coastal Studies Center, Bowdoin College, Brunswick, Maine, United States of America
- School of Marine Sciences and Darling Marine Center, University of Maine, Walpole, Maine, United States of America
| | - David B. Carlon
- Department of Biology & Schiller Coastal Studies Center, Bowdoin College, Brunswick, Maine, United States of America
| | - Michael Gantsevich
- Department of Invertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr Strelkov
- St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Monitoring and Conservation of Natural Arctic Ecosystems, Murmansk Arctic State University, Murmansk, Russia
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15
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Development and Validation of a Multi-Locus PCR-HRM Method for Species Identification in Mytilus Genus with Food Authenticity Purposes. Foods 2021; 10:foods10081684. [PMID: 34441462 PMCID: PMC8391999 DOI: 10.3390/foods10081684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/06/2021] [Accepted: 07/06/2021] [Indexed: 11/17/2022] Open
Abstract
DNA-based methods using informative markers such as single nucleotide polymorphism (SNPs) are suitable for reliable species identification (SI) needed to enforce compliance with seafood labelling regulations (EU No.1379/2013). We developed a panel of 10 highly informative SNPs to be genotyped by PCR-High resolution melting (HRM) for SI in the Mytilus genus through in silico and in vitro stages. Its fitness for purpose and concordance were assessed by an internal validation process and by the transference to a second laboratory. The method was applicable to identify M. chilensis, M. edulis, M. galloprovincialis and M. trossulus mussels, fresh, frozen and canned with brine, oil and scallop sauce, but not in preserves containing acetic acid (wine vinegar) and tomato sauce. False-positive and negative rates were zero. Sensitivity, expressed as limit of detection (LOD), ranged between 5 and 8 ng/μL. The method was robust against small variations in DNA quality, annealing time and temperature, primer concentration, reaction volume and HRM kit. Reference materials and 220 samples were tested in an inter-laboratory assay obtaining an “almost perfect agreement” (κ = 0.925, p < 0.001). In conclusion, the method was suitable for the intended use and to be applied in the seafood industry.
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Michalek K, Vendrami DLJ, Bekaert M, Green DH, Last KS, Telesca L, Wilding TA, Hoffman JI. Mytilus trossulus introgression and consequences for shell traits in longline cultivated mussels. Evol Appl 2021; 14:1830-1843. [PMID: 34295367 PMCID: PMC8288009 DOI: 10.1111/eva.13245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/30/2021] [Accepted: 04/14/2021] [Indexed: 01/13/2023] Open
Abstract
Mussels belonging to the Mytilus species complex (M. edulis, ME; M. galloprovincialis, MG; and M. trossulus, MT) often occur in sympatry, facilitating introgressive hybridization. This may be further promoted by mussel aquaculture practices, with MT introgression often resulting in commercially unfavourable traits such as low meat yield and weak shells. To investigate the relationship between genotype and shell phenotype, genetic and morphological variability was quantified across depth (1 m to 7 m) along a cultivation rope at a mussel farm on the West coast of Scotland. A single nuclear marker (Me15/16) and a novel panel of 33 MT-diagnostic single nucleotide polymorphisms were used to evaluate stock structure and the extent of MT introgression across depth. Variation in shell strength, determined as the maximum compression force for shell puncture, and shell shape using geometric morphometric analysis were evaluated in relation to cultivation depth and the genetic profiles of the mussels. Overall, ME was the dominant genotype across depth, followed by ME × MG hybrids and smaller quantities of ME × MT hybrids and pure MT individuals. In parallel, we identified multiple individuals that were either predominantly homozygous or heterozygous for MT-diagnostic alleles, likely representing pure MT and first-generation ME × MT hybrids, respectively. Both the proportion of individuals carrying MT alleles and MT allele frequency declined with depth. Furthermore, MT-introgressed individuals had significantly weaker and more elongate shells than nonintrogressed individuals. This study provides detailed insights into stock structure along a cultivation rope and suggests that practical methods to assess shell strength and shape of cultivated mussels may facilitate the rapid identification of MT, limiting the impact of this commercially damaging species.
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Affiliation(s)
| | | | - Michaël Bekaert
- Institute of AquacultureFaculty of Natural SciencesUniversity of StirlingStirlingUK
| | | | - Kim S. Last
- The Scottish Association for Marine ScienceObanUK
| | - Luca Telesca
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
- British Antarctic SurveyCambridgeUK
- Present address:
Lamont‐Doherty Earth Observatory of Columbia UniversityPalisadesNYUSA
| | | | - Joseph I. Hoffman
- Department of Animal BehaviourUniversity of BielefeldBielefeldGermany
- British Antarctic SurveyCambridgeUK
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17
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Vendrami DLJ, De Noia M, Telesca L, Brodte E, Hoffman JI. Genome-wide insights into introgression and its consequences for genome-wide heterozygosity in the Mytilus species complex across Europe. Evol Appl 2020; 13:2130-2142. [PMID: 32908609 PMCID: PMC7463347 DOI: 10.1111/eva.12974] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/24/2020] [Indexed: 11/26/2022] Open
Abstract
The three mussel species comprising the Mytilus complex are widespread across Europe and readily hybridize when they occur in sympatry, resulting in a mosaic of populations with varying genomic backgrounds. Two of these species, M. edulis and M. galloprovincialis, are extensively cultivated across Europe, with annual production exceeding 230,000 tonnes. The third species, M. trossulus, is considered commercially damaging as hybridization with this species results in weaker shells and poor meat quality. We therefore used restriction site associated DNA sequencing to generate high-resolution insights into the structure of the Mytilus complex across Europe and to resolve patterns of introgression. Inferred species distributions were concordant with the results of previous studies based on smaller numbers of genetic markers, with M. edulis and M. galloprovincialis predominating in northern and southern Europe respectively, while introgression between these species was most pronounced in northern France and the Shetland Islands. We also detected traces of M. trossulus ancestry in several northern European populations, especially around the Baltic and in northern Scotland. Finally, genome-wide heterozygosity, whether quantified at the population or individual level, was lowest in M. edulis, intermediate in M. galloprovincialis, and highest in M. trossulus, while introgression was positively associated with heterozygosity in M. edulis but negatively associated with heterozygosity in M. galloprovincialis. Our study will help to inform mussel aquaculture by providing baseline information on the genomic backgrounds of different Mytilus populations across Europe and by elucidating the effects of introgression on genome-wide heterozygosity, which is known to influence commercially important traits such as growth, viability, and fecundity in mussels.
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Affiliation(s)
| | - Michele De Noia
- Department of Animal BehaviorUniversity of BielefeldBielefeldGermany
- Institute of Biodiversity, Animal Health & Comparative MedicineCollege of Medical Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
| | - Luca Telesca
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
- British Antarctic Survey, High CrossCambridgeUK
| | | | - Joseph I. Hoffman
- Department of Animal BehaviorUniversity of BielefeldBielefeldGermany
- British Antarctic Survey, High CrossCambridgeUK
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18
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Der Sarkissian C, Möller P, Hofman CA, Ilsøe P, Rick TC, Schiøtte T, Sørensen MV, Dalén L, Orlando L. Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00037] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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19
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Larraín MA, González P, Pérez C, Araneda C. Comparison between single and multi-locus approaches for specimen identification in Mytilus mussels. Sci Rep 2019; 9:19714. [PMID: 31873129 PMCID: PMC6928075 DOI: 10.1038/s41598-019-55855-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/30/2019] [Indexed: 01/19/2023] Open
Abstract
Mytilus mussels have been the object of much research given their sentinel role in coastal ecosystems and significant value as an aquaculture resource appreciated for both, its flavour and nutritional content. Some of the most-studied Mytilus species are M. edulis, M. galloprovincialis, M. chilensis and M. trossulus. As species identification based on morphological characteristics of Mytilus specimens is difficult, molecular markers are often used. Single-locus markers can give conflicting results when used independently; not all markers differentiate among all species, and the markers target genomic regions with different evolutionary histories. We evaluated the concordance between the PCR-RFLP markers most commonly-used for species identification in mussels within the Mytilus genus (Me15-16, ITS, mac-1, 16S rRNA and COI) when used alone (mono-locus approach) or together (multi-locus approach). In this study, multi-locus strategy outperformed the mono-locus methods, clearly identifying all four species and also showed similar specimen identification performance than a 49 SNPs panel. We hope that these findings will contribute to a better understanding of DNA marker-based analysis of Mytilus taxa. These results support the use of a multi-locus approach when studying this important marine resource, including research on food quality and safety, sustainable production and conservation.
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Affiliation(s)
- María Angélica Larraín
- Food Quality Research Center, Universidad de Chile, Santiago, Chile.
- Departamento de Ciencia de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
| | - Pía González
- Food Quality Research Center, Universidad de Chile, Santiago, Chile
- Programa de Magister en Alimentos. Mención Gestión, Calidad e Inocuidad de los Alimentos. Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Claudio Pérez
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Cristián Araneda
- Food Quality Research Center, Universidad de Chile, Santiago, Chile
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
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20
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Cunha M, Martins C, Grosso AR, Costa PM. Mytilus galloprovincialis CYP1A-like mRNAs reveal closer proximity of mytilid CYP1A to the eumetazoan CYP2 family. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 214:105260. [PMID: 31336222 DOI: 10.1016/j.aquatox.2019.105260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/15/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
Due to the role of Cytochrome P450, Family 1, Subfamily A (CYP1A) in the detoxification of many polycyclic aromatic hydrocarbons (PAHs), there has been an effort to characterise the gene and the products from its expression in organisms that are relevant for biomonitoring and toxicity testing procedures. Nonetheless, the existence of functional homologues in aquatic invertebrates is not entirely consensual, especially in bivalve molluscs, which pose as one of the most important models for aquatic toxicologists, especially mytilids. After isolation and sequencing of CYP1A-like mRNA from the Mediterranean mussel, Mytilus galloprovincialis, phylogenetics incorporating homologues from molluscs and other eumetazoans, vertebrates included, yielded notorious similarity to sequences belonging to the CYP2 Family. Altogether, the findings further indicate that CYP1A-like CYPs may be absent in bivalves, in lieu of Families CYP2, 3 and 4, suggesting caution when interpreting data from common biomarkers of exposure to aromatic hydrocarbons that have been developed for CYP1A activity and expression in higher deuterostomes.
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Affiliation(s)
- M Cunha
- UCIBIO -Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - C Martins
- UCIBIO -Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - A R Grosso
- UCIBIO -Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - P M Costa
- UCIBIO -Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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21
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Zbawicka M, Gardner JPA, Wenne R. Cryptic diversity in smooth-shelled mussels on Southern Ocean islands: connectivity, hybridisation and a marine invasion. Front Zool 2019; 16:32. [PMID: 31406494 PMCID: PMC6685288 DOI: 10.1186/s12983-019-0332-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/24/2019] [Indexed: 01/08/2023] Open
Abstract
Background Large numbers of endemic species inhabit subantarctic continental coasts and islands that are characterised by highly variable environmental conditions. Southern hemisphere populations of taxa that are morphologically similar to northern counterparts have traditionally been considered to be extensions of such Northern hemisphere taxa, and may not exhibit differentiation amongst geographically isolated populations in the Southern Ocean. Smooth-shelled blue mussels of the genus Mytilus that exhibit an anti-tropical distribution are a model group to study phylogeography, speciation and hybridisation in the sea, and contribute to the theory and practice of marine biosecurity. Methods We used a single nucleotide polymorphism (SNPs) panel that has the ability to accurately identify reference Northern and Southern hemisphere Mytilus taxa to test for evolutionary differentiation amongst native Southern Ocean island populations. Results Native mussels from the Falkland Islands and the Kerguelen Islands exhibited greatest affinity to native M. platensis d’Orbigny 1846 from the Atlantic coast of South America. The major Southern Ocean current flow from west to east is likely to explain the spreading of M. platensis to remote offshore islands, as adults via the process of rafting or perhaps directly as larvae. SNPs variation revealed that mussels from Tasmania were native and clearly differentiated from all other blue mussel groups in the Southern and Northern hemispheres. The native mussels M. planulatus from Tasmania and from mainland New Zealand (NZ), and tentatively M. aoteanus from the two NZ Southern Ocean offshore island groups (the Auckland Islands and Campbell Island), formed a distinct M. galloprovincialis–like Southern hemisphere group with closest affinity to Northern hemisphere M. galloprovincialis from the Mediterranean Sea. In all cases, the SNPs revealed evidence of hybridisation between two or more distinct taxa. The invasive Northern hemisphere M. galloprovincialis was identified only in Tasmania, amongst native mussels of a distinct Australian M. planulatus lineage. Conclusion Overall, our results reveal that Southern hemisphere island mussels have mixed genome ancestry and are native, not introduced by human activities. The preservation of distinct evolutionary lineages of Southern hemisphere species needs to be an ongoing focus of conservation efforts, given that population sizes on some of the remote offshore oceanic islands will be small and may be more easily adversely affected by invasion and subsequent hybridisation and introgression than larger populations elsewhere. Electronic supplementary material The online version of this article (10.1186/s12983-019-0332-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Małgorzata Zbawicka
- 1Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Jonathan P A Gardner
- 2School of Biological Sciences, Victoria University of Wellington, P O Box 600, Wellington, 6140 New Zealand
| | - Roman Wenne
- 1Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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