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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Asorey CM, Jilberto F, Haase I, Schubbert R, Angélica Larraín M, Araneda C. Comparison of two commercial methods for smooth-shelled mussels ( Mytilus spp.) species identification. Food Chem (Oxf) 2022; 5:100121. [PMID: 35865713 PMCID: PMC9294527 DOI: 10.1016/j.fochms.2022.100121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/14/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Seafood international trade has increased the labeling requirements in standards and regulations to include product information that enable traders and consumers to make informed choices. The European Union (EU) Regulation No. 1379/2013 imposes the declaration of an official commercial designation and scientific names for all the fishery and aquaculture products to be offered for sale to the final consumers. DNA analyses are used to enforce this regulation and to test authenticity in processed foods. We compared the performance of two mono-locus approaches for species identification (SI) in 61 Mytilus mussels: the high-resolution melting analysis of the polyphenolic adhesive protein gene and the partial sequencing of the histone H1C gene. The H1C sequences were analyzed with five different methods. Both approaches show discrepancies in the identification of putative hybrids (0.0 < κ < 0.687 and 0.0 < MCC < 0.724). Excluding putative hybrids, methods show substantial to perfect agreement (0.772 < κ < 1.0 and 0.783 < MCC < 1.0). This study highlights the need to use standardized molecular tools, as well as to use multi-locus methods for SI of Mytilus mussels in testing laboratories.
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Affiliation(s)
- Cynthia M. Asorey
- Food Quality Research Center. Universidad de Chile, Santiago, Chile
- Universidad Católica del Norte, Facultad de Ciencias del Mar, Sala de Colecciones Biológicas, Departamento de Biología Marina, Larrondo 1281, Coquimbo, Chile
| | - Felipe Jilberto
- Food Quality Research Center. Universidad de Chile, Santiago, Chile
- Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Animal, Avenida Santa Rosa 11315, La Pintana, Santiago, Chile
- Universidad de Chile, Facultad de Ciencias Químicas y Farmacéuticas, Departamento de Ciencia de los Alimentos y Tecnología Química, Santiago, Chile
| | - Ilka Haase
- Eurofins Genomics, Anzinger Str. 7a, 85560 Ebersberg, Germany
| | | | - María Angélica Larraín
- Food Quality Research Center. Universidad de Chile, Santiago, Chile
- Universidad de Chile, Facultad de Ciencias Químicas y Farmacéuticas, Departamento de Ciencia de los Alimentos y Tecnología Química, Santiago, Chile
| | - Cristián Araneda
- Food Quality Research Center. Universidad de Chile, Santiago, Chile
- Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Animal, Avenida Santa Rosa 11315, La Pintana, Santiago, Chile
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Giusti A, Malloggi C, Tosi F, Boldini P, Larraín Barth MA, Araneda C, Arcangeli G, Armani A. Mislabeling assessment and species identification by PCR-RFLP of mussel-based products (Mytilus spp.) sold on the Italian market. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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del Rio-Lavín A, Jiménez E, Pardo MÁ. SYBR-Green real-time PCR assay with melting curve analysis for the rapid identification of Mytilus species in food samples. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Gense K, Peterseil V, Licina A, Wagner M, Cichna-Markl M, Dobrovolny S, Hochegger R. Development of a DNA Metabarcoding Method for the Identification of Bivalve Species in Seafood Products. Foods 2021; 10:2618. [PMID: 34828894 DOI: 10.3390/foods10112618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022] Open
Abstract
The production of bivalve species has been increasing in the last decades. In spite of strict requirements for species declaration, incorrect labelling of bivalve products has repeatedly been detected. We present a DNA metabarcoding method allowing the identification of bivalve species belonging to the bivalve families Mytilidae (mussels), Pectinidae (scallops), and Ostreidae (oysters) in foodstuffs. The method, developed on Illumina instruments, targets a 150 bp fragment of mitochondrial 16S rDNA. We designed seven primers (three primers for mussel species, two primers for scallop species and a primer pair for oyster species) and combined them in a triplex PCR assay. In each of eleven reference samples, the bivalve species was identified correctly. In ten DNA extract mixtures, not only the main component (97.0-98.0%) but also the minor components (0.5-1.5%) were detected correctly, with only a few exceptions. The DNA metabarcoding method was found to be applicable to complex and processed foodstuffs, allowing the identification of bivalves in, e.g., marinated form, in sauces, in seafood mixes and even in instant noodle seafood. The method is highly suitable for food authentication in routine analysis, in particular in combination with a DNA metabarcoding method for mammalian and poultry species published recently.
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Quintrel M, Jilberto F, Sepúlveda M, Marín ME, Véliz D, Araneda C, Larraín MA. Development and Validation of a Multi-Locus PCR-HRM Method for Species Identification in Mytilus Genus with Food Authenticity Purposes. Foods 2021; 10:1684. [PMID: 34441462 DOI: 10.3390/foods10081684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Colihueque N, Espinoza R, Parraguez M. Authentication of Frozen Chilean Blue Mussel (Mytilus chilensis) Commercialized in the Town of Osorno, Southern Chile, Using PCR-RFLP Analysis. Recent Pat Food Nutr Agric 2021; 11:49-55. [PMID: 30599114 DOI: 10.2174/2212798410666181231154406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/08/2018] [Accepted: 12/17/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND DNA-based technologies are reliable authentication methods for food products, enabling the detection of fraud, non-intentional substitution and control of mislabeling. The Chilean blue mussel (Mytilus chilensis) is a seafood commercialized in Chile under different formats, including packages of frozen specimens. In this format, the valves of mussels are removed during processing, thus impeding identification of the product by the consumer due to the lack of external characters. OBJECTIVE To assess the authenticity of frozen Chilean blue mussels commercialized in southern Chile, particularly in the town of Osorno. METHODS Six commercial brands of frozen Chilean blue mussel were authenticated by the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method, based on the analysis of an 18S rDNA fragment. RESULTS Restriction patterns obtained indicate that three brands (50%) proved to be 100% authentic, given that all specimens contained in the package were Chilean blue mussels. The other three brands (50%) contained specimens of other commercial mytilids, particularly the cholga mussel (Aulacomya ater), in a variable percentage (12.5-50%). CONCLUSION This study based on the PCR-RFLP method provides evidence that Chilean blue mussels commercialized in a town located in southern Chile lack authenticity. This finding highlights the necessity for national producers to improve the production and/or packaging processes of this seafood. The authentication of commercial mussels is a matter of consumer interest and has been described in a recent patent on this issue that proposes an alternative methodology.
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Affiliation(s)
- Nelson Colihueque
- Laboratorio de Biologia Molecular y Citogenetica, Departamento de Ciencias Biologicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - René Espinoza
- Departamento de Acuicultura y Recursos Agroalimentarios, Universidad de Los Lagos, Osorno, Chile
| | - Margarita Parraguez
- Laboratorio de Genetica, Acuicultura y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
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Chen C, Ding Y, Wang Y, Jiang Q, Wang F, Lu C, Zhang L, Zhu C. High-Resolution Melting Analysis of COI Sequences Distinguishes Pufferfish Species ( Takifugu spp.) in China. J Agric Food Chem 2021; 69:794-804. [PMID: 33401907 DOI: 10.1021/acs.jafc.0c06584] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pufferfish is a traditional, delicious dish in Asia. However, eating wild or improperly processed pufferfish causes serious poisoning. This study aimed to exploit the high-resolution melting (HRM) method for authenticating four species of Takifugu pufferfish (Takifugu xanthopterus, T. fasciatus, T. flavidus, and T. rubripes). Candidate DNA barcodes, including the cytochrome c oxidase subunit I (COI), cytochrome oxidase b (Cytb), and the control region (D-loop), were analyzed, with COI selected as the optimal DNA barcode. An HRM method was developed to identify 57 commercial fish samples in China, including 33 commercial pufferfish products and 24 unlabeled fish products. The findings revealed that the pufferfish products were T. rubripes or T. fasciatus, and four T. xanthopterus samples were detected in unlabeled fish products. These results showed that DNA barcode coupled with HRM analysis was a rapid and efficient tool to identify pufferfish, which might aid in the prevention of consumer fraud or mislabeling of fish products.
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Affiliation(s)
- Chengtong Chen
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yanfei Ding
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yi Wang
- Hangzhou Neoline Technology Co., Ltd., Hangzhou 310004, China
| | - Qiong Jiang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Feijuan Wang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Chenze Lu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Leilei Zhang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Cheng Zhu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
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Giusti A, Tosi F, Tinacci L, Guardone L, Corti I, Arcangeli G, Armani A. Mussels (Mytilus spp.) products authentication: A case study on the Italian market confirms issues in species identification and arises concern on commercial names attribution. Food Control 2020; 118:107379. [DOI: 10.1016/j.foodcont.2020.107379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Abstract
Global trade of seafood has increased in the last decade, leading to significant concerns associated with seafood fraud. Seafood fraud involves the intentional misrepresentation of fish or shellfish for the purpose of economic gain and includes acts such as species substitution, illegal transshipment, overtreatment/short weighting, and mislabeling country of origin or production method. These fraudulent acts have had economic, environmental, and public health consequences on a global level. DNA-based techniques for seafood authentication are utilized by regulatory agencies and can be employed as part of a food fraud risk mitigation plan. This chapter will focus specifically on the use of DNA-based methods for the detection of seafood species substitution. Various methods have been developed for DNA-based species identification of seafood, including polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), species-specific PCR, real-time PCR, Sanger sequencing, microarrays, and high-resolution melting (HRM). Emerging techniques for seafood authentication include droplet digital PCR, isothermal amplification, PCR-enzyme-linked immunosorbent assay (ELISA), and high-throughput or next-generation sequencing. Some of these DNA-based methods target specific species, such as real-time PCR and droplet digital PCR, while other methods allow for simultaneous differentiation of a wide range of fish species, including Sanger sequencing and high-throughput sequencing. This chapter will begin with an introduction on seafood fraud and species substitution, followed by an analysis of the main DNA-based authentication methods and emerging techniques for species identification.
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Affiliation(s)
| | - Joana S. Amaral
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Isabel Mafra
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Zhao Y, Song W, Li R, Wang C, Mu C. A high-resolution melting analysis method for the effective discrimination of three Sepia species. J Verbrauch Lebensm 2020; 15:383-5. [DOI: 10.1007/s00003-020-01289-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Maggioni D, Tatulli G, Montalbetti E, Tommasi N, Galli P, Labra M, Pompa PP, Galimberti A. From DNA barcoding to nanoparticle-based colorimetric testing: a new frontier in cephalopod authentication. Appl Nanosci 2020; 10:1053-60. [DOI: 10.1007/s13204-020-01249-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Verrez-Bagnis V, Sotelo CG, Mendes R, Silva H, Kappel K, Schröder U. Methods for Seafood Authenticity Testing in Europe. Bioactive Molecules in Food 2019. [DOI: 10.1007/978-3-319-78030-6_69] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Worasilchai N, Permpalung N, Chindamporn A. High-resolution melting analysis: A novel approach for clade differentiation in Pythium insidiosum and pythiosis. Med Mycol 2018; 56:868-876. [PMID: 29228389 DOI: 10.1093/mmy/myx123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/12/2017] [Indexed: 01/02/2023] Open
Abstract
Pythium insidiosum causes life-threatening human pythiosis. Based on phylogenetic analysis using internal transcribed spacer (ITS) region, mitochondrial cytochrome C oxidase II (COX2) gene, intergenic spacer (IGS) region and exo-1,3-β-glucanase gene (exo1), P. insidiosum is classified into clade ATH, BTH, and CTH related to geographic distribution. At present, polymerase chain reaction in any of these specific regions with DNA sequencing is the only technique to provide clade diagnosis. In this study, P. insidiosum-specific primers targeting COX2 gene were designed and used in real-time quantitative polymerase chain reaction (qPCR) with subsequent high-resolution melting (HRM) to provide rapid identification as well as clade classification for P. insidiosum. Based on the qPCR-HRM method, 15 P. insidiosum isolates could be differentiated from 28 related organisms with 100% specificity and 1 pg limit of detection. This technique was, in addition, directly tested on clinical samples from proved human pythiosis cases: nine corneal scrapes and six arterial clots. The qPCR-HRM results of all nine corneal samples were a 100% match with the results from the conventional PCR at clade level. However, the qPCR-HRM results of arterial clot samples were only matched with the nucleotide sequencing results from the conventional PCR at species level. In conclusion, the qPCR-HRM is a simple one closed tube, inexpensive and user-friendly method to identify P. insidiosum into clade level.
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Affiliation(s)
- Navaporn Worasilchai
- Interdisciplinary Program, Medical Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Nitipong Permpalung
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina, USA
| | - Ariya Chindamporn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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Larraín MA, Zbawicka M, Araneda C, Gardner JPA, Wenne R. Native and invasive taxa on the Pacific coast of South America: Impacts on aquaculture, traceability and biodiversity of blue mussels (Mytilusspp.). Evol Appl 2017. [DOI: 10.1111/eva.12553] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Maria A. Larraín
- Departamento de Ciencia de los Alimentos y Tecnología Química; Facultad de Ciencias Químicas y Farmacéuticas; Universidad de Chile; Santiago Chile
| | | | - Cristian Araneda
- Departamento de Producción Animal; Facultad de Ciencias Agronómicas; Universidad de Chile; Santiago Chile
| | - Jonathan P. A. Gardner
- School of Biological Sciences; Victoria University of Wellington; Wellington New Zealand
| | - Roman Wenne
- Institute of Oceanology; Polish Academy of Sciences; Sopot Poland
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