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Alvarenga M, D'Elia AKP, Rocha G, Arantes CA, Henning F, de Vasconcelos ATR, Solé-Cava AM. Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic. BMC Genomics 2024; 25:215. [PMID: 38413941 PMCID: PMC10898094 DOI: 10.1186/s12864-024-10035-5] [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: 10/27/2023] [Accepted: 01/21/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Phylogenetic gaps of public databases of reference sequences are a major obstacle for comparative genomics and management of marine resources, particularly in the Global South, where economically important fisheries and conservation flagship species often lack closely-related references. We applied target-enrichment to obtain complete mitochondrial genomes of marine ichthyofauna from the Brazilian coast selected based on economic significance, conservation status and lack of phylogenetically-close references. These included sardines (Dorosomatidae, Alosidae), mackerels (Scombridae) croakers (Sciaenidae), groupers (Epinephelidae) and snappers (Lutjanidae). RESULTS Custom baits were designed to enrich mitochondrial DNA across a broad phylogenetic range of fishes. Sequencing generated approximately 100k reads per sample, which were assembled in a total of 70 complete mitochondrial genomes and include fifty-two new additions to GenBank, including five species with no previous mitochondrial data. Departures from the typical gene content and order occurred in only three taxa and mostly involved tRNA gene duplications. Start-codons for all genes, except Cytochrome C Oxidase subunit I (COI), were consistently ATG, whilst a wide range of stop-codons deviated from the prevailing TAA. Phylogenetic analysis confirmed assembly accuracy and revealed signs of cryptic diversification within the Mullus genus. Lineage delimitation methods using Sardinella aurita and S. brasiliensis mitochondrial genomes support a single Operational Taxonomic Unit. CONCLUSIONS Target enrichment was highly efficient, providing complete novel mitochondrial genomes with little sequencing effort. These sequences are deposited in public databases to enable subsequent studies in population genetics and adaptation of Latin American fish species and serve as a vital resource for conservation and management programs that rely on molecular data for species and genus-level identification.
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Affiliation(s)
- Marcela Alvarenga
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, 4485-661, Portugal
| | - Ananda Krishna Pereira D'Elia
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
| | - Graciane Rocha
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
| | - Clara Alvarez Arantes
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
| | - Frederico Henning
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil.
| | | | - Antonio Mateo Solé-Cava
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
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2
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Mislabeling in seafood products sold on the Italian market: A systematic review and meta-analysis. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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3
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Munguia-Vega A, Terrazas-Tapia R, Dominguez-Contreras JF, Reyna-Fabian M, Zapata-Morales P. DNA barcoding reveals global and local influences on patterns of mislabeling and substitution in the trade of fish in Mexico. PLoS One 2022; 17:e0265960. [PMID: 35421106 PMCID: PMC9009668 DOI: 10.1371/journal.pone.0265960] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/10/2022] [Indexed: 11/18/2022] Open
Abstract
Mislabeling of seafood is a global phenomenon that can misrepresent the status and level of consumption of wild fish stocks while concealing the use of many other wild species or those originating from aquaculture and sold as substitutes. We conducted a DNA barcoding study in three cities within Mexico (Mazatlan, Mexico City and Cancun) and sequenced the COI gene in 376 fish samples sold as 48 distinct commercial names at fish markets, grocery stores, and restaurants. Our goal was to identify the main species sold, their mislabeling rates and the species most used as substitutes. Overall, the study-wide mislabeling rate was 30.8% (95% CI 26.4–35.6). Half of the samples collected belonged to five species traded globally (yellowfin tuna, Atlantic salmon, mahi, swai, and tilapia), most of them with important aquaculture or ranching production levels. These species were commonly used as substitutes for other species and showed low mislabeling rates themselves (≤ 11%, except mahi mahi with 39% mislabeling). The other half of the samples revealed nearly 100 species targeted by small-scale fishers in Mexico and sold under 42 distinct commercial names. Popular local commercial names (dorado, marlin, mero, robalo, mojarra, huachinango, pargo, sierra) showed the highest mislabeling rates (36.3% to 94.4%) and served to sell many of the 53 species identified as substitutes in our study. We discuss the observed patterns in relation to landing and import data showing differences in availability of commercial species and the links to explain observed mislabeling rates and the use of a species as a substitute for other species. We also outline some of the implications of establishing a labeling and traceability standard as an alternative to improve transparency in the trade of seafood products in Mexico.
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Affiliation(s)
- Adrian Munguia-Vega
- Conservation Genetics Laboratory & Desert Laboratory on Tumamoc Hill, The University of Arizona, Tucson, Arizona, United States of America
- Applied Genomics Lab, La Paz, Baja California Sur, México
- * E-mail:
| | | | - Jose F. Dominguez-Contreras
- Instituto Politécnico Nacional–Centro Interdisciplinario de Ciencias Marinas (IPN- CICIMAR), La Paz, Baja California Sur, México
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, La Paz, Baja California Sur, México
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4
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Illegal, Unreported, and Unregulated Fisheries Threatening Shark Conservation in African Waters Revealed from High Levels of Shark Mislabelling in Ghana. Genes (Basel) 2021; 12:genes12071002. [PMID: 34210039 PMCID: PMC8305889 DOI: 10.3390/genes12071002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022] Open
Abstract
Mislabelling of fish and fish products has attracted much attention over the last decades, following public awareness of the practice of substituting high-value with low-value fish in markets, restaurants, and processed seafood. In some cases, mislabelling includes illegal, unreported, and unregulated (IUU) fishing, contributing to overexploit substitute species that are undetectable when sold under wrong names. This is the first study of DNA barcoding to assess the level of mislabelling in fish marketed in Ghana, focusing on endangered shark species. Genetic identification was obtained from 650 base pair sequences within the cytochrome c oxidase I (COI) gene. All except one of 17 shark fillets analysed were wrongly labelled as compared with none of 28 samples of small commercial pelagic fish and 14 commercial shark samples purchased in Europe. Several substitute shark species in Ghana are endangered (Carcharhinus signatus and Isurusoxyrinchus) and critically endangered (Squatina aculeata). Shark products commercialized in Europe (n = 14) did not reveal mislabelling, thus specific shark mislabelling cannot be generalized. Although based on a limited number of samples and fish markets, the results that reveal trade of endangered sharks in Ghana markets encourage Ghanaian authorities to improve controls to enforce conservation measures.
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5
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Blanco-Fernandez C, Ardura A, Masiá P, Rodriguez N, Voces L, Fernandez-Raigoso M, Roca A, Machado-Schiaffino G, Dopico E, Garcia-Vazquez E. Fraud in highly appreciated fish detected from DNA in Europe may undermine the Development Goal of sustainable fishing in Africa. Sci Rep 2021; 11:11423. [PMID: 34075165 PMCID: PMC8169655 DOI: 10.1038/s41598-021-91020-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/20/2021] [Indexed: 01/19/2023] Open
Abstract
Despite high effort for food traceability to ensure safe and sustainable consumption, mislabeling persists on seafood markets. Determining what drives deliberate fraud is necessary to improve food authenticity and sustainability. In this study, the relationship between consumer's appreciation and fraudulent mislabeling was assessed through a combination of a survey on consumer's preferences (N = 1608) and molecular tools applied to fish samples commercialized by European companies. We analyzed 401 samples of fish highly consumed in Europe and worldwide (i.e. tuna, hake, anchovy, and blue whiting) through PCR-amplification and sequencing of a suite of DNA markers. Results revealed low mislabeling rate (1.9%), with a higher mislabeling risk in non-recognizable products and significant mediation of fish price between consumer´s appreciation and mislabeling risk of a species. Furthermore, the use of endangered species (e.g. Thunnus thynnus), tuna juveniles for anchovy, and still not regulated Merluccius polli hake as substitutes, points towards illegal, unreported and/or unregulated fishing from African waters. These findings reveal a worrying intentional fraud that hampers the goal of sustainable seafood production and consumption, and suggest to prioritize control efforts on highly appreciated species.
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Affiliation(s)
| | - Alba Ardura
- Department of Functional Biology, University of Oviedo, Oviedo, Spain
| | - Paula Masiá
- Department of Functional Biology, University of Oviedo, Oviedo, Spain
| | - Noemi Rodriguez
- Department of Education Sciences, University of Oviedo, Oviedo, Spain
| | - Laura Voces
- Department of Functional Biology, University of Oviedo, Oviedo, Spain
| | | | - Agustín Roca
- Department of Functional Biology, University of Oviedo, Oviedo, Spain
| | | | - Eduardo Dopico
- Department of Education Sciences, University of Oviedo, Oviedo, Spain
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6
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Dimitrakopoulou ME, Vantarakis A. Does Traceability Lead to Food Authentication? A Systematic Review from A European Perspective. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2021.1923028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Apostolos Vantarakis
- Department of Public Health, Medical School, University of Patras, Patras, Greece
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7
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Blanco-Fernandez C, Garcia-Vazquez E, Machado-Schiaffino G. Seventeen years analysing mislabelling from DNA barcodes: Towards hake sustainability. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Wang N, Xing RR, Zhou MY, Sun RX, Han JX, Zhang JK, Zheng WJ, Chen Y. Application of DNA barcoding and metabarcoding for species identification in salmon products. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2021; 38:754-768. [PMID: 33783328 DOI: 10.1080/19440049.2020.1869324] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mislabelling is a significant manifestation of food fraud. Traditional Sanger sequencing technology is the gold standard for seafood species identification. However, this method is not suitable for analysing processed samples that may contain more than one species. This study tested the feasibility of next-generation sequencing in identifying mixed salmon products. Salmon samples containing up to eight species were amplified using 16S rRNA mini-barcode primers, and sequenced on an Illumina HiSeq2500 platform. All species were accurately identified, and mixtures as low as 1% (w/w) could be detected. Furthermore, this study conducted a market survey of 32 products labelled as salmon. For pure and mixed fish products, Sanger and next-generation sequencing techniques were respectively used for species identification, and for NGS results, we also used real-time PCR method to cross-validate the mixed products to further verify the accuracy of the DNA metabarcoding technology established in this study. DNA barcoding and metabarcoding of commercial salmon food products revealed the presence of mislabelling in 16 of 32 (50%) samples. The developed DNA barcoding and metabarcoding methods are useful for the identification of salmon species in food and can be used for quality control of various types of salmon products.
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Affiliation(s)
- Nan Wang
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Ran-Ran Xing
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Meng-Yue Zhou
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China.,College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Rui-Xue Sun
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China.,College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jian-Xun Han
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Jiu-Kai Zhang
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Wen-Jie Zheng
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Ying Chen
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China
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9
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Parrondo M, López S, Aparicio-Valencia A, Fueyo A, Quintanilla-García P, Arias A, Borrell Y. Almost never you get what you pay for: Widespread mislabeling of commercial “zamburiñas” in northern Spain. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Fernandes TJR, Amaral JS, Mafra I. DNA barcode markers applied to seafood authentication: an updated review. Crit Rev Food Sci Nutr 2020; 61:3904-3935. [DOI: 10.1080/10408398.2020.1811200] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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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11
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Pardo MÁ, Jiménez E. DNA barcoding revealing seafood mislabeling in food services from Spain. J Food Compost Anal 2020. [DOI: 10.1016/j.jfca.2020.103521] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Muñoz-Colmenero M, Rahman S, Martínez JL, Garcia-Vazquez E. High variability in parvalbumin beta 1 genes offers new molecular options for controlling the mislabeling in commercial Salmonids. Eur Food Res Technol 2019. [DOI: 10.1007/s00217-019-03278-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Horreo JL, Fitze PS, Jiménez-Valverde A, Noriega JA, Pelaez ML. Amplification of 16S rDNA reveals important fish mislabeling in Madrid restaurants. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.09.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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15
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Xiong X, Yao L, Ying X, Lu L, Guardone L, Armani A, Guidi A, Xiong X. Multiple fish species identified from China's roasted Xue Yu fillet products using DNA and mini-DNA barcoding: Implications on human health and marine sustainability. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.12.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Baeza JA, Behringer DC. Integrative taxonomy of the ornamental 'peppermint' shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide. PeerJ 2017; 5:e3786. [PMID: 28948100 PMCID: PMC5607919 DOI: 10.7717/peerj.3786] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/18/2017] [Indexed: 11/20/2022] Open
Abstract
The ornamental trade is a worldwide industry worth >15 billion USD with a problem of rampant product misidentification. Minimizing misidentification is critical in the face of overexploitation of species in the trade. We surveyed the peppermint shrimp ornamental marketplace in the southeastern USA, the most intense market for peppermint shrimps worldwide, to characterize the composition of species in the trade, reveal the extent of misidentification, and describe the population genetics of the true target species. Shrimps were bought from aquarium shops in FL, GA, SC, and NC. We demonstrated, contrary to popular belief (information from dealers), that the most heavily traded species in the market was Lysmata boggessi, an endemic species to the eastern Gulf of Mexico, and not Lysmata wurdemanni. Importantly, only when color pattern or genetic markers in conjunction with morphological traits were employed, was it was possible to unequivocally identify L. boggessi as the only species in the trade. The intensity of the market for peppermint shrimps in the USA has led to L. boggessi being the most traded species worldwide. Misidentification in the shrimp aquarium trade is accidental and involuntary, and is explained by remarkable similarity among congeneric species. Using sequences of the 16S-mt-DNA marker, we found no indication of population genetic structure in the endemic L. boggessi across 550 km of linear coast. Therefore, this species can be considered genetically homogeneous and a single fished stock. Still, we argue in favor of additional studies using more powerful markers (e.g., SNPs) capable of revealing genetic structure at a finer spatial-scale. Our results will help advance management and conservation policies in this lucrative yet understudied fishery. Future studies of other ornamental fisheries will benefit from using an integrative taxonomic approach, as we demonstrate here.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America.,Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL, United States of America.,Departamento de Biologia Marina, Universidad Catolica del Norte, Coquimbo, IV Region, Chile
| | - Donald C Behringer
- Program in Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL, United States of America.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America
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White fish authentication by COIBar-RFLP: Toward a common strategy for the rapid identification of species in convenience seafood. Food Control 2016. [DOI: 10.1016/j.foodcont.2016.05.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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19
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Muñoz‐Colmenero M, Martínez JL, Roca A, Garcia‐Vazquez E. Detection of Different DNA Animal Species in Commercial Candy Products. J Food Sci 2016; 81:T801-9. [DOI: 10.1111/1750-3841.13225] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/22/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Marta Muñoz‐Colmenero
- Laboratory of Genetics of Natural Resources, Area of Genetics, Dept. of Functional BiologyUniv. of Oviedo Asturias Spain
| | | | - Agustín Roca
- Laboratory of Genetics of Natural Resources, Area of Genetics, Dept. of Functional BiologyUniv. of Oviedo Asturias Spain
| | - Eva Garcia‐Vazquez
- Laboratory of Genetics of Natural Resources, Area of Genetics, Dept. of Functional BiologyUniv. of Oviedo Asturias Spain
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