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Li T, Zhong S, Wen B, Jiang L, Zhang M. Comparative Analysis of Complete Mitochondrial Genomes of Five Chromodorididae Species (Nudibranchia:Doridina). Biochem Genet 2024:10.1007/s10528-024-10878-3. [PMID: 38954214 DOI: 10.1007/s10528-024-10878-3] [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: 03/13/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
Mitochondrial genome is an important molecular marker for exploring the phylogenetic relationships of species and revealing molecular evolution. In the present study, 5 mitogenomes of Chromodorididae (Chromodoris lochi, Chromodoris colemani, Chromodoris elisabethina, Chromodoris annae and Hypselodoris whitei) were systemically investigated. The lengths of the mitogenomes sequences were 14248 bp, 14257 bp, 14252 bp, 14254 bp and 14856 bp, respectively. Most protein-coding genes (PCGs) were initiated with the common ATG codon and terminated with the TAA and TAG. We calculated Ka/Ks values for all 13 PCGs of Chromodorididae species, all ratios were less than 1, indicating selection by purification. Phylogenetic relationships were constructed by Bayesian inference (BI) and maximum likelihood (ML) methods based on all complete genomes of 50 species, primarily from the family Chromodorididae (Doridina) and 2 outgroups. This phylogenetic tree provided further additional references for the classification of the suborder Doridina. Gene rearrangement suggested a more conserved pattern of gene sequences in the superfamily Chromodoridoidea. These results and newly sequenced will contribute to a better understanding of Chromodorididae and provide reference for further phylogenetic studies.
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Affiliation(s)
- Tianyu Li
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Shengping Zhong
- Guangxi Key Laboratory of Marine Drugs, Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Beihua Wen
- School of Marine Sciences, School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China
| | - Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Man Zhang
- School of Marine Sciences, School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China.
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Singh M, Young RG, Hellberg RS, Hanner RH, Corradini MG, Farber JM. Twenty-three years of PCR-based seafood authentication assay development: What have we learned? Compr Rev Food Sci Food Saf 2024; 23:e13401. [PMID: 39073284 DOI: 10.1111/1541-4337.13401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/27/2024] [Accepted: 06/14/2024] [Indexed: 07/30/2024]
Abstract
Seafood is a prime target for fraudulent activities due to the complexity of its supply chain, high demand, and difficult discrimination among species once morphological characteristics are removed. Instances of seafood fraud are expected to increase due to growing demand. This manuscript reviews the application of DNA-based methods for commercial fish authentication and identification from 2000 to 2023. It explores (1) the most common types of commercial fish used in assay development, (2) the type of method used, (3) the gene region most often targeted, (4) provides a case study of currently published assays or primer-probe pairs used for DNA amplification, for specificity, and (5) makes recommendations for ensuring standardized assay-based reporting for future studies. A total of 313 original assays for the detection and authentication of commercial fish species from 191 primary articles published over the last 23 years were examined. The most explored DNA-based method was real-time polymerase chain reaction (qPCR), followed by DNA sequencing. The most targeted gene regions were cytb (cytochrome b) and COI (cytochrome c oxidase 1). Tuna was the most targeted commercial fish species. A case study of published tuna assays (n = 19) targeting the cytb region found that most assays were not species-specific through in silico testing. This was conducted by examining the primer mismatch for each assay using multiple sequence alignment. Therefore, there is need for more standardized DNA-based assay reporting in the literature to ensure specificity, reproducibility, and reliability of results. Factors, such as cost, sensitivity, quality of the DNA, and species, should be considered when designing assays.
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Affiliation(s)
- Maleeka Singh
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Robert G Young
- Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Rosalee S Hellberg
- Schmid College of Science and Technology, Food Science Program, Chapman University, Orange, California, USA
| | - Robert H Hanner
- Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Maria G Corradini
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
- Arrell Food Institute, University of Guelph, Guelph, Ontario, Canada
| | - Jeffrey M Farber
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada
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Tinacci L, Stratev D, Strateva M, Zhelyazkov G, Kyuchukova R, Armani A. An Authentication Survey on Retail Seafood Products Sold on the Bulgarian Market Underlines the Need for Upgrading the Traceability System. Foods 2023; 12:1070. [PMID: 36900583 PMCID: PMC10000581 DOI: 10.3390/foods12051070] [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: 01/26/2023] [Revised: 02/13/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Economically motivated or accidental species substitutions lead to economic and potential health damage to consumers with a loss of confidence in the fishery supply chain. In the present study, a three-year survey on 199 retail seafood products sold on the Bulgarian market was addressed to assess: (1) product authenticity by molecular identification; (2) trade name compliance to the list of official trade names accepted in the territory; (3) adherence of the list in force to the market supply. DNA barcoding on mitochondrial and nuclear genes was applied for the identification of whitefish (WF), crustaceans (C) and mollusks (cephalopods-MC; gastropods-MG; bivalves-MB) except for Mytilus sp. products for which the analysis was conducted with a previously validated RFLP PCR protocol. Identification at the species level was obtained for 94.5% of the products. Failures in species allocation were reconducted due to low resolution and reliability or the absence of reference sequences. The study highlighted an overall mislabeling rate of 11%. WF showed the highest mislabeling rate (14%), followed by MB (12.5%), MC (10%) and C (7.9%). This evidence emphasized the use of DNA-based methods as tools for seafood authentication. The presence of non-compliant trade names and the ineffectiveness of the list to describe the market species varieties attested to the need to improve seafood labeling and traceability at the national level.
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Affiliation(s)
- Lara Tinacci
- Department of Veterinary Sciences, University of Pisa, Via delle Piagge 2, 56124 Pisa, Italy
| | - Deyan Stratev
- Department of Food Quality and Safety and Veterinary Legislation, Faculty of Veterinary Medicine, Trakia University, 6000 Stara Zagora, Bulgaria
| | - Mariyana Strateva
- Department of Veterinary Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, Trakia University, 6000 Stara Zagora, Bulgaria
| | - Georgi Zhelyazkov
- Department of Animal Husbandry—Non-Ruminants and Other Animals, Faculty of Agriculture, Trakia University, 6000, Stara Zagora, Bulgaria
| | - Ralica Kyuchukova
- Department of Food Quality and Safety and Veterinary Legislation, Faculty of Veterinary Medicine, Trakia University, 6000 Stara Zagora, Bulgaria
| | - Andrea Armani
- Department of Veterinary Sciences, University of Pisa, Via delle Piagge 2, 56124 Pisa, Italy
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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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Mottola A, Piredda R, Catanese G, Lorusso L, Ciccarese G, Di Pinto A. Species authentication of canned mackerel: Challenges in molecular identification and potential drivers of mislabelling. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Nimbkar S, Auddy M, Manoj I, Shanmugasundaram S. Novel Techniques for Quality Evaluation of Fish: A Review. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2021.1925291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shubham Nimbkar
- Planning and Monitoring Cell, Indian Institute of Food Processing Technology (IIFPT), Ministry of Food Processing Industries, Govt. Of India, Thanjavur, Tamil Nadu, India
| | - Manoj Auddy
- Planning and Monitoring Cell, Indian Institute of Food Processing Technology (IIFPT), Ministry of Food Processing Industries, Govt. Of India, Thanjavur, Tamil Nadu, India
| | - Ishita Manoj
- Planning and Monitoring Cell, Indian Institute of Food Processing Technology (IIFPT), Ministry of Food Processing Industries, Govt. Of India, Thanjavur, Tamil Nadu, India
| | - S Shanmugasundaram
- Planning and Monitoring Cell, Indian Institute of Food Processing Technology (IIFPT), Ministry of Food Processing Industries, Govt. Of India, Thanjavur, Tamil Nadu, India
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Rapid detection of fraudulence in seven commercial shrimp products by species-specific PCR assays. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107871] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Tinacci L, Stratev D, Zhelyazkov G, Kyuchukova R, Strateva M, Nucera D, Armani A. Nationwide survey of the Bulgarian market highlights the need to update the official seafood list based on trade inputs. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History. Int J Mol Sci 2020; 21:ijms21051874. [PMID: 32182936 PMCID: PMC7084342 DOI: 10.3390/ijms21051874] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genome is a powerful molecule marker to explore phylogenetic relationships and reveal molecular evolution in ichthyological studies. Gerres species play significant roles in marine fishery, but its evolution has received little attention. To date, only two Gerres mitochondrial genomes were reported. In the present study, three mitogenomes of Gerres (Gerres filamentosus, Gerres erythrourus, and Gerres decacanthus) were systemically investigated. The lengths of the mitogenome sequences were 16,673, 16,728, and 16,871 bp for G. filamentosus, G. erythrourus, and G. decacanthus, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA codon, and the incomplete termination codon T/TA could be detected in the three species. The majority of AT-skew and GC-skew values of the 13 PCGs among the three species were negative, and the amplitude of the GC-skew was larger than the AT-skew. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, were which most likely due to the difference in their living environment. The phylogenetic tree was constructed by molecular method (Bayesian Inference (BI) and maximum Likelihood (ML)), providing further supplement to the scientific classification of fish. Three Gerres species were differentiated in late Cretaceous and early Paleogene, and their evolution might link with the geological events that could change their survival environment.
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Tinacci L, Guardone L, Castro-Palomino Rubio J, Riina M, Stratev D, Guidi A, Armani A. Labelling compliance and species identification of herring products sold at large scale retail level within the Italian market. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.106707] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Molecular identification of seahorse and pipefish species sold as dried seafood in China: A market-based survey to highlight the actual needs for a proper trade. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Ceruso M, Mascolo C, Anastasio A, Pepe T, Sordino P. Frauds and fish species authentication: Study of the complete mitochondrial genome of some Sparidae to provide specific barcode markers. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.03.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Guardone L, Nucera D, Rosellini N, Tinacci L, Acutis P, Guidi A, Armani A. Occurrence, distribution and viability of Anisakis spp. larvae in various kind of marketed herring products in Italy. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.02.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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