1
|
Venuti I, Ceruso M, Muscariello T, Ambrosio RL, Di Pinto A, Pepe T. Mitochondrial Analysis of Sparidae Species to Detect a New DNA Barcoding Marker for Dentex gibbosus to Utilize against Fraud. Foods 2023; 12:3441. [PMID: 37761149 PMCID: PMC10530232 DOI: 10.3390/foods12183441] [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: 08/09/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Dentex gibbosus (Pink dentex) is a fish species of increasing economic interest in the Mediterranean Sea that is consumed both whole and processed. The growing value of this sparid in European markets is responsible for its substitution with fraudulent species. The distinctive morphologic feature of D. gibbosus is the conspicuous hump on the forehead in the older and larger specimens. However, the head is regularly convex in young individuals, requiring high skills and competencies for correct identification. Authentication becomes even more challenging in the case of prepared and processed products. Therefore, the molecular characterization of Pink dentex plays a crucial role in preventing commercial fraud with species substitution. This paper proposes a comparative mitogenome analysis between 19 sparid species of commercial interest as a tool to accurately design species-specific primers targeting a fragment of the NAD2 gene for the identification of D. gibbosus. We successfully detected Pink dentex DNA both using endpoint and real-time PCR. The findings showed the high specificity of the designed primers, demonstrating this a suitable, fast, and cost-effective method that could be used for the unambiguous identification of Pink dentex. This innovative approach for sparid authentication is expected to contribute to seafood traceability, public health assurance, integrity, and the credibility of the seafood industry.
Collapse
Affiliation(s)
- Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via F. Delpino, n. 1, 80137 Naples, Italy; (I.V.); (T.M.); (R.L.A.); (T.P.)
| | - Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via F. Delpino, n. 1, 80137 Naples, Italy; (I.V.); (T.M.); (R.L.A.); (T.P.)
| | - Tiziana Muscariello
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via F. Delpino, n. 1, 80137 Naples, Italy; (I.V.); (T.M.); (R.L.A.); (T.P.)
| | - Rosa Luisa Ambrosio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via F. Delpino, n. 1, 80137 Naples, Italy; (I.V.); (T.M.); (R.L.A.); (T.P.)
| | - Angela Di Pinto
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima, Km 3, Valenzano, 70010 Bari, Italy;
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via F. Delpino, n. 1, 80137 Naples, Italy; (I.V.); (T.M.); (R.L.A.); (T.P.)
| |
Collapse
|
2
|
Filonzi L, Ardenghi A, Rontani PM, Voccia A, Ferrari C, Papa R, Bellin N, Nonnis Marzano F. Molecular Barcoding: A Tool to Guarantee Correct Seafood Labelling and Quality and Preserve the Conservation of Endangered Species. Foods 2023; 12:2420. [PMID: 37372635 DOI: 10.3390/foods12122420] [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: 05/04/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The recent increase in international fish trade leads to the need for improving the traceability of fishery products. In relation to this, consistent monitoring of the production chain focusing on technological developments, handling, processing and distribution via global networks is necessary. Molecular barcoding has therefore been suggested as the gold standard in seafood species traceability and labelling. This review describes the DNA barcoding methodology for preventing food fraud and adulteration in fish. In particular, attention has been focused on the application of molecular techniques to determine the identity and authenticity of fish products, to discriminate the presence of different species in processed seafood and to characterize raw materials undergoing food industry processes. In this regard, we herein present a large number of studies performed in different countries, showing the most reliable DNA barcodes for species identification based on both mitochondrial (COI, cytb, 16S rDNA and 12S rDNA) and nuclear genes. Results are discussed considering the advantages and disadvantages of the different techniques in relation to different scientific issues. Special regard has been dedicated to a dual approach referring to both the consumer's health and the conservation of threatened species, with a special focus on the feasibility of the different genetic and genomic approaches in relation to both scientific objectives and permissible costs to obtain reliable traceability.
Collapse
Affiliation(s)
- Laura Filonzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Alessia Ardenghi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Pietro Maria Rontani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Andrea Voccia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Claudio Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Riccardo Papa
- Department Biology, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico
| | - Nicolò Bellin
- Department Biology, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico
| | - Francesco Nonnis Marzano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| |
Collapse
|
3
|
Osca D, Caputi L, Tanduo V, Sepe RM, Liberti A, Tiralongo F, Venuti I, Ceruso M, Crocetta F, Sordino P, Pepe T. The complete mitochondrial genome of the zebra seabream Diplodus cervinus (Perciformes, Sparidae) from the Mediterranean Sea. Mitochondrial DNA B Resour 2022; 7:2006-2008. [DOI: 10.1080/23802359.2022.2145174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- David Osca
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Luigi Caputi
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Valentina Tanduo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Rosa Maria Sepe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Assunta Liberti
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Francesco Tiralongo
- Department of Biological, Geological and Environmental Sciences, University of Catania, Italy
- Scientific Organization for Research and Conservation of Marine Biodiversity, Ente Fauna Marina Mediterranea, Avola, Italy
| | - Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy
| | - Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy
| | - Fabio Crocetta
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy
| |
Collapse
|
4
|
Multiplex PCR Assay for Simultaneous Identification of Five Types of Tuna (Katsuwonus pelamis, Thunnus alalonga, T. albacares, T. obesus and T. thynnus). Foods 2022; 11:foods11030280. [PMID: 35159432 PMCID: PMC8834044 DOI: 10.3390/foods11030280] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 01/27/2023] Open
Abstract
There is a need to identify the species of similar types of fish, especially those that are commercially sold. Particularly, the price of tuna varies depending on its type, which is difficult to determine as they are sold in cut or processed forms. This study developed a multiplex polymerase chain reaction (PCR) assay to identify the five most common tuna species: bigeye, skipjack, Atlantic bluefin, albacore, and yellowfin tunas. Newly designed species-specific primer sets for these five tuna species were created. Subsequently, the amplicon sizes obtained were 270, 238, 200, 178, and 127 base pairs for bigeye, skipjack, Atlantic bluefin, albacore, and yellowfin tunas, respectively. Each primer’s specificity was further tested using 15 other fish species, and no cross-reactivity was observed. To identify multiple targets in a single reaction, multiplex PCR was optimized to increase its resolution and accuracy. The detection levels of the multiplex PCR assay were confirmed to be 1 pg for all the five tunas. Additionally, it was successfully applied to 32 types of commercial tuna products. Therefore, this multiplex PCR assay could be an efficient identification method for various tuna species.
Collapse
|
5
|
Yu X, Yang H, Liu J, Qi Y, Sun L, Tian X. A strategy for a high enrichment of insect mitochondrial DNA for mitogenomic analysis. Gene 2022; 808:145986. [PMID: 34600050 DOI: 10.1016/j.gene.2021.145986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/04/2022]
Abstract
Next-generation sequencing has dramatically fostered insect mitogenomic research in recent years. However, studies on the insect mitochondrial genome (mitogenome) assembly mainly rely on the sequencing data from total DNA, which is not cost-effective as a huge data from nuclear DNA are wasted. Besides, many mitogenomic studies require genomic information from individual organisms, whereas the DNA yield from small individual insects is too low to meet the sequencing requirements. Here, we describe a strategy for a high enrichment of insect mitochondrial DNA (mtDNA) using rolling circle amplification (RCA) technique. This strategy consists of standard DNA extraction, RCA enrichment, next-generation sequencing and mitogenome assembly. We have evaluated the performance of this strategy on nine insect species representing eight families of insecta, three other invertebrates, and even two vertebrate specimens. Results show that our strategy is especially suitable for insects, which allows almost all tested insect mtDNA contents to reach 80% and above. A further examination of enrichment efficiency of our strategy among different taxa shows that it is also applicable to other invertebrates and even some vertebrates such as Rhacophorus and ptyas species, although its enrichment efficiency in these groups is lower than that of insects. After treatment with our strategy, small flux sequencing data can realize the assembly of mitogenome with deep coverage, providing a solid base for subsequent mitogenome-based studies.
Collapse
Affiliation(s)
- Xiaolei Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hongxia Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jie Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; GemPharmatech Co. Ltd, Jiangsu, China
| | - Yingju Qi
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; Genetron Health (Beijing) Co. Ltd, Beijing, China
| | - Liran Sun
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; Novogene Co, Ltd, Tianjin, China
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China.
| |
Collapse
|
6
|
Fish intended for human consumption: from DNA barcoding to a next-generation sequencing (NGS)-based approach. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2021.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
7
|
Venuti I, Ceruso M, Palma G, Smaldone G, Pepe T. DNA barcoding and nutritional analysis as a tool for promoting the market of inland fish species. Ital J Food Saf 2021; 10:9565. [PMID: 34733801 PMCID: PMC8513186 DOI: 10.4081/ijfs.2021.9565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 07/06/2021] [Indexed: 11/23/2022] Open
Abstract
The increasing world market demand for seafood requires an expansion of product categories available to consumers. Inland fish are usually considered having unmarked taste and are less appreciated by consumers; thus, they have low commercial value. Therefore, the marketing of the lake's fresh and processed fish is limited to the local market and consumers are currently uninformed and mistrustful about these species. In this study, six different fish species were caught in the Fondi lake (Lazio, central Italy): Anguilla anguilla, Tinca tinca, Carassius gibelio, Cyprinus carpio, Micropterus salmoides, Chelon ramada. All the samples were subjected to nutritional and DNA barcoding analysis. Moisture, protein, fat, carbohydrates, ash, and sodium content were measured. As regards the fatty acids profile, the most abundant were MUFAs with the highest value in Anguilla anguilla (45.97%). Oleic acid (C18: 1 n9 cis) was particularly high in Cyprinus carpio (55.46%). The fraction of polyunsaturated fatty acids (PUFA) revealed a higher DHA content (C22: 6 n3) in Anguilla anguilla than the other species (>12 %) while Chelon ramada presented both higher EPA content (C 20: 5 n3) and total fraction of omega 3 PUFAs. Concerning molecular analysis, a 655 bp fragment of cytochrome C oxidase subunit I (COI) gene was successfully used for the identification at the species level using both BOLD and BLAST public databases. The present study gives the basis for improving the knowledge and promoting inland fish' market and traceability along the supply chain.
Collapse
Affiliation(s)
- Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples
| | - Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples
| | | | - Giorgio Smaldone
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples
| |
Collapse
|
8
|
Caputi L, Osca D, Ceruso M, Venuti I, Sepe RM, Anastasio A, D'Aniello S, Crocetta F, Pepe T, Sordino P. The complete mitochondrial genome of the white seabream Diplodus sargus (Perciformes: Sparidae) from the Tyrrhenian sea. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2581-2583. [PMID: 34409152 PMCID: PMC8366610 DOI: 10.1080/23802359.2021.1915209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The white seabream Diplodus sargus (Linnaeus, 1758) is a species of interest for commercial fisheries throughout its range of distribution and it is also reared using aquaculture techniques. Herein, we present the first complete sequence and annotation of the mitochondrial genome of this species. The D. sargus mitogenome is 16,515 base pairs in length and contains 13 protein-coding genes, 2 rRNA, 22 tRNA, and 2 non-coding regions (D-loop and L-origin). The overall nucleotide composition is: 27.3% A, 28.9% C, 26.8% T, and 17.0% G. Maximum likelihood analyses placed D. sargus as a sister species of Diplodus puntazzo. This study provides valuable information for further studying identification methods and evolutionary relationships of Sparidae species.
Collapse
Affiliation(s)
- Luigi Caputi
- Biology and Evolution of Marine Organisms, Naples, Italy
| | - David Osca
- Integrative Marine Ecology, Naples, Italy
| | - Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University 'Federico II', Naples, Italy
| | - Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University 'Federico II', Naples, Italy
| | | | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, University 'Federico II', Naples, Italy
| | | | | | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University 'Federico II', Naples, Italy
| | - Paolo Sordino
- Biology and Evolution of Marine Organisms, Naples, Italy.,Biology and Evolution of Marine Organisms, Sicily Marine Centre, Messina, Italy
| |
Collapse
|
9
|
Ceruso M, Mascolo C, De Luca P, Venuti I, Biffali E, Ambrosio RL, Smaldone G, Sordino P, Pepe T. Dentex dentex Frauds: Establishment of a New DNA Barcoding Marker. Foods 2021; 10:foods10030580. [PMID: 33802000 PMCID: PMC8000392 DOI: 10.3390/foods10030580] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 11/16/2022] Open
Abstract
The common dentex (Dentex dentex (Linnaeus, 1758)) is an iconic fish in the Mediterranean diet. Due to its commercial and organoleptic importance, this sparid is highly appreciated in European markets and is often subjected to species substitution frauds. Comparative mitogenomics is a suitable approach for identifying new and effective barcode markers. This study aimed to find a molecular tag useful for unequivocally discriminating the sparid species D. dentex. The comparison of the complete mitochondrial DNA (mtDNA) sequences of 16 sparid species allowed us to highlight the potential of the NAD2 gene for direct identification purposes. Common dentex-specific primers were created and successfully evaluated by end-point and real-rime PCR (Polymerase Chain Reaction) for several fish species, achieving amplification only in the D. dentex. The method proposed in this study appears fast, simple, and inexpensive and requires affordable instrumentation. This approach provides unambiguous results for the common dentex authentication without the sequencing step. The presence/absence assay for D. dentex can be executed in a few hours of lab work. Therefore, national authorities responsible for food safety and traceability could apply and make full use of DNA-testing methods for deterring operators from false seafood declarations.
Collapse
Affiliation(s)
- Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (R.L.A.)
| | - Celestina Mascolo
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (R.L.A.)
| | - Pasquale De Luca
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (P.D.L.); (E.B.)
| | - Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (R.L.A.)
| | - Elio Biffali
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (P.D.L.); (E.B.)
| | - Rosa Luisa Ambrosio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (R.L.A.)
| | - Giorgio Smaldone
- Department Agricultural Sciences, University of Naples Federico II, via Università, n.100, Portici, 80055 Naples, Italy;
| | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, via Consolare Pompea, 29, Villaggio Pace, 98167 Messina, Italy;
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (R.L.A.)
- Correspondence: ; Tel.: +39-081-2533905
| |
Collapse
|
10
|
Fisher KE, Bradbury SP, Coates BS. Prediction of mitochondrial genome-wide variation through sequencing of mitochondrion-enriched extracts. Sci Rep 2020; 10:19123. [PMID: 33154458 PMCID: PMC7645498 DOI: 10.1038/s41598-020-76088-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/19/2020] [Indexed: 11/08/2022] Open
Abstract
Although mitochondrial DNA (mtDNA) haplotype variation is often applied for estimating population dynamics and phylogenetic relationships, economical and generalized methods for entire mtDNA genome enrichment prior to high-throughput sequencing are not readily available. This study demonstrates the utility of differential centrifugation to enrich for mitochondrion within cell extracts prior to DNA extraction, short-read sequencing, and assembly using exemplars from eight maternal lineages of the insect species, Ostrinia nubilalis. Compared to controls, enriched extracts showed a significant mean increase of 48.2- and 86.1-fold in mtDNA based on quantitative PCR, and proportion of subsequent short sequence reads that aligned to the O. nubilalis reference mitochondrial genome, respectively. Compared to the reference genome, our de novo assembled O. nubilalis mitochondrial genomes contained 82 intraspecific substitution and insertion/deletion mutations, and provided evidence for correction of mis-annotated 28 C-terminal residues within the NADH dehydrogenase subunit 4. Comparison to a more recent O. nubilalis mtDNA assembly from unenriched short-read data analogously showed 77 variant sites. Twenty-eight variant positions, and a triplet ATT codon (Ile) insertion within ATP synthase subunit 8, were unique within our assemblies. This study provides a generalizable pipeline for whole mitochondrial genome sequence acquisition adaptable to applications across a range of taxa.
Collapse
Affiliation(s)
- Kelsey E Fisher
- Department of Entomology, Iowa State University, Ames, IA, 50011, USA.
| | - Steven P Bradbury
- Department of Entomology, Iowa State University, Ames, IA, 50011, USA
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, 50011, USA
| | - Brad S Coates
- Department of Agriculture, Agriculture Research Station, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| |
Collapse
|
11
|
Ceruso M, Mascolo C, De Luca P, Venuti I, Smaldone G, Biffali E, Anastasio A, Pepe T, Sordino P. A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds. Foods 2020; 9:E1397. [PMID: 33023115 PMCID: PMC7600753 DOI: 10.3390/foods9101397] [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: 09/16/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
The commercialization of porgies or seabreams of the family Sparidae has greatly increased in the last decade, and some valuable species have become subject to seafood substitution. DNA regions currently used for fish species identification in fresh and processed products belong to the mitochondrial (mt) genes cytochrome b (Cytb), cytochrome c oxidase I (COI), 16S and 12S. However, these markers amplify for fragments with lower divergence within and between some species, failing to provide informative barcodes. We adopted comparative mitogenomics, through the analysis of complete mtDNA sequences, as a compatible approach toward studying new barcoding markers. The intent is to develop a specific and rapid assay for the identification of the common pandora Pagellus erythrinus, a sparid species frequently subject to fraudulent replacement. The genetic diversity analysis (Hamming distance, p-genetic distance, gene-by-gene sequence variability) between 16 sparid mtDNA genomes highlighted the discriminating potential of a 291 bp NAD2 gene fragment. A pair of species-specific primers were successfully designed and tested by end-point and real-time PCR, achieving amplification only in P. erythrinus among several fish species. The use of the NAD2 barcoding marker provides a rapid presence/absence method for the identification of P. erythrinus.
Collapse
Affiliation(s)
- Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Celestina Mascolo
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Pasquale De Luca
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (P.D.L.); (E.B.)
| | - Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Giorgio Smaldone
- Department Agricultural Sciences, University of Naples Federico II, via Università, n.100, Portici, 80055 Naples, Italy;
| | - Elio Biffali
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (P.D.L.); (E.B.)
| | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| |
Collapse
|
12
|
Ceruso M, Venuti I, Osca D, Caputi L, Anastasio A, Crocetta F, Sordino P, Pepe T. The complete mitochondrial genome of the sharpsnout seabream Diplodus puntazzo (Perciformes: Sparidae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2379-2381. [PMID: 33457799 PMCID: PMC7782139 DOI: 10.1080/23802359.2020.1775509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The sharpsnout seabream Diplodus puntazzo Walbaum, 1792 is a target species of small-scale fishery activities and is cage-cultured for human consumption. Nonetheless, genetic information on this species is limited. We here first sequence its complete mitochondrial genome. The sequence is composed of 16,638 base pairs, accounting for 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions (D-loop and L-origin). The overall nucleotide composition is: 27.4% A, 28.9% C, 26.9% T, and 16.8% G. Maximum likelihood analyses placed D. puntazzo close to Acanthopagrus and some Pagellus species.
Collapse
Affiliation(s)
- Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University "Federico II", Naples, Italy
| | - Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University "Federico II", Naples, Italy
| | - David Osca
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Luigi Caputi
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, University "Federico II", Naples, Italy
| | - Fabio Crocetta
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Paolo Sordino
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University "Federico II", Naples, Italy
| |
Collapse
|
13
|
Minich JJ, Petrus S, Michael JD, Michael TP, Knight R, Allen EE. Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus. mSphere 2020; 5:e00401-20. [PMID: 32434844 PMCID: PMC7380571 DOI: 10.1128/msphere.00401-20] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], and pyloric ceca) from 229 Pacific chub mackerel, Scomber japonicus, collected across 38 time points spanning 1 year from the Scripps Institution of Oceanography Pier (La Jolla, CA). Mucosal sites had unique microbial communities significantly different from the surrounding seawater and sediment communities with over 10 times more total diversity than seawater. The external surfaces of skin and gill were more similar to seawater, while digesta was more similar to sediment. Alpha and beta diversity of the skin and gill was explained by environmental and biological factors, specifically, sea surface temperature, chlorophyll a, and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by regional migration of chub mackerel subpopulations by nanopore sequencing a 14,769-bp region of the 16,568-bp mitochondria across all temporal fish specimens. A cosmopolitan pathogen, Photobacterium damselae, was prevalent across multiple body sites all year but highest in the skin, GI, and digesta between June and September, when the ocean is warmest. The longitudinal fish microbiome study evaluates the extent to which the environment and host biology drives mucosal microbial ecology and establishes a baseline for long-term surveys linking environment stressors to mucosal health of wild marine fish.IMPORTANCE Pacific chub mackerel, Scomber japonicus, are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean.
Collapse
Affiliation(s)
- Jeremiah J Minich
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Semar Petrus
- J. Craig Venter Institute, La Jolla, California, USA
| | | | - Todd P Michael
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- J. Craig Venter Institute, La Jolla, California, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| |
Collapse
|
14
|
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]
|