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Corradini B, Gianfreda D, Ferri G, Ferrari F, Borciani I, Santunione AL, Cecchi R. Forensic species identification: practical guide for animal and plant DNA analysis. Int J Legal Med 2024:10.1007/s00414-024-03284-2. [PMID: 38985195 DOI: 10.1007/s00414-024-03284-2] [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: 04/09/2024] [Accepted: 06/29/2024] [Indexed: 07/11/2024]
Abstract
The importance of non-human DNA in the forensic field has increased greatly in recent years, together with the type of applications. The molecular species identification of animal and botanical material may be crucial both for wildlife trafficking and crime scene investigation. However, especially for forensic botany, several challenges slow down the implementation of the discipline in the routine.Although the importance of molecular analysis of animal origin samples is widely recognized and the same value is acknowledged to the botanical counterpart, the latter does not find the same degree of application.The availability of molecular methods, especially useful in cases where the material is fragmented, scarce or spoiled preventing the morphological identification, is not well known. This work is intended to reaffirm the relevance of non-human forensic genetics (NHFG), highlighting differences, benefits and pitfalls of the current most common molecular analysis workflow for animal and botanical samples, giving a practical guide. A flowchart describing the analysis paths, divided in three major working areas (inspection and sampling, molecular analysis, data processing and interpretation), is provided. More real casework examples of the utility of non-human evidence in forensic investigations should be shared by the scientific community, especially for plants. Moreover, concrete efforts to encourage initiatives in order to promote quality and standardization in the NHFG field are also needed.
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Affiliation(s)
- Beatrice Corradini
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy.
| | - Denise Gianfreda
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Gianmarco Ferri
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Ilaria Borciani
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Anna Laura Santunione
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Rossana Cecchi
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
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2
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Jourdan J, Bundschuh M, Copilaș-Ciocianu D, Fišer C, Grabowski M, Hupało K, Jemec Kokalj A, Kabus J, Römbke J, Soose LJ, Oehlmann J. Cryptic Species in Ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1889-1914. [PMID: 37314101 DOI: 10.1002/etc.5696] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/20/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023]
Abstract
The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Jonas Jourdan
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, University of Kaiserslautern-Landau, Landau, Germany
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Denis Copilaș-Ciocianu
- Laboratory of Evolutionary Ecology of Hydrobionts, Nature Research Centre, Vilnius, Lithuania
| | - Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michał Grabowski
- Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Kamil Hupało
- Department of Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anita Jemec Kokalj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Kabus
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie, Flörsheim am Main, Germany
| | - Laura J Soose
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Oehlmann
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
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Mthethwa S, Bester‐van der Merwe AE, Roodt‐Wilding R. Addressing the complex phylogenetic relationship of the Gempylidae fishes using mitogenome data. Ecol Evol 2023; 13:e10217. [PMID: 37351481 PMCID: PMC10283032 DOI: 10.1002/ece3.10217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
The Gempylidae (snake mackerels) family, belonging to the order Perciformes, consists of about 24 species described in 16 genera primarily distributed in tropical, subtropical, and temperate seas worldwide. Despite substantial research on this family utilizing morphological and molecular approaches, taxonomy categorization in this group has remained puzzling for decades prompting the need for further investigation into the underlying evolutionary history among the gempylids using molecular tools. In this study, we assembled eight complete novel mitochondrial genomes for five Gempylidae species (Neoepinnula minetomai, Neoepinnula orientalis, Rexea antefurcata, Rexea prometheoides, and Thyrsites atun) using Ion Torrent sequencing to supplement publicly available mitogenome data for gempylids. Using Bayesian inference and maximum-likelihood tree search methods, we investigated the evolutionary relationships of 17 Gempylidae species using mitogenome data. In addition, we estimated divergence times for extant gempylids. We identified two major clades that formed approximately 48.05 (35.89-52.04) million years ago: Gempylidae 1 (Thyrsites atun, Promethichthys prometheus, Nealotus tripes, Diplospinus multistriatus, Paradiplospinus antarcticus, Rexea antefurcata, Rexea nakamurai, Rexea prometheoides, Rexea solandri, Thyrsitoides marleyi, Gempylus serpens, and Nesiarchus nasutus) and Gempylidae 2 (Lepidocybium flavobrunneum, Ruvettus pretiosus, Neoepinnula minetomai, Neoepinnula orientalis, and Epinnula magistralis). The present study demonstrated the superior performance of complete mitogenome data compared with individual genes in phylogenetic reconstruction. By including T. atun individuals from different regions, we demonstrated the potential for the application of mitogenomes in species phylogeography.
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Affiliation(s)
- Siphesihle Mthethwa
- Molecular Breeding and Biodiversity Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| | | | - Rouvay Roodt‐Wilding
- Molecular Breeding and Biodiversity Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
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Kawakami T, Yamazaki A, Asami M, Goto Y, Yamanaka H, Hyodo S, Ueno H, Kasai A. Evaluating the sampling effort for the metabarcoding‐based detection of fish environmental DNA in the open ocean. Ecol Evol 2023; 13:e9921. [PMID: 36969932 PMCID: PMC10037434 DOI: 10.1002/ece3.9921] [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: 09/06/2022] [Revised: 02/24/2023] [Accepted: 03/03/2023] [Indexed: 03/26/2023] Open
Abstract
Clarifying the effect of the sampling protocol on the detection of environmental DNA (eDNA) is essential for appropriately designing biodiversity research. However, technical issues influencing eDNA detection in the open ocean, which consists of water masses with varying environmental conditions, have not been thoroughly investigated. This study evaluated the sampling effort for the metabarcoding‐based detection of fish eDNA using replicate sampling with filters of different pore sizes (0.22 and 0.45 μm) in the subtropical and subarctic northwestern Pacific Ocean and Arctic Chukchi Sea. The asymptotic analysis predicted that the accumulation curves for detected taxa did not saturate in most cases, indicating that our sampling effort (7 or 8 replicates, corresponding to 10.5–40 L of filtration in total) was insufficient to fully assess the species diversity in the open ocean and that tens of replicates or a substantial filtration volume were required. The Jaccard dissimilarities between filtration replicates were comparable with those between the filter types at any site. In subtropical and subarctic sites, turnover dominated the dissimilarity, suggesting that the filter pore size had a negligible effect. In contrast, nestedness dominated the dissimilarity in the Chukchi Sea, implying that the 0.22 μm filter could collect a broader range of eDNA than the 0.45 μm filter. Therefore, the effect of filter selection on the collection of fish eDNA likely varies depending on the region. These findings highlight the highly stochastic nature of fish eDNA collection in the open ocean and the difficulty of standardizing the sampling protocol across various water masses.
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Affiliation(s)
- Tatsuya Kawakami
- Faculty of Fisheries SciencesHokkaido UniversityHakodateHokkaidoJapan
| | - Aya Yamazaki
- Research and Educational Unit for Studies on Connectivity of Hills, Humans and OceansKyoto UniversityKyotoJapan
| | - Maki Asami
- Center for Biodiversity ScienceRyukoku UniversityOtsuShigaJapan
| | - Yuko Goto
- Center for Biodiversity ScienceRyukoku UniversityOtsuShigaJapan
| | - Hiroki Yamanaka
- Center for Biodiversity ScienceRyukoku UniversityOtsuShigaJapan
- Faculty of Advanced Science and TechnologyRyukoku UniversityOtsuShigaJapan
| | - Susumu Hyodo
- Atmosphere and Ocean Research Institute, The University of TokyoKashiwaChibaJapan
| | - Hiromichi Ueno
- Faculty of Fisheries SciencesHokkaido UniversityHakodateHokkaidoJapan
| | - Akihide Kasai
- Faculty of Fisheries SciencesHokkaido UniversityHakodateHokkaidoJapan
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5
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New Sets of Primers for DNA Identification of Non-Indigenous Fish Species in the Volga-Kama Basin (European Russia). WATER 2022. [DOI: 10.3390/w14030437] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Adequate species’ identification is critical for the detection and monitoring of biological invasions. In this study, we proposed and assessed the efficiency of newly created primer sets for the genetic identification of non-indigenous species (NIS) of fishes in the Volga basin based on: (a) a “long” fragment of cytochrome c oxidase subunit one of the mitochondrial gene (COI) (0.7 kb), used in “classical” DNA barcoding; (b) a short 3’-fragment (0.3 kb) of COI, suitable for use in high-throughput sequencing systems (i.e., for dietary analysis); (c) fragment of 16S mitochondrial rRNA, including those designed to fill the library of reference sequences for work on the metabarcoding of communities and eDNA studies; (d) a fragment of 18S nuclear rRNA, including two hypervariable regions V1-V2, valuable for animal phylogeny. All four sets of primers demonstrated a high amplification efficiency and high specificity for freshwater fish. Also, we proposed the protocols for the cost-effective isolation of total DNA and purification of the PCR product without the use of commercial kits. We propose an algorithm to carry out extremely cheap studies on the assessment of biological diversity without expensive equipment. We also present original data on the genetic polymorphism of all mass NIS fish species in the Volga-Kama region. The high efficiency of DNA identification based on our primers is shown relative to the traditional monitoring of biological invasions.
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Development of loop-mediated isothermal amplification (LAMP) assay for rapid screening of skipjack tuna (Katsuwonus pelamis) in processed fish products. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.104038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Lea-Charris E, Castro LR, Villamizar N. DNA barcoding reveals fraud in commercial common snook ( Centropomus undecimalis) products in Santa Marta, Colombia. Heliyon 2021; 7:e07095. [PMID: 34095587 PMCID: PMC8165420 DOI: 10.1016/j.heliyon.2021.e07095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/30/2021] [Accepted: 05/13/2021] [Indexed: 10/31/2022] Open
Abstract
The common snook Centropomus undecimalis is one of the main commercial fish species in the Caribbean region, including Colombia, where its populations have drastically decreased due to overfishing and environmental degradation. Thus, there is a market imbalance between the availability of snook products and their demand by consumers, which creates an opening for fraudulent actions such as species substitutions. Legislation in Colombia (and most Caribbean countries) lacks effective tools for the easy and rapid detection of frauds. Furthermore, there are very few studies published in scientific journals addressing this issue, of which none include C. undecimalis as the target species. Therefore, in order to investigate the existence of mislabeling in common snook products in Santa Marta, the present study analysed 44 frozen snook fillets from the five commercial brands available in the city. Moreover, 15 fresh snook fillets from six of the main fish markets were also analysed. To discover the frequency of possible frauds in labeling, samplings were carried out in July, September and November of 2019. Sample analyses involved the identification of each fillet at species level through molecular barcodes (16S-rRNA and COI), whose sequences were verified using BLAST and BOLD, and corroborated by a phylogenetic analysis. As a result, an astonishing 98% of the supermarkets fillets were found to be fraudulent, contrasting with a single case registered in the fish shop samples. The species used to substitute snook include the Pacific bearded brotula Brotula clarkae (38 samples), the Nile perch Lates niloticus (4 samples) and the acoupa weakfish Cynoscion acoupa (1 sample). Based on these results, there is a high rate of fraudulent labeling in the marketing of common snook in the city of Santa Marta, which calls for urgent actions to be taken by the corresponding authorities.
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Affiliation(s)
- Edison Lea-Charris
- Evolution, Systematics and Molecular Ecology Research Group with - GIESEMOL, Universidad del Magdalena, Santa Marta, Colombia
| | - Lyda R Castro
- Evolution, Systematics and Molecular Ecology Research Group with - GIESEMOL, Universidad del Magdalena, Santa Marta, Colombia
| | - Natalia Villamizar
- Biodiversity and Applied Ecology Research Group - GIBEA, Universidad del Magdalena, Carrera 32 No 22 - 08, 47001, Santa Marta, Colombia
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Modernizing the Toolkit for Arthropod Bloodmeal Identification. INSECTS 2021; 12:insects12010037. [PMID: 33418885 PMCID: PMC7825046 DOI: 10.3390/insects12010037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 11/24/2022]
Abstract
Simple Summary The ability to identify the source of vertebrate blood in mosquitoes, ticks, and other blood-feeding arthropod vectors greatly enhances our knowledge of how vector-borne pathogens are spread. The source of the bloodmeal is identified by analyzing the remnants of blood remaining in the arthropod at the time of capture, though this is often fraught with challenges. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification with a focus on progress made in the field over the past decade. We highlight genome regions that can be used to identify the vertebrate source of arthropod bloodmeals as well as technological advances made in other fields that have introduced innovative new ways to identify vertebrate meal source based on unique properties of the DNA sequence, protein signatures, or residual molecules present in the blood. Additionally, engineering progress in miniaturization has led to a number of field-deployable technologies that bring the laboratory directly to the arthropods at the site of collection. Although many of these advancements have helped to address the technical challenges of the past, the challenge of successfully analyzing degraded DNA in bloodmeals remains to be solved. Abstract Understanding vertebrate–vector interactions is vitally important for understanding the transmission dynamics of arthropod-vectored pathogens and depends on the ability to accurately identify the vertebrate source of blood-engorged arthropods in field collections using molecular methods. A decade ago, molecular techniques being applied to arthropod blood meal identification were thoroughly reviewed, but there have been significant advancements in the techniques and technologies available since that time. This review highlights the available diagnostic markers in mitochondrial and nuclear DNA and discusses their benefits and shortcomings for use in molecular identification assays. Advances in real-time PCR, high resolution melting analysis, digital PCR, next generation sequencing, microsphere assays, mass spectrometry, and stable isotope analysis each offer novel approaches and advantages to bloodmeal analysis that have gained traction in the field. New, field-forward technologies and platforms have also come into use that offer promising solutions for point-of-care and remote field deployment for rapid bloodmeal source identification. Some of the lessons learned over the last decade, particularly in the fields of DNA barcoding and sequence analysis, are discussed. Though many advancements have been made, technical challenges remain concerning the prevention of sample degradation both by the arthropod before the sample has been obtained and during storage. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification and reviews how advances in molecular technology over the past decade have been applied in this unique biomedical context.
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Chan AHE, Chaisiri K, Dusitsittipon S, Jakkul W, Charoennitiwat V, Komalamisra C, Thaenkham U. Mitochondrial ribosomal genes as novel genetic markers for discrimination of closely related species in the Angiostrongylus cantonensis lineage. Acta Trop 2020; 211:105645. [PMID: 32702297 DOI: 10.1016/j.actatropica.2020.105645] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/17/2020] [Accepted: 07/19/2020] [Indexed: 11/23/2022]
Abstract
The Angiostrongylus cantonensis lineage (Nematoda: Metastrongyloidea) consists of the closely related species A. cantonensis, Angiostrongylus malaysiensis, and Angiostrongylus mackerrasae. Various genetic markers have been used for species discrimination in molecular phylogenetic studies of this lineage. However, despite showing potential in other organisms, mitochondrial 12S and 16S ribosomal RNA (rRNA) genes have not been used for Angiostrongylus species discrimination. Therefore, this study assessed these genes' suitability for inter- and intraspecies discrimination in the A. cantonensis lineage. The ultimate aim was to provide a novel genetic marker to support existing phylogenies. Sixty adult Angiostrongylus spp. worms from four geographic locations in Thailand were identified morphologically before molecular identification with 12S and 16S rRNA genes. Neighbor-joining and maximum likelihood algorithms were used for phylogenetic analyzes, and sequence variation was calculated to determine whether the genes could be used to discriminate among species. Furthermore, sequence variation was compared among previously used genetic markers to evaluate the robustness of the 12S and 16S rRNA genes as markers. Using both markers, the A. cantonensis lineage formed a monophyletic clade with a clear separation between A. cantonensis, A. malaysiensis, and A. mackerrasae. From our representative A. cantonensis and A. malaysiensis specimens, the genetic distance between the two clades was 6.8% -7.9% and 7.9% -10.0% for 12S and 16S rRNA genes, respectively, which is sufficient interspecific genetic variation for species discrimination. Higher levels of genetic variation were observed for the 16S rRNA gene, with 12 haplotypes and an intraspecific variation ≤2.2%. Thus, as a genetic marker, the 16S rRNA gene is comparable to mitochondrial protein-coding genes, which are commonly used in intra-level Angiostrongylus spp. studies. In conclusion, mitochondrial 12S and 16S rRNA genes can discriminate among closely related species in the A. cantonensis lineage, and they represent novel genetic markers for supporting existing phylogenies and verifying the phylogenetic position of A. mackerrasae.
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Affiliation(s)
- Abigail Hui En Chan
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Kittipong Chaisiri
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Sirilak Dusitsittipon
- Department of Parasitology and Entomology, Faculty of Public Health, Mahidol University, Bangkok, Thailand.
| | - Wallop Jakkul
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Chalit Komalamisra
- Mahidol Bangkok School of Tropical Medicine (Mahidol-BSTM), Faculty of Tropical Medicine, Mahidol University, Thailand.
| | - Urusa Thaenkham
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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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.
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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;
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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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Gaber A, Hassan MM, Boland C, Alsuhaibany A, Babbington J, Pereira J, Budd J, Shobrak M. Molecular identification of Todiramphus chloris subspecies on the Arabian Peninsula using three mitochondrial barcoding genes and ISSR markers. Saudi J Biol Sci 2020; 27:480-488. [PMID: 31889874 PMCID: PMC6933276 DOI: 10.1016/j.sjbs.2019.11.014] [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: 05/23/2019] [Revised: 10/20/2019] [Accepted: 11/17/2019] [Indexed: 11/03/2022] Open
Abstract
The Collared Kingfisher (Todiramphus chloris) is widely distributed across the Indian and western Pacific Oceans and consists of about 50 subspecies. Two different subspecies of T. chloris occur in the Arabian Peninsula: T. c. abyssinicus from the Red Sea coast and T. c. kalbaensis from the Arabian Sea coast in the United Arab Emirates and Oman. The aim of this study was to determine the molecular relationship between the two Arabian subspecies and to establish the first DNA barcodes from the Arabian Peninsula for this species. Three different mitochondrial genes were used: (i) cytochrome c oxidase subunit I (COI), (ii) 12S rRNA (12S) and (iii) NADH dehydrogenase-1 (ND1). The COI gene sequences of the two subspecies were 100% identical, while the 12S and ND1 gene sequences revealed a unique single nucleotide variation between the two subspecies. Thus, this single nucleotide variation can be used as a DNA barcode to discriminate between two subspecies. Furthermore, the genetic profile or fingerprint for both subspecies were compared using ten primers of the highly polymorphic nuclear markers (Inter Simple Sequence Repeat, ISSR). As expected, the DNA analysis of the ISSR markers was able to distinguish between the specimens of the two subspecies. These results suggest that T. c. abyssinicus and T. c. kalbaensis are not identical and thus belong to different subspecies. Besides, the sequences of the COI gene for T. c. abyssinicus and T. c. kalbaensis differs by only 1.28% from T. sanctus suggesting that the Arabian subspecies are closely related to the Sacred Kingfisher (T. sanctus).
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Affiliation(s)
- Ahmed Gaber
- Department of Biology, Faculty of Science, Taif University, Saudi Arabia.,Department of Genetics, Faculty of Agriculture, Cairo University, Egypt
| | - Mohamed M Hassan
- Department of Biology, Faculty of Science, Taif University, Saudi Arabia.,Department of Genetics, Faculty of Agriculture, Menoufia University, Egypt
| | - Christopher Boland
- Saudi Aramco, Environmental Protection Department, Dhahran, Saudi Arabia
| | - Abdullah Alsuhaibany
- Ministry of Environment, Water, and Agriculture, National Wildlife Center, Riyadh, Saudi Arabia
| | - Jem Babbington
- Saudi Aramco, EXPEC Advance Research Center, Dhahran, Saudi Arabia
| | - John Pereira
- Environment & Protected Areas Authority, Sharjah, United Arab Emirates
| | - Jane Budd
- Environment & Protected Areas Authority, Sharjah, United Arab Emirates
| | - Mohammed Shobrak
- Department of Biology, Faculty of Science, Taif University, Saudi Arabia.,Saudi Wildlife Authority, Prince Saud Al Faisal Research Center, Taif, Saudi Arabia
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13
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Arisuryanti T, Rumahorbo Y, Amaliya Rha’ifa F, Hakim L. Detection of 16S mitochondrial sequence polymorphism and haplotype network of Ophiocara porocephala (Valenciennes, 1837) from Tekolok Estuary (NTB, Indonesia) using DnaSP and NETWORK. BIO WEB OF CONFERENCES 2020. [DOI: 10.1051/bioconf/20202801002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The two genetic software, DnaSP and NETWORK, is commonly used to analyse gene polymorphism and haplotype network which is useful for the understanding pattern of genetic variation and genetic relationship. In this study, the two software were applied to detect polymorphism of 16S sequence gene of Ophiocara paracephala from Tekolok Estuary (NTB, Indonesia) which has not been investigated. This study used a PCR method with 16Sar and 16Sbr primers. The results revealed two haplotypes and two variable sites with one parsimony informative within O.paracephala from Tekolok Estuary population. Next, if the 16S sequence data of O.paracephala from Tekolok Estuary was combined with the 16S gene data of O.paracephala from GenBank, three haplotypes were detected with five variables sites and one parsimony informative. This finding showed intra-population and intraspecific genetic variation of O.paracephala. In addition, haplotype network using NETWORK and a phylogenetic tree using Neighbor Joining and Maximum Likelihood methods exhibited that O.paracephala from Tekolok Estuary has a close genetic relationship with O.paracephala from Japan.
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14
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Chen C, Lin Y, Tao R, Xia R, Zhang X, Zhang J, Yang Z, Li C, Zhang S. An enhanced DNA amplification method to detect the species origins of the rootless hair shafts. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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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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16
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Kinebuchi T, Idota N, Tsuboi H, Takaso M, Bando R, Ikegaya H. The genome profiling method can be applied for species identification of biological materials collected at crime scenes. BMC Genet 2019; 20:50. [PMID: 31182029 PMCID: PMC6558897 DOI: 10.1186/s12863-019-0753-9] [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: 09/11/2018] [Accepted: 05/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Various biological materials unrelated to humans are found at crime scenes and it is often important to elucidate the origin of these materials. A genetic locus common to several species is conventionally PCR-amplified with universal primers to identify species. However, not all species can be identified using a single locus. In this study, DNA from 13 commonly handled taxa was analyzed to identify species by a genome profiling (GP) method, which involves random PCR and temperature gradient gel electrophoresis. RESULTS In a clustering analysis, we successfully obtained a single cluster for each species. CONCLUSION The GP method is cost-effective and does not require advanced techniques and knowledge in molecular biology. The random sampling of the whole genome using multiple primers provides substantial genomic information. Therefore, the method is effective for classifying a wide range of species, including animals, plants, and insects, and is useful for crime scene investigations.
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Affiliation(s)
- Takako Kinebuchi
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Nozomi Idota
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Hajime Tsuboi
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Marin Takaso
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Risa Bando
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Hiroshi Ikegaya
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan.
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17
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Comparison of mitochondrial DNA enrichment and sequencing methods from fish tissue. Food Chem 2019; 294:333-338. [PMID: 31126471 DOI: 10.1016/j.foodchem.2019.05.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 01/06/2023]
Abstract
Sparid fish species have different commercial values related to their organoleptic features. Mitochondrial (mt) DNA provides a potential tool to distinguish species, but the enrichment of high-quality mtDNA from total genomic DNA is critical to obtain entire mtDNA sequences. Conventional mtDNA isolation is relatively low-cost and proficient. However, high numbers of PCR cycles can lead to artefacts (10-6 mutations/bp). We describe a rapid protocol for mtDNA extraction and enrichment from fish tissues, based on conventional miniprep columns and paramagnetic bead-based purification, without the need to employ PCR amplification. This newly described method generates a substrate for next-generation sequencing (NGS) analysis and is likely to have wider applications for mitochondrial studies in other fish families to help ensure traceability and differentiation of fish with high commercial values.
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18
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Galal-Khallaf A, Osman AGM, El-Ganainy A, Farrag MM, Mohammed-AbdAllah E, Moustafa MA, Mohammed-Geba K. Mitochondrial genetic markers for authentication of major Red Sea grouper species (Perciformes: Serranidae) in Egypt: A tool for enhancing fisheries management and species conservation. Gene 2018; 689:235-245. [PMID: 30572096 DOI: 10.1016/j.gene.2018.12.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/29/2018] [Accepted: 12/12/2018] [Indexed: 11/26/2022]
Abstract
Groupers are coral fish species of prime ecological and economic significance. The interactions among them and other coral reefs organisms aid the healthiness and species balance in this fundamental marine niches. Also, groupers are among the top priced fisheries species. The Egyptian habitats of the Red Sea are lacking genetic studies that assess species diversity for the final goal of conservation and fisheries management. Moreover, morphological similarities among these organisms sometimes hinder a proper species identification. Hence, more accurate groupers authentication methods are crucially required. Sixteen grouper species belonging to the genera Epinephelus, Anyperodon, Cephaolopholes, Aethaloperca, Variola, and Plectropomus, present in the Red Sea in Egypt, were investigated for species authentication through mitochondrial DNA variations, applying cytochrome oxidase subunit I (COI) and 12srRNA genes sequencing. GenBank comparisons, phylogenetic analyses and comparisons of pairwise distances were carried out. All these analyses aimed to species authentication and identifying their relations at the international scale. The results exhibited >98% identity with E. fasciatus, A. rogaa, C. oligosticta, E. areolatus, V. louti, P. areolatus, E. malabaricus, C. sexmaculata, E. summana, E. chlorostigma, E. polyphekadion, C. miniataus, A. leucogrammicus, E. tauvina, C. argus, C. hemistiktos. Pairwise distances showed a clear increase upon raising comparison level from among species to among-genera. Combined 12srRNA and COI genes sequencing resulted in an accurate tool for Egyptian Red Sea grouper species unambiguous discrimination. This can provide vital aid to the active efforts for these species conservation and fisheries management in Egypt and the world.
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Affiliation(s)
- Asmaa Galal-Khallaf
- Genetic Engineering and Molecular Biology Division, Department of Zoology, Faculty of Science, Menoufia University, 32511 Shebin El-Kom, Menoufia, Egypt.
| | - Alaa G M Osman
- Department of Zoology, Faculty of Science, Al-Azhar University, Assiut Branch, 71524 Assiut, Egypt
| | - Azza El-Ganainy
- National Institute of Oceanography and Fisheries, Fisheries Division, Egypt
| | - Mahmoud M Farrag
- Department of Zoology, Faculty of Science, Al-Azhar University, Assiut Branch, 71524 Assiut, Egypt
| | - Ezzat Mohammed-AbdAllah
- Department of Zoology, Faculty of Science, Al-Azhar University, Assiut Branch, 71524 Assiut, Egypt
| | - Mohsen A Moustafa
- Department of Zoology, Faculty of Science, Al-Azhar University, Assiut Branch, 71524 Assiut, Egypt
| | - Khaled Mohammed-Geba
- Genetic Engineering and Molecular Biology Division, Department of Zoology, Faculty of Science, Menoufia University, 32511 Shebin El-Kom, Menoufia, Egypt.
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19
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Marquina D, Andersson AF, Ronquist F. New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods. Mol Ecol Resour 2018; 19:90-104. [PMID: 30226026 PMCID: PMC7379581 DOI: 10.1111/1755-0998.12942] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/27/2018] [Accepted: 09/07/2018] [Indexed: 11/29/2022]
Abstract
Insect metabarcoding has been mainly based on PCR amplification of short fragments within the “barcoding region” of the gene cytochrome oxidase I (COI). However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ecoprimers and degeprime) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein‐coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon‐based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.
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Affiliation(s)
- Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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20
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Chen JY, Chang YW, Zheng SZ, Lu MX, Du YZ. Comparative analysis of the Liriomyza chinensis mitochondrial genome with other Agromyzids reveals conserved genome features. Sci Rep 2018; 8:8850. [PMID: 29892001 PMCID: PMC5995824 DOI: 10.1038/s41598-018-27213-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 05/29/2018] [Indexed: 12/03/2022] Open
Abstract
Liriomyza chinensis is a serious pest of onions in many countries, especially in East Asia. We sequenced the complete mitochondrial genome of this species and compared it with five other Agromyzidae species. The L. chinensis mitogenome is a double-stranded 16,175 bp circular molecule with an A + T content of 78.3%. It contains 37 genes and a control region as do the sequenced Liriomyza species. The mitogenomes of L. chinensis and other Agromyzidae species showed a clear bias in nucleotide composition with a positive AT-skew. Most PCGs used standard ATN as start codons, and TAN as termination codons. The tRNAs exhibited the typical clover-leaf structure, except for tRNASer(AGN) and the two rRNA genes are conserved with those of other Agromyzids. The L. chinensis mitogenome control region included several conserved regions, including a poly-T, two (TA)n and one poly-A stretch, which are considered important replication and transcription. The 13 PCGs were used to study the phylogeny of L. chinensis and five related Agromyzids. Analysis by maximum likelihood, Bayesian inference and genetic distance suggest congruent phylogenetic relationships in Liriomyza spp. and provide a useful supplement to taxonomic classification by morphology.
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Affiliation(s)
- Jing-Yun Chen
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, 225009, China.,Suzhou Customs (formerly Suzhou Entry-Exit Inspection and Quarantine Bureau), Suzhou, 215000, China
| | - Ya-Wen Chang
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, 225009, China
| | - Si-Zhu Zheng
- Suzhou Customs (formerly Suzhou Entry-Exit Inspection and Quarantine Bureau), Suzhou, 215000, China
| | - Ming-Xing Lu
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, 225009, China
| | - Yu-Zhou Du
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, 225009, China. .,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China.
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21
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Giusti A, Tinacci L, Sotelo CG, Marchetti M, Guidi A, Zheng W, Armani A. Seafood Identification in Multispecies Products: Assessment of 16SrRNA, cytb, and COI Universal Primers' Efficiency as a Preliminary Analytical Step for Setting up Metabarcoding Next-Generation Sequencing Techniques. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:2902-2912. [PMID: 28290697 DOI: 10.1021/acs.jafc.6b05802] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Few studies applying NGS have been conducted in the food inspection field, particularly on multispecies seafood products. A preliminary study screening the performance and the potential application in NGS analysis of 14 "universal primers" amplifying 16SrRNA, cytb, and COI genes in fish and cephalopods was performed. Species used in surimi preparation were chosen as target. An in silico analysis was conducted to test primers' coverage capacity by assessing mismatches (number and position) with the target sequences. The 9 pairs showing the best coverage capacity were tested in PCR on DNA samples of 53 collected species to assess their amplification performance (amplification rate and amplicon concentration). The results confirm that primers designed for the 16SrRNA gene amplification are the most suitable for NGS analysis also for identification of multispecies seafood products. In particular, the primer pair of Chapela et al. (2002) is the best candidate.
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Affiliation(s)
- Alice Giusti
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
| | - Lara Tinacci
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
| | - Carmen G Sotelo
- Instituto de Investigaciones Marinas (IIM-CSIC) , Eduardo Cabello 6, 36208 Vigo, Spain
| | - Martina Marchetti
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
| | - Alessandra Guidi
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
| | - Wenjie Zheng
- Tianjin Entry-Exit Inspection and Quarantine Bureau of the People's Republic of China , Jingmen Road 158, Free trade Zone, Tianjin Port, 300461 Tianjin, China
| | - Andrea Armani
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
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22
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Gao L, Yin Y, Li J, Yuan Y, Jiang C, Gao W, Zhang X, Huang L. Identification of traditional Chinese medicinal pipefish and exclusion of common adulterants by multiplex PCR based on 12S sequences of specific alleles. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:340-346. [PMID: 28129724 DOI: 10.1080/24701394.2016.1278538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We aimed to establish a rapid and accurate allele-specific diagnostic Polymerase Chain Reaction (PCR) method for medicinal pipefish. To achieve this, pipefish genomic DNA was extracted, sequenced bi-directionally, and the data were analyzed. On this basis, specific identification primers were designed and a facile multiplex PCR system was established and optimized. Phylogenetic tree analysis showed that the six species of pipefish were strictly clustered in separate single branches. The reaction was optimized for ease of application, to be used in a reaction volume of 20 μL with template DNA amounts in the range of 5-100 ng, and an annealing temperature from 43 to 55 °C. The reactions conducted using authentic samples of Syngnathoides biaculeatus, Solenognathus hardwickii, and Syngnathus acus produced clear single DNA bands of 240 bp, 318 bp, and 139 bp, respectively. The observed amplicons correspond very well to the specific identification primers HLN, HLD, HLJ, as designed. Thus, it can be concluded that our identification system is specific and stable, and can be used to quickly and accurately identify complex multi-source pipefish samples. We hope that the system will not only ensure the quality of traditional Chinese medicinal ingredients, but also help conservation efforts by offering a quick and easy identification method for pipefish.
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Affiliation(s)
- Linhui Gao
- a School of Traditional Chinese Medicine, Capital Medical University , Beijing , China
| | - Yan Yin
- b School of Pharmaceutical Sciences, Guizhou University , Guiyang , China
| | - Jia Li
- a School of Traditional Chinese Medicine, Capital Medical University , Beijing , China
| | - Yuan Yuan
- c State Key Laboratory Breeding Base of Dao-di Herbs , National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing , China
| | - Chao Jiang
- c State Key Laboratory Breeding Base of Dao-di Herbs , National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing , China
| | - Wei Gao
- a School of Traditional Chinese Medicine, Capital Medical University , Beijing , China
| | - Xianan Zhang
- a School of Traditional Chinese Medicine, Capital Medical University , Beijing , China
| | - Luqi Huang
- c State Key Laboratory Breeding Base of Dao-di Herbs , National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing , China
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23
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Huang Y, Hu J, Wang B, Song Z, Zhou C, Jiang J. Integrative taxonomy helps to reveal the mask of the genus Gynandropaa (Amphibia: Anura: Dicroglossidae). Integr Zool 2016; 11:134-50. [PMID: 26531851 DOI: 10.1111/1749-4877.12169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Species of the genus Gynandropaa within the family Dicroglossidae are typical spiny frogs whose taxonomic status has long been in doubt. We used integrative methods, involving morphological and molecular analyses, to elucidate the phylogenetic relationships, and to determine identities and the geographic distribution of each valid species. We obtained DNA sequence data of 5 species of Gynandropaa (complete sequences of the mitochondrial NADH dehydrogenase subunit 2 [ND2] gene, and 890 bp of 12S rRNA and 16S rRNA partial sequences) from 37 localities (including the topotypes of 5 described species) and constructed Bayesian and maximum-likelihood trees to examine the patterns of phylogeography. A total of 28 morphological variables were taken on 624 specimens. Three clades with clear geographic patterns were recognized: clade C (from south-western Sichuan Province and central Yunnan Province), clade E (western Guizhou Province and eastern to central Yunnan Province) and clade W (western to southern Yunnan Province). Integrating morphological characteristics and distribution information, the clades W, E and C represent Gynandropaa yunnanensis, G. phrynoides and G. sichuanensis, respectively. We draw the following conclusions: (i) the taxon G. phrynoides, formerly evaluated as a junior synonym of G. yunnanensis, is revalidated herein at the rank of species; (ii) G. liui is a junior synonym of G. sichuanensis; and (iii) G. yunnanensis is a valid species while G. bourreti is probably a subspecies of G. yunnanensis, with the distribution range from Vietnam to southern Yunnan Province. This study clears up the taxonomic status of Gynandropaa and provides important information for understanding the evolution and conservation of these spiny frogs.
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Affiliation(s)
- Yan Huang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,College of Life Science, Sichuan University, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Southwest China Wildlife Resources Conservation, China West Normal University, Ministry of Education, Nanchong, China
| | - Junhua Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Bin Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhaobin Song
- College of Life Science, Sichuan University, Chengdu, China
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation, China West Normal University, Ministry of Education, Nanchong, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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24
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Falade MO, Opene AJ, Benson O. DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria. F1000Res 2016; 5:1268. [PMID: 27990256 PMCID: PMC5133684 DOI: 10.12688/f1000research.7895.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 11/20/2022] Open
Abstract
DNA barcoding has been adopted as a gold standard rapid, precise and unifying identification system for animal species and provides a database of genetic sequences that can be used as a tool for universal species identification. In this study, we employed mitochondrial genes 16S rRNA (16S) and cytochrome oxidase subunit I (COI) for the identification of some Nigerian freshwater catfish and Tilapia species. Approximately 655 bp were amplified from the 5' region of the mitochondrial cytochrome C oxidase subunit I (COI) gene whereas 570 bp were amplified for the 16S rRNA gene. Nucleotide divergences among sequences were estimated based on Kimura 2-parameter distances and the genetic relationships were assessed by constructing phylogenetic trees using the neighbour-joining (NJ) and maximum likelihood (ML) methods. Analyses of consensus barcode sequences for each species, and alignment of individual sequences from within a given species revealed highly consistent barcodes (99% similarity on average), which could be compared with deposited sequences in public databases. The nucleotide distance between species belonging to different genera based on COI ranged from 0.17% between Sarotherodonmelanotheron and Coptodon zillii to 0.49% between Clarias gariepinus and C. zillii, indicating that S. melanotheron and C. zillii are closely related. Based on the data obtained, the utility of COI gene was confirmed in accurate identification of three fish species from Southwest Nigeria.
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Affiliation(s)
- Mofolusho O. Falade
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
| | - Anthony J. Opene
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
| | - Otarigho Benson
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
- Department of Biological Science, Edo University, Iyamho, Edo State, Nigeria
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25
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Towards more sustainable surimi? PCR-cloning approach for DNA barcoding reveals the use of species of low trophic level and aquaculture in Asian surimi. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.09.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Cawthorn DM, Duncan J, Kastern C, Francis J, Hoffman LC. Fish species substitution and misnaming in South Africa: An economic, safety and sustainability conundrum revisited. Food Chem 2015; 185:165-81. [PMID: 25952855 DOI: 10.1016/j.foodchem.2015.03.113] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 03/16/2015] [Accepted: 03/29/2015] [Indexed: 10/23/2022]
Abstract
While fish species mislabelling has emerged as a global problem, the tracking of improvements or deteriorations in seafood trading practices is challenging without a consistent basis for monitoring. The aim of this study was to develop a robust, repeatable species authentication protocol that could be used to benchmark the current and future incidences of fish mislabelling in South Africa. Using this approach, 149 fish samples collected from restaurants and retailers in three provinces (KwaZulu-Natal, Western Cape and Gauteng) were identified using DNA barcoding, supplemented in certain cases with mitochondrial control region sequencing. Overall, 18% of samples were incorrectly described in terms of species, with similar misrepresentation rates in restaurants (18%) and retail outlets (19%). While there appears to be some improvement in the transparency of local seafood marketing compared to previous studies, the results remain of concern and signal the need for enhanced seafood labelling regulations, monitoring and law enforcement.
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Affiliation(s)
- Donna-Mareè Cawthorn
- Department of Animal Sciences, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
| | - John Duncan
- World Wildlife Fund South Africa - Southern African Sustainable Seafood Initiative (WWF-SASSI), PO Box 23273, Claremont 7735, South Africa
| | - Chris Kastern
- World Wildlife Fund South Africa - Southern African Sustainable Seafood Initiative (WWF-SASSI), PO Box 23273, Claremont 7735, South Africa
| | - Junaid Francis
- World Wildlife Fund South Africa - Southern African Sustainable Seafood Initiative (WWF-SASSI), PO Box 23273, Claremont 7735, South Africa
| | - Louwrens C Hoffman
- Department of Animal Sciences, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
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27
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Armani A, Tinacci L, Xiong X, Castigliego L, Gianfaldoni D, Guidi A. Fish species identification in canned pet food by BLAST and Forensically Informative Nucleotide Sequencing (FINS) analysis of short fragments of the mitochondrial 16s ribosomal RNA gene (16S rRNA). Food Control 2015. [DOI: 10.1016/j.foodcont.2014.10.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Sangthong P, Ngernsiri L, Sangthong D. Identification of Puffer Fish of the GenusLagocephalus: L. lunaris, L. spadiceusandL. inermis, Using Multiplex PCR. FOOD BIOTECHNOL 2014. [DOI: 10.1080/08905436.2014.931865] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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A universal method for species identification of mammals utilizing next generation sequencing for the analysis of DNA mixtures. PLoS One 2013; 8:e83761. [PMID: 24358309 PMCID: PMC3865308 DOI: 10.1371/journal.pone.0083761] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 11/07/2013] [Indexed: 11/19/2022] Open
Abstract
Species identification can be interesting in a wide range of areas, for example, in forensic applications, food monitoring and in archeology. The vast majority of existing DNA typing methods developed for species determination, mainly focuses on a single species source. There are, however, many instances where all species from mixed sources need to be determined, even when the species in minority constitutes less than 1 % of the sample. The introduction of next generation sequencing opens new possibilities for such challenging samples. In this study we present a universal deep sequencing method using 454 GS Junior sequencing of a target on the mitochondrial gene 16S rRNA. The method was designed through phylogenetic analyses of DNA reference sequences from more than 300 mammal species. Experiments were performed on artificial species-species mixture samples in order to verify the method's robustness and its ability to detect all species within a mixture. The method was also tested on samples from authentic forensic casework. The results showed to be promising, discriminating over 99.9 % of mammal species and the ability to detect multiple donors within a mixture and also to detect minor components as low as 1 % of a mixed sample.
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Yang F, Du Y, Cao J, Huang F. Analysis of three leafminers' complete mitochondrial genomes. Gene 2013; 529:1-6. [PMID: 23954222 DOI: 10.1016/j.gene.2013.08.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/01/2013] [Accepted: 08/04/2013] [Indexed: 10/26/2022]
Abstract
Liriomyza trifolii (Burgess), Liriomyza huidobrensis (Blanchard), and Liriomyza bryoniae (Kaltenbach), are three closely related and economically important leafminer pests in the world. This study examined the complete mitochondrial genomes of L. trifolii, L. huidobrensis and L. bryoniae, which were 16,141 bp, 16,236 bp and 16,183 bp in length, respectively. All of them displayed 37 typical animal mitochondrial genes and an A+T-rich region. The genomes were highly compact with only 60-68 bp of non-coding intergenic spacer. However, considerable differences in the A+T-rich region were detected among the three species. Results of this study also showed the two ribosomal RNA genes of the three species had very limited variable sites and thus should not provide much information in the study of population genetics of these species. Data generated from three leafminers' complete mitochondrial genomes should provide valuable information in studying phylogeny of Diptera, and developing genetic markers for species identification in leafminers.
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Affiliation(s)
- Fei Yang
- College of Horticulture and Plant Protection and Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, PR China; Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
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Paital B, Samanta L. A comparative study of hepatic mitochondrial oxygen consumption in four vertebrates by using Clark-type electrode. ACTA BIOLOGICA HUNGARICA 2013; 64:152-60. [PMID: 23739884 DOI: 10.1556/abiol.64.2013.2.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The present study was undertaken to establish a comparative account on hepatic mitochondrial oxygen consumption of Clarias gariepinus (fish), Bufo melanostictus (amphibian), Gallus gallus (bird) and Rattus norvegicus (mammal) and to correlate it with their specific metabolic rate (SMR). Mitochondrial oxygen consumption was measured with a Clarke-type electrode with succinate and pyruvate/malate as substrates. ADP was used to start state-III respiration. The results show that rats and chickens have higher oxygen consumption rate than that of fish and toads. Similarly, a species and substrate specific difference was also noticed in P/O (phosphate utilized per oxygen atom) ratio and respiratory control index. In case of rat, a significant negative correlation was noticed between P/O ratio and SMR with succinate as substrate. It is surmised that the observed difference in the mitochondrial respiration and P/O ratio in the above vertebrates is due to the difference in their metabolic activities.
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Affiliation(s)
- B Paital
- Utkal University Department of Zoology and Biotechnology, Bhubaneswar, India.
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