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Frigerio J, Campone L, Giustra MD, Buzzelli M, Piccoli F, Galimberti A, Cannavacciuolo C, Ouled Larbi M, Colombo M, Ciocca G, Labra M. Convergent technologies to tackle challenges of modern food authentication. Heliyon 2024; 10:e32297. [PMID: 38947432 PMCID: PMC11214499 DOI: 10.1016/j.heliyon.2024.e32297] [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: 04/11/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 07/02/2024] Open
Abstract
The authentication process involves all the supply chain stakeholders, and it is also adopted to verify food quality and safety. Food authentication tools are an essential part of traceability systems as they provide information on the credibility of origin, species/variety identity, geographical provenance, production entity. Moreover, these systems are useful to evaluate the effect of transformation processes, conservation strategies and the reliability of packaging and distribution flows on food quality and safety. In this manuscript, we identified the innovative characteristics of food authentication systems to respond to market challenges, such as the simplification, the high sensitivity, and the non-destructive ability during authentication procedures. We also discussed the potential of the current identification systems based on molecular markers (chemical, biochemical, genetic) and the effectiveness of new technologies with reference to the miniaturized systems offered by nanotechnologies, and computer vision systems linked to artificial intelligence processes. This overview emphasizes the importance of convergent technologies in food authentication, to support molecular markers with the technological innovation offered by emerging technologies derived from biotechnologies and informatics. The potential of these strategies was evaluated on real examples of high-value food products. Technological innovation can therefore strengthen the system of molecular markers to meet the current market needs; however, food production processes are in profound evolution. The food 3D-printing and the introduction of new raw materials open new challenges for food authentication and this will require both an update of the current regulatory framework, as well as the development and adoption of new analytical systems.
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Affiliation(s)
- Jessica Frigerio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20216, Milano, Italy
| | - Luca Campone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20216, Milano, Italy
| | - Marco Davide Giustra
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20216, Milano, Italy
| | - Marco Buzzelli
- Department of Informatics Systems and Communication, University of Milano-Bicocca, viale Sarca, 336, 20216, Milano, Italy
| | - Flavio Piccoli
- Department of Informatics Systems and Communication, University of Milano-Bicocca, viale Sarca, 336, 20216, Milano, Italy
| | - Andrea Galimberti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20216, Milano, Italy
| | - Ciro Cannavacciuolo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20216, Milano, Italy
| | - Malika Ouled Larbi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20216, Milano, Italy
| | - Miriam Colombo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20216, Milano, Italy
| | - Gianluigi Ciocca
- Department of Informatics Systems and Communication, University of Milano-Bicocca, viale Sarca, 336, 20216, Milano, Italy
| | - Massimo Labra
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20216, Milano, Italy
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Matoute A, Maestri S, Saout M, Laghoe L, Simon S, Blanquart H, Hernandez Martinez MA, Pierre Demar M. Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana. Curr Issues Mol Biol 2024; 46:3810-3821. [PMID: 38785505 PMCID: PMC11119736 DOI: 10.3390/cimb46050237] [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: 02/09/2024] [Revised: 03/06/2024] [Accepted: 04/03/2024] [Indexed: 05/25/2024] Open
Abstract
French Guiana, located in the Guiana Shield, is a natural reservoir for many zoonotic pathogens that are of considerable medical or veterinary importance. Until now, there has been limited data available on the description of parasites circulating in this area, especially on protozoan belonging to the phylum Apicomplexa; conversely, the neighbouring countries describe a high parasitic prevalence in animals and humans. Epidemiological surveillance is necessary, as new potentially virulent strains may emerge from these forest ecosystems, such as Amazonian toxoplasmosis. However, there is no standard tool for detecting protozoa in wildlife. In this study, we developed Meat-Borne-Parasite, a high-throughput meta-barcoding workflow for detecting Apicomplexa based on the Oxford Nanopore Technologies sequencing platform using the 18S gene of 14 Apicomplexa positive samples collected in French Guiana. Sequencing reads were then analysed with MetONTIIME pipeline. Thanks to a scoring rule, we were able to classify 10 samples out of 14 as Apicomplexa positive and reveal the presence of co-carriages. The same samples were also sequenced with the Illumina platform for validation purposes. For samples identified as Apicomplexa positive by both platforms, a strong positive correlation at up to the genus level was reported. Overall, the presented workflow represents a reliable method for Apicomplexa detection, which may pave the way for more comprehensive biomonitoring of zoonotic pathogens.
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Affiliation(s)
- Adria Matoute
- Tropical Biome and Immunopathophysiology (TBIP), Université de Guyane, 97300 Cayenne, France; (A.M.); (S.M.); (M.S.); (L.L.); (S.S.)
- U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Université Lille, 59000 Lille, France
| | - Simone Maestri
- Tropical Biome and Immunopathophysiology (TBIP), Université de Guyane, 97300 Cayenne, France; (A.M.); (S.M.); (M.S.); (L.L.); (S.S.)
| | - Mona Saout
- Tropical Biome and Immunopathophysiology (TBIP), Université de Guyane, 97300 Cayenne, France; (A.M.); (S.M.); (M.S.); (L.L.); (S.S.)
- U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Université Lille, 59000 Lille, France
| | - Laure Laghoe
- Tropical Biome and Immunopathophysiology (TBIP), Université de Guyane, 97300 Cayenne, France; (A.M.); (S.M.); (M.S.); (L.L.); (S.S.)
- U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Université Lille, 59000 Lille, France
| | - Stéphane Simon
- Tropical Biome and Immunopathophysiology (TBIP), Université de Guyane, 97300 Cayenne, France; (A.M.); (S.M.); (M.S.); (L.L.); (S.S.)
- U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Université Lille, 59000 Lille, France
| | | | - Miguel Angel Hernandez Martinez
- Laboratoire Associé du CNR Leishmaniose, Laboratoire Hospitalo-Universitaire de Parasitologie et Mycologie, Centre Hospitalier Andrée Rosemon, 97300 Cayenne, France;
| | - Magalie Pierre Demar
- Tropical Biome and Immunopathophysiology (TBIP), Université de Guyane, 97300 Cayenne, France; (A.M.); (S.M.); (M.S.); (L.L.); (S.S.)
- U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Université Lille, 59000 Lille, France
- Laboratoire Associé du CNR Leishmaniose, Laboratoire Hospitalo-Universitaire de Parasitologie et Mycologie, Centre Hospitalier Andrée Rosemon, 97300 Cayenne, France;
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Vasilita C, Feng V, Hansen AK, Hartop E, Srivathsan A, Struijk R, Meier R. Express barcoding with NextGenPCR and MinION for species-level sorting of ecological samples. Mol Ecol Resour 2024; 24:e13922. [PMID: 38240168 DOI: 10.1111/1755-0998.13922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 03/06/2024]
Abstract
The use of DNA barcoding is well established for specimen identification and large-scale biodiversity discovery, but remains underutilized for time-sensitive applications such as rapid species discovery in field stations, identifying pests, citizen science projects, and authenticating food. The main reason is that existing express barcoding workflows are either too expensive or can only be used in very well-equipped laboratories by highly-trained staff. We here show an alternative workflow combining rapid DNA extraction with HotSHOT, amplicon production with NextGenPCR thermocyclers, and sequencing with low-cost MinION sequencers. We demonstrate the power of the approach by generating 250 barcodes for 285 specimens within 6 h including specimen identification through BLAST. The workflow required only the following major equipment that easily fits onto a lab bench: Thermocycler, NextGenPCR, microplate sealer, Qubit, and MinION. Based on our results, we argue that simplified barcoding workflows for species-level sorting are now faster, more accurate, and sufficiently cost-effective to replace traditional morpho-species sorting in many projects.
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Affiliation(s)
| | - Vivian Feng
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
- Humboldt-Universität zu Berlin, Institut für Biologie, Berlin, Germany
| | - Aslak Kappel Hansen
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Emily Hartop
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Robin Struijk
- Molecular Biology Systems B.V., Goes, The Netherlands
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
- Humboldt-Universität zu Berlin, Institut für Biologie, Berlin, Germany
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Srivathsan A, Feng V, Suárez D, Emerson B, Meier R. ONTbarcoder 2.0: rapid species discovery and identification with real-time barcoding facilitated by Oxford Nanopore R10.4. Cladistics 2024; 40:192-203. [PMID: 38041646 DOI: 10.1111/cla.12566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 12/03/2023] Open
Abstract
Most arthropod species are undescribed and hidden in specimen-rich samples that are difficult to sort to species using morphological characters. For such samples, sorting to putative species with DNA barcodes is an attractive alternative, but needs cost-effective techniques that are suitable for use in many laboratories around the world. Barcoding using the portable and inexpensive MinION sequencer produced by Oxford Nanopore Technologies (ONT) could be useful for presorting specimen-rich samples with DNA barcodes because it requires little space and is inexpensive. However, similarly important is user-friendly and reliable software for analysis of the ONT data. It is here provided in the form of ONTbarcoder 2.0 that is suitable for all commonly used operating systems and includes a Graphical User Interface (GUI). Compared with an earlier version, ONTbarcoder 2.0 has three key improvements related to the higher read quality obtained with ONT's latest flow cells (R10.4), chemistry (V14 kits) and basecalling model (super-accuracy model). First, the improved read quality of ONT's latest flow cells (R10.4) allows for the use of primers with shorter indices than those previously needed (9 bp vs. 12-13 bp). This decreases the primer cost and can potentially improve PCR success rates. Second, ONTbarcoder now delivers real-time barcoding to complement ONT's real-time sequencing. This means that the first barcodes are obtained within minutes of starting a sequencing run; i.e. flow cell use can be optimized by terminating sequencing runs when most barcodes have already been obtained. The only input needed by ONTbarcoder 2.0 is a demultiplexing sheet and sequencing data (raw or basecalled) generated by either a Mk1B or a Mk1C. Thirdly, we demonstrate that the availability of R10.4 chemistry for the low-cost Flongle flow cell is an attractive option for users who require only 200-250 barcodes at a time.
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Affiliation(s)
- Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Invalidenstraße 43, 10115, Berlin, Germany
| | - Vivian Feng
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Invalidenstraße 43, 10115, Berlin, Germany
| | - Daniel Suárez
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, 38206, Spain
- School of Doctoral and Postgraduate Studies, University of La Laguna, 38200 La Laguna, Tenerife, Canary Islands, 38200, Spain
| | - Brent Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Invalidenstraße 43, 10115, Berlin, Germany
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
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Srivathsan A, Meier R. Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing. Methods Mol Biol 2024; 2744:223-238. [PMID: 38683322 DOI: 10.1007/978-1-0716-3581-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
DNA barcodes are useful in biodiversity research, but sequencing barcodes with dye termination methods ("Sanger sequencing") has been so time-consuming and expensive that DNA barcodes are not as widely used as they should be. Fortunately, MinION sequencers from Oxford Nanopore Technologies have recently emerged as a cost-effective and efficient alternative for barcoding. MinION barcodes are now suitable for large-scale species discovery and enable specimen identification when the target species are represented in barcode databases. With a MinION, it is possible to obtain 10,000 barcodes from a single flow cell at a cost of less than 0.10 USD per specimen. Additionally, a Flongle flow cell can be used for small projects requiring up to 300 barcodes (0.50 USD per specimen). We here describe a cost-effective laboratory workflow for obtaining tagged amplicons, preparing ONT libraries, sequencing amplicon pools, and analyzing the MinION reads with the software ONTbarcoder. This workflow has been shown to yield highly accurate barcodes that are 99.99% identical to Sanger barcodes. Overall, we propose that the use of MinION for DNA barcoding is an attractive option for all researchers in need of a cost-effective and efficient solution for large-scale species discovery and specimen identification.
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Affiliation(s)
- Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany.
- Institute for Biology, Humboldt University, Berlin, Germany.
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Giusti A, Malloggi C, Magagna G, Filipello V, Armani A. Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin? A systematic review. Compr Rev Food Sci Food Saf 2024; 23:e13256. [PMID: 38284609 DOI: 10.1111/1541-4337.13256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 01/30/2024]
Abstract
Food authentication using molecular techniques is of great importance to fight food fraud. Metabarcoding, based on the next-generation sequencing (NGS) technologies, allowing large-scale taxonomic identification of complex samples via massive parallel sequencing of fragments (called DNA barcodes) simultaneously, has become increasingly popular in many scientific fields. A systematic review to answer the question "Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin?" is presented. The inclusion criteria were focused on the selection of scientific papers (SPs) only applying metabarcoding to foodstuff of animal origin collected on the market. The 23 included SPs were first analyzed with respect to the metabarcoding phases: library preparation (target genes, primer pairs, and fragment length), sequencing (NGS platforms), and final data analysis (bioinformatic pipelines). Given the importance of primer selection, the taxonomic coverage of the used primers was also evaluated. In addition, the SPs were scored based on the use of quality control measures (procedural blanks, positive controls, replicates, curated databases, and thresholds to filter the data). A lack of standardized protocols, especially with respect to the target barcode/s and the universal primer/s, and the infrequent application of the quality control measures, leads to answer that metabarcoding is not ripe enough for authenticating foodstuff of animal origin. However, the observed trend of the SP quality improvement over the years is encouraging. Concluding, a proper protocol standardization would allow a wider use of metabarcoding by both official and private laboratories, enabling this method to become the primary for the authentication of foodstuffs of animal origin.
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Affiliation(s)
- Alice Giusti
- FishLab, Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - Chiara Malloggi
- FishLab, Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - Giulia Magagna
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Virginia Filipello
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Andrea Armani
- FishLab, Department of Veterinary Sciences, University of Pisa, Pisa, Italy
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Srivathsan A, Loh RK, Ong EJ, Lee L, Ang Y, Kutty SN, Meier R. Network analysis with either Illumina or MinION reveals that detecting vertebrate species requires metabarcoding of iDNA from a diverse fly community. Mol Ecol 2023; 32:6418-6435. [PMID: 36326295 DOI: 10.1111/mec.16767] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
DNA obtained from invertebrates (iDNA) can be metabarcoded in order to survey vertebrate communities. However, little attention has been paid to the interaction between the invertebrate and vertebrate species. Here, we tested for specialization by sampling the dung and carrion fly community of a swamp forest remnant along a disturbance gradient (10 sites: 80-310 m from a road). Approximately, 60% of the baited 407 flies yielded 294 vertebrate identifications based on two COI fragments and 16S. A bipartite network analysis found no statistically significant specialization in the interactions between fly and vertebrate species, but uncommon fly species can carry the signal for vertebrate species that are otherwise difficult to detect with iDNA. A spatial analysis revealed that most of the 20 vertebrate species reported in this study could be detected within 150 m of the road (18 spp.) and that the fly community sourced for iDNA was unexpectedly rich (24 species, 3 families). They carried DNA for rare and common species inhabiting different layers of the forest (ground-dwelling: wild boar, Sunda pangolin, skinks, rats; arboreal: long-tailed macaque, Raffles' banded langur; flying: pin-striped tit-babbler, olive-winged bulbul). All our results were obtained with a new, greatly simplified iDNA protocol that eliminates DNA extraction by obtaining template directly through dissolving fly faeces and regurgitates with water. Lastly, we show that MinION- and Illumina-based metabarcoding yield similar results. We conclude by urging more studies that use different baits and involve experiments that are capable of revealing the dispersal capabilities of the flies carrying the iDNA.
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Affiliation(s)
- Amrita Srivathsan
- Centre for Integrative Biodiversity Discovery, Museum für Naturkunde, Berlin, Germany
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rebecca Ker Loh
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Elliott James Ong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Leshon Lee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yuchen Ang
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | | | - Rudolf Meier
- Centre for Integrative Biodiversity Discovery, Museum für Naturkunde, Berlin, Germany
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Goymer A, Steele K, Jenkins F, Burgess G, Andrews L, Baumgartner N, Gubili C, Griffiths AM. For R-eel?! Investigating international sales of critically endangered species in freshwater eel products with DNA barcoding. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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Socorro TR, Joran V, Sofie D. Evaluation of DNA metabarcoding using Oxford Nanopore sequencing for authentication of mixed seafood products. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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De Vivo M, Lee HH, Huang YS, Dreyer N, Fong CL, de Mattos FMG, Jain D, Wen YHV, Mwihaki JK, Wang TY, Machida RJ, Wang J, Chan BKK, Tsai IJ. Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum. Sci Rep 2022; 12:9973. [PMID: 35705661 PMCID: PMC9200733 DOI: 10.1038/s41598-022-14121-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing of six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course. The students were able to produce mitogenomes from sampling to annotation using existing protocols and programs. Approximately 4 Gb of sequence was produced from 16 Flongle and one MinION flow cells, averaging 235 Mb and N50 = 4.4 kb per flow cell. Five of the six 14.1-18 kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing revealed that the ONT assemblies spanned over highly AT rich sequences in the control region that were otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8-346.7 bp under the fast mode basecalling with the majority occurring at homopolymer regions. Our findings suggest that the portable MinION device can be used to rapidly produce low-cost mitogenomes onsite and tailored to genomics-based training in biodiversity research.
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Affiliation(s)
- Mattia De Vivo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei, Taiwan
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Yu-Sin Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Niklas Dreyer
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Natural History Museum of Denmark, University of Copenhagen, Faculty of Science, Copenhagen, Denmark
| | - Chia-Ling Fong
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Felipe Monteiro Gomes de Mattos
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Dharmesh Jain
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, Taiwan
| | - Yung-Hui Victoria Wen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
| | - John Karichu Mwihaki
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Benny K K Chan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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12
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Egeter B, Veríssimo J, Lopes-Lima M, Chaves C, Pinto J, Riccardi N, Beja P, Fonseca NA. Speeding up the detection of invasive bivalve species using environmental DNA: a Nanopore and Illumina sequencing comparison. Mol Ecol Resour 2022; 22:2232-2247. [PMID: 35305077 DOI: 10.1111/1755-0998.13610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 02/09/2022] [Accepted: 03/02/2022] [Indexed: 11/30/2022]
Abstract
Traditional detection of aquatic invasive species via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools (msi package) to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves while comparing it with Illumina-based sequencing. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. Samples were extracted, amplified, and sequenced by the two platforms. The mean agreement between sequencing methods was 69% and the difference between methods was non-significant. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples.
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Affiliation(s)
- Bastian Egeter
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,NatureMetrics, Bakeham Lane, Egham, Surrey, TW20 9TY, U.K
| | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Manuel Lopes-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,IUCN SSC Mollusc Specialist Group, c/o 219 Huntingdon Road, Cambridge, CB3 0DL, U.K
| | - Cátia Chaves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Joana Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | | | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,CIBIO/InBIO, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Nuno A Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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Piredda R, Mottola A, Cipriano G, Carlucci R, Ciccarese G, Di Pinto A. Next Generation Sequencing (NGS) approach applied to species identification in mixed processed seafood products. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108590] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Nijman V, Stein FM. Meta-analyses of molecular seafood studies identify the global distribution of legal and illegal trade in CITES-regulated European eels. Curr Res Food Sci 2022; 5:191-195. [PMID: 35106483 PMCID: PMC8784285 DOI: 10.1016/j.crfs.2022.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/29/2021] [Accepted: 01/09/2022] [Indexed: 11/28/2022] Open
Abstract
Authentication of seafood products by means of molecular techniques has relevance for food sustainability and security, as well as international trade regulation, linked to transparency in food manufacturing. We focus on the molecular detection of the depleted European eel Anguilla anguilla, a species for which strict international trade regulations are in place since 2010, in studies conducted outside Europe. We found thirteen studies from nine countries (Canada, China, Japan, Malaysia, Peru, Singapore, South Korea, Taiwan, and USA) for which, on average, 59 ± 28% of the 330 sequenced eel samples comprised European eel. Only China, Japan, South Korea, and USA reported the import of European eel in the years prior to sampling. The authentication of eel products demonstrates a global, in part illegal, trade in European eel, covered up by incomplete or fraudulent labelling. This calls into question the compliance with existing national and international trade regulations and its implications for food safety and sustainability. Existing seafood studies enable meta-analysis, identifying global distribution. Observed distribution of European eel is not evident in trade statistics. Regulations are insufficiently enforced, impacting food sustainability and security.
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Affiliation(s)
- Vincent Nijman
- Oxford Wildlife Trade Research Group, School of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Florian Martin Stein
- Oxford Wildlife Trade Research Group, School of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Institut für Geoökologie, Technische Universität Braunschweig, Langer Kamp 19c, Braunschweig, DE, 38106, Germany
- Corresponding author. Oxford Wildlife Trade Research Group, School of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK.
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15
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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]
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16
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Xing RR, Hu RR, Wang N, Zhang JK, Ge YQ, Chen Y. Authentication of sea cucumber products using NGS-based DNA mini-barcoding. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Srivathsan A, Lee L, Katoh K, Hartop E, Kutty SN, Wong J, Yeo D, Meier R. ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biol 2021; 19:217. [PMID: 34587965 PMCID: PMC8479912 DOI: 10.1186/s12915-021-01141-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, and allows fast turnaround from specimen to sequence by using the portable MinION sequencer. RESULTS We describe how tagged amplicons can be obtained and sequenced with the real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for > 10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (> 99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018. CONCLUSIONS We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.
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Affiliation(s)
- Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Leshon Lee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kazutaka Katoh
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Artificial Intelligence Research Center, AIST, Tokyo, Japan
| | - Emily Hartop
- Zoology Department, Stockholms Universitet, Stockholm, Sweden
- Station Linné, Öland, Sweden
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Johnathan Wong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Berlin, Germany.
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Cutler Ii WD, Bradshaw AJ, Dentinger BTM. What's for dinner this time?: DNA authentication of "wild mushrooms" in food products sold in the USA. PeerJ 2021; 9:e11747. [PMID: 34414024 PMCID: PMC8340906 DOI: 10.7717/peerj.11747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 06/19/2021] [Indexed: 12/30/2022] Open
Abstract
Mushrooms have been consumed by humans for thousands of years, and while some have gastronomic and nutritional value, it has long been recognized that only select species of mushrooms are suitable for consumption. Adverse health effects of consuming poisonous mushrooms range from mild illness to death. Many valuable edible mushrooms are either impractical or unable to be grown commercially, requiring them to be harvested from the wild. In the U.S., products containing these wild-collected mushrooms are often sold with the nonspecific and undefined label “wild mushrooms,” although in some cases particular species are listed in the ingredients. However, the ambiguity of the definition of “wild mushrooms” in foods makes it impossible to know which species are involved or whether they are truly wild-collected or cultivated varieties. As a consequence, any individual adverse reactions to consuming the mushrooms in these products cannot be traced to the source due to the minimal regulations around the harvest and sale of wild mushrooms. For this study, we set out to shed light on what species of fungi are being sold as “wild mushrooms” using DNA metabarcoding to identify fungal contents of various food products acquired from locally sourced grocers and a large online retail site. Twenty-eight species of mushroom were identified across 16 food products, ranging from commonly cultivated species to wild species not represented in global DNA databases. Our results demonstrate that “wild mushroom” ingredients often consist entirely or in part of cultivated species such as the ubiquitous white and brown “button” mushrooms and portabella (Agaricus bisporus), oyster (Pleurotus spp.) and shiitake (Lentinula edodes). In other cases truly wild mushrooms were detected but they were not always consistent with the species on the label. More alarmingly, a few products with large distribution potential contained species whose edibility is at best dubious, and at worst potentially toxic.
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Affiliation(s)
- W Dalley Cutler Ii
- Natural History Museum of Utah & School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
| | - Alexander J Bradshaw
- Natural History Museum of Utah & School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
| | - Bryn T M Dentinger
- Natural History Museum of Utah & School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
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19
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Nanopores: a versatile tool to study protein dynamics. Essays Biochem 2021; 65:93-107. [PMID: 33296461 DOI: 10.1042/ebc20200020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022]
Abstract
Proteins are the active workhorses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now readily available, observing the functional cycle of proteins - involving conformational changes and interactions - remains very challenging, e.g., due to ensemble averaging. However, time-resolved information is crucial to gain a mechanistic understanding of protein function. Single-molecule techniques such as FRET and force spectroscopies provide answers but can be limited by the required labelling, a narrow time bandwidth, and more. Here, we describe electrical nanopore detection as a tool for probing protein dynamics. With a time bandwidth ranging from microseconds to hours, nanopore experiments cover an exceptionally wide range of timescales that is very relevant for protein function. First, we discuss the working principle of label-free nanopore experiments, various pore designs, instrumentation, and the characteristics of nanopore signals. In the second part, we review a few nanopore experiments that solved research questions in protein science, and we compare nanopores to other single-molecule techniques. We hope to make electrical nanopore sensing more accessible to the biochemical community, and to inspire new creative solutions to resolve a variety of protein dynamics - one molecule at a time.
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Chang JJM, Ip YCA, Ng CSL, Huang D. Takeaways from Mobile DNA Barcoding with BentoLab and MinION. Genes (Basel) 2020; 11:E1121. [PMID: 32987804 PMCID: PMC7598690 DOI: 10.3390/genes11101121] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters' Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50-60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended.
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Affiliation(s)
- Jia Jin Marc Chang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
| | - Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
| | - Chin Soon Lionel Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
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