Recent Advances in Closed-Tube Barcoding for FastFish-ID.
Closed-Tube Barcoding
FastFish-ID
Fluorescent Signature
Interdiction of IUU Fishing
Intraspecies Variants
Portable Barcoding Platform
Seafood Fraud
Species Identification
Synthetic Reference Target DNA
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2024
2024
Historique:
medline:
29
4
2024
pubmed:
29
4
2024
entrez:
29
4
2024
Statut:
ppublish
Résumé
FastFish-ID for rapid and accurate identification of fish species was conceived at Brandeis University based on pioneering work on Closed-Tube Barcoding (Rice et al., Mitochondrial DNA Part A 27(2):1358-1363, 2016; Sirianni et al., Genome 59:1049-1061, 2016). FastFish-ID was subsequently validated and commercialized at Thermagenix, Inc. using a portable device and high-precision PCR (Naaum et al., Food Res Int 141:110035, 2021). The motivation for these efforts was the pressing need for a technology that could be widely used throughout the seafood supply chain to combat IUU Fishing (Helyar et al., PLOS ONE 9, 2014) and overfishing (FAO, State of the World Fisheries and Aquaculture 2018. http://www.fao.org/documents/card/en/c/I9540EN/ , 2018), along with seafood fraud and mislabeling (Watson et al., Fish Fish 17:585-595, 2015). These destructive practices are wasting fish stocks, frustrating attempts to achieve seafood sustainability, endangering oceanic ecosystems, and causing consumers billions of dollars each year (Porterfield et al., Oceana: February, 2022). During the past three Covid19 pandemic years, EcologeniX, LLC has taken over further development and optimization of FastFish-ID. The present chapter provides an overview of the improvements introduced throughout the FastFish-ID process.
Identifiants
pubmed: 38683325
doi: 10.1007/978-1-0716-3581-0_17
doi:
Substances chimiques
DNA, Mitochondrial
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
267-278Informations de copyright
© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Rice LM, Reis AH Jr, Wangh LJ (2016) Virtual Barcoding using LATE-PCR and Lights-on/Lights-off probes: identification of nematode species in a closed-tube reaction. Mitochondrial DNA Part A 27(2):1358–1363
doi: 10.3109/19401736.2014.947581
Sirianni NM, Yuan H, Rice JE, Kaufman RS et al (2016) Closed-tube barcoding. Genome 59:1049–1061. https://doi.org/10.1139/gen-2016-0026
doi: 10.1139/gen-2016-0026
pubmed: 27809602
Naaum AM, Cusa M, Singh M, Bleicher Z et al (2021) Validation of FASTFISH-ID: A new commercial platform for rapid fish species authentication via universal closed-tube barcoding. Food Res Int 141:110035. https://doi.org/10.1016/j.foodres.2020.110035
doi: 10.1016/j.foodres.2020.110035
pubmed: 33641956
Helyar SJ, Lloyd HD, de Bruyn M, Leake J, Bennett N et al (2014) Fish product mislabelling: failings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU) fishing. PLoS One 9(6):e98691. https://doi.org/10.1371/journal.pone.0098691
doi: 10.1371/journal.pone.0098691
pubmed: 24921655
pmcid: 4055496
FAO (2018) State of the World Fisheries and Aquaculture 2018. http://www.fao.org/documents/card/en/c/I9540EN/
Watson RA, Green BS, Tracey SR et al (2015) Provenance of global seafood. Fish Fish 17:585–595. https://doi.org/10.1111/faf.12129
doi: 10.1111/faf.12129
Porterfield E, Valentine M, Mustain P, Lowell B (2022) Loopholes put illegally caught seafood on Americans’ plates. Oceana: February 2022, https://doi.org/10.5281/zenodo.6014994
Sanchez JA, Pierce KE, Rice JE, Wangh LJ (2004) Linear-after-the-exponential (LATE)-PCR: an advanced method of asymmetric PCR and its uses in quantitative real-time analysis. Proc Natl Acad Sci U S A 101:1933–1938
doi: 10.1073/pnas.0305476101
pubmed: 14769930
pmcid: 357030
Pierce KE, Sanchez JA, Rice JE, Wangh LJ (2005) Linear-After-The-Exponential (LATE)-PCR: primer design criteria for high yields of specific single-stranded DNA and improved real-time detection. Proc Natl Acad Sci U S A 102:8609–8614
doi: 10.1073/pnas.0501946102
pubmed: 15937116
pmcid: 1150831
Rice JE, Reis AH Jr, Rice LM, Carver-Brown RK, Wangh LJ (2012) Fluorescent signatures for variable DNA sequences. Nucleic Acids Res 40(21):e164
doi: 10.1093/nar/gks731
pubmed: 22879378
pmcid: 3505974
Handy SM, Deeds JR, Ivanova NV, Hebert PD et al (2011) A single laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance. J AOAC Int 94:201–210
doi: 10.1093/jaoac/94.1.201
pubmed: 21391497
Ratnasingham S, Hebert PD (2007) BOLD: the barcode of life data system. Mol Ecol Notes 7:355–364
doi: 10.1111/j.1471-8286.2007.01678.x
pubmed: 18784790
pmcid: 1890991
Chakraborty M, Dhar B, Ghosh SK (2017) Design of character-based DNA barcode motif for species identification: a computational approach and its validation in fishes. Mol Ecol Resour 17:1359–1370
doi: 10.1111/1755-0998.12671
pubmed: 28332322
Shokralla S, Hellberg RS, Handy SM et al (2015) DNA mini-barcoding system for authentication of processed fish products. Sci Rep 5:1589. https://doi.org/10.1038/srep15894
doi: 10.1038/srep15894
Sultana S, Ali ME, Hossain MAM, Asing NN, Zaidul ISM (2018) Universal mini COI barcode for the identification of fish species in processed products. Food Res Int 105:19–28
doi: 10.1016/j.foodres.2017.10.065
pubmed: 29433207
Larsson A (2014) AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30:3276–3278
doi: 10.1093/bioinformatics/btu531
pubmed: 25095880
pmcid: 4221126
Tetrault SM, Rice JE, Wangh LJ, Sanchez JA (2014) Single-tube mutation scanning of the epidermal growth factor receptor gene using multiplex LATE-PCR and Lights-On/Lights-Off probes. J Mol Biomark Diagn 5(3):1000175. https://doi.org/10.4172/2155-9929.1000175
doi: 10.4172/2155-9929.1000175
pubmed: 25411647
pmcid: 4234171
Boyd CE, McNevin AA, Davis RP (2022) The contribution of fisheries and aquaculture to the global protein. Supply Food Security 14:805–827. https://doi.org/10.1007/s12571-021-01246-9
doi: 10.1007/s12571-021-01246-9
pubmed: 35075379
Myers SL, Chang A, Watkins D, Fu C (2022) How China targets the global fish supply. New York Times, September 26. https://www.nytimes.com/interactive/2022/09/26/world/asia/china-fishing-south-america.html
Godfrey M (2021) Major seafood players alleged to be connected to IUU fishing in Planet Tracker report. SeafoodSource December 8
Goodman J (2022) Chinese fishing vessels involved in standoff with US Coast Guard on the high seas. SeafoodSource, November 3
Dean S, Goillandeau M (2021) UK PM calls French threats in fishing dispute “completely unjustified” in meeting with EU president. CNN 11:15 a.m. ET, October 30
Bryce E (2022) Millions of tonnes of dead animals: the growing scandal of fish waste. The Guardian: Mon 9 May 01.15 EDT
Blank C (2022) US seafood inflation outpaces record grocery inflation. SeafoodSource, August 12
Cawthorn D, Baillie C, Mariani S (2018) Generic names and mislabeling conceal high species diversity in global fisheries markets. Conserv Lett 11:e12573. https://doi.org/10.1111/conl.12573
doi: 10.1111/conl.12573
Desrochers E (2022) Conclusion of CITES leads to new protection of sharks and guitarfishes. SeafoodSource, December 1
Prasetyo AP, Cusa M, Murray JM et al (2023) Universal closed-tube barcoding for 1 monitoring the shark and ray trade in megadiverse conservation hotspots. bioRxiv preprint. https://doi.org/10.1101/2022.11.30.518468
Schiller H, Deng J, Lai E, Fulton C, Wangh LJ (2017) Closed-Tube DNA Barcoding analysis of the species and global distribution of Naegleria: a worldwide genus of single-celled amoeboflagellates. Genome 60(11):994–995
Carver-Brown RK, Reis AH Jr, Rice LM et al (2012) Design and construction of a single-tube, LATE-PCR, multiplex endpoint assay with Lights-On/Lights-Off probes for the detection of pathogens associated with sepsis. J Pathogens 2012:424808. https://doi.org/10.1155/2012/424808
doi: 10.1155/2012/424808
Whitfield MG, Marras SAE, Warren RM et al (2020) Rapid pyrazinamide drug susceptibility testing using a closed-tube PCR assay of the entire pncA gene. Sci Rep 10:4234. https://doi.org/10.1038/s41598-020-61286-7
doi: 10.1038/s41598-020-61286-7
pubmed: 32144379
pmcid: 7060184