MinION sequencing of seafood in Singapore reveals creatively labelled flatfishes, confused roe, pig DNA in squid balls, and phantom crustaceans

Abstract

Food mislabelling is a growing world-wide problem that is increasingly addressed through the authentication of ingredients via techniques like mass spectrometry or DNAsequencing. However, traditional DNA sequencing methods are slow, expensive, and require well-equipped laboratories. We here test whether these problems can be overcome through the use of Nanopore sequencing. We sequenced 92 single and 13 mixed-species samples bought in supermarkets and restaurants in Singapore which has a large and diverse seafood trade. We successfully obtained DNA barcodes for 94% and 100% of the single-and mixed-species products after correcting the numerous sequencing errors of MinION reads with a correction pipeline optimized for DNA barcodes. We find comparatively low levels of clear-cut mislabelling for single-species samples (7.6 %) while the rates are higher for mixed-species samples (38.5 %). These low rates are somewhat deceptive, however, because of the widespread use of vague common species names that do not allow for a precise assessment of the expected ingredients. With regard to the clearly mislabelled single-species products, higher-value products (e.g., prawn roe, wild-caught Atlantic salmon, halibut) are replaced with lowervalue ingredients (e.g., fish roe, Pacific salmon, arrowtooth flounder) while more serious problems are observed for mixed-species samples. Cuttlefish and prawn balls repeatedly contained pig DNA and 100% of all mixed samples labelled as containing crustaceans ('crab', 'prawn', 'lobster') only yielded fish barcodes. We conclude that there is a need for more regular testing of seafood samples and suggest that due to speed and low-cost, MinION would be a good instrument for this purpose. We also emphasize the need for developing clearer labelling guidelines..

Seeking life in sedimented waters: Environmental DNA from diverse habitat types reveals ecologically significant species in a tropical marine environment

“…We thus selected the 3% threshold for collapsing sequence haplotypes into MOTUs. This was in agreement with stability thresholds applied in previous studies (Baloğlu et al, 2018;Ho et al, 2020;Yeo et al, 2018).…”

Diversity and origins of giant guitarfish and wedgefish products in Singapore

“…GenBank and BOLD) are very likely to yield informative matches (Meusnier et al, 2008;Appleyard et al, 2018;Wannell et al, 2020). Though DNA degradation during processing of food products may limit recovery of full-length barcodes, sequencing shorter fragments, or mini-barcoding (Shokralla et al, 2015), has been shown to be effective in identifying species in various types of preserved and processed meats (Hellberg, Hernandez & Hernandez, 2017;Ho et al, 2020).…”

“…In addition, 'shovelnose ray' refers to other species of guitarfishes belonging in the genus Aptychotrema but has been applied on fresh fillets identified here as R. australiae. As unremarkable as it may seem, labelling is an important issue that has direct impacts on consumers' health and their ethical and religious beliefs, especially in the context of Singapore's multicultural and multi-religious society (Ho et al, 2020).…”

“…To increase the throughput and accuracy of these processes, robust sampling and test kits that can handle numerous samples should be utilized as soon as they are available and effective for customs surveillance of trade in endangered species. With rapid, affordable, and high-capacity DNA sequencing tools such as MinION (Oxford Nanopore Technologies; Johri et al, 2019;Chang et al, 2020a;Chang et al, 2020b), large volumes (up to 1,000) of mixed-species products can be analysed in one flow cell at the low cost of <US$10 per sample (Ho et al, 2020).…”

“…However, fillets and fins in dried and cooked forms and when packaged with other meats are generally impossible to visually identify to species (Moore, 2017). Indeed, mislabelling of products is a well-known issue in the elasmobranch trade globally (Almerón-Souza et al, 2018;Wainwright et al, 2018;Pazartzi et al, 2019), with many instances where products are vaguely labelled in order to meet loose labelling regulations (Donlan & Luque, 2013;Ho et al, 2020). Inappropriate labelling impacts the sustainability of elasmobranch populations, as sales of at-risk species are obscured even if they are protected under existing trade regulations.…”