Nanopore sequencing facilitates screening of diversity and provenance of seafood and marine wildlife

Abstract

The soaring global demand for seafood has placed unprecedented pressure on fisheries, leading to the exploitation of vulnerable marine resources and data-deficient species. Over the past few decades, a surge of molecular methods has enabled identification of traded marine animal products that may be otherwise unrecognizable through morphological analysis. While universal DNA barcoding remains a powerful authentication and traceability tool, its application still requires lengthy procedures, established facilities, and assay development. In this study, we explored some of the uses and advantages of cutting-edge nanopore sequencing, a rapid and portable alternative method. We first tested the method to identify ten opportunistically sampled fishery products obtained in two different contexts: five fish fillets marketed in the UK, four shark specimens traded in Indonesia and one fish collected as part of a scientific survey. We present a full analytical workflow to produce accurate species identification based on direct, PCR-free long-read sequencing of the DNA extracted from each specimen. We then used the nanopore sequencing output to mine whole mitogenomes from samples of varying DNA quality. Finally, we used the extensive additional genomic information produced by the sequencing to pinpoint the geographic origin of two of the identified specimens for which robust baseline data existed. In the face of increasing threats to biodiversity, and the need to control exploitation and supply of fisheries and wildlife globally, this rapid and portable approach is poised to revolutionize the monitoring of seafood supply and the trade in endangered marine wildlife, contributing to the sustainable management of aquatic resources.