Establishing a DNA reference library for the identification of elasmobranchs in the Indian Ocean using Oxford Nanopore Sequencing

Abstract

Elasmobranchs, comprising sharks and rays, are among the most threatened species globally. The first elasmobranchs were added to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) in 2002. Since then, the number of species listed has increased to 151, highlighting the urgent conservation challenges faced by these species. In Sri Lanka, where over 100 species have been recorded, the demand for elasmobranch products drives significant export and import activities, complicating conservation efforts. Accurate species identification is crucial for fisheries monitoring, trade regulation, and conservation management. However, relying solely on morphological characteristics is challenging, especially since key identifying features are unavailable in certain derivatives like meat and oil in market samples. This study aims to develop a robust DNA reference library for elasmobranch species in Sri Lanka and to showcase the application of Oxford Nanopore Technology (ONT) as a reliable tool for fisheries monitoring and conservation. Using DNA barcoding and ONT sequencing, we analysed 49 elasmobranch species, focusing on the Cytochrome Oxidase I (COI) and 12S ribosomal ribonucleic acid (rRNA) genes to develop a DNA reference library. The creation of reliable barcode reference libraries is essential for effective species identification in biomonitoring because it facilitates the assessment of population trends and the effectiveness of fishing and trade regulations. We conducted a phylogenetic analysis to assess the robustness of reference sequences in species discrimination. All DNA reference sequences are publicly accessible through GenBank. This study enhances the capacity to monitor and regulate the elasmobranch trade in Sri Lanka and beyond.