Species Identification of Caviar Using ONT Sequencing—A Case Study

The high commercial value and the increasing demand for caviar make it susceptible to illegal trade and fraudulent activities, while mislabelling can occur both deliberately and unintentionally. Therefore, reliable methods are urgently needed to distinguish even closely related sturgeon species for the authentication of declared species in caviar products. In this study, we explore the effectiveness of ONT sequencing combined with nanopore adaptive sampling (NAS) to recover mitochondrial genomes from genomic DNA extracted from two caviar samples. NAS yielded similar percentages of mitochondrial reads as sequencing experiments without using the NAS option. However, NAS substantially increased the percentage of bases that could be mapped against a mitochondrial reference genome, demonstrating its effectiveness in enriching ONT sequencing data for mitochondrial sequences. The percentage of mapped mitochondrial reads varied between two samples in our sequencing experiments, ranging between 2.37% and 10.46%, which is exceptionally high compared to previous studies focusing on the recovery of mitochondrial genomes from genomic DNA. This increase may be attributed to the extraction of genomic DNA from individual fish eggs. To determine the taxonomic identities of the two caviar samples, a phylogenetic analysis was performed that included all available acipenseriform mitochondrial genomes from GenBank, as well as the newly recovered mitochondrial genomes. During this process, four problematic mitochondrial genomes obtained from GenBank were identified, which were characterized by either suggestively low sequence quality, chimeric sequence information, or potential misidentification. This underscores the need for reviewing sequencing data before database submission to avoid negative impacts on research and DNA-based species authentication.