Miss Maddalena Tibone1,2, Dr. Sergio Stefanni2, Dr. Jacopo Aguzzi2,3, Dr. Bernadette O’Neill1, Dr. Luca Mirimin1,2
1Marine and Freshwater Research Centre, Atlantic Technological University, Galway, Ireland, 2Stazione Zoologica Anton Dohrn, Napoli, Italy, 3Marine Science Institute, ICM-CSIC, Barcelona, Spain
Biography:
Maddalena Tibone is a PhD student at Atlantic Technological University in Galway (Ireland) and holds an international master’s degree in marine Biological Resources. Her project focuses on the coupling of optoacoustic technologies and environmental DNA analysis to develop and implement augmented assessment approaches in support to marine biodiversity conservation efforts and fisheries surveys. Maddalena has participated in five oceanographic/fisheries surveys, during which she was in charge of the collection and processing of environmental DNA samples. She has been awarded, as principal investigator, two trans-national access grants to conduct projects at the Acqua Alta platform in the Northern Adriatic Sea. Lastly, she has participated in four national and international conferences/symposiums during her PhD to disseminate her research findings.
Abstract:
Environmental DNA (eDNA) metabarcoding is a molecular technique that has been increasingly used to study marine fish communities. Recent technological advances have produced portable high-throughput sequencers (i.e. Oxford Nanopore devices) that allow cost-effective and rapid sample processing. The lower quality outputs of Nanopore sequencing, compared to established sequencing platforms (i.e. Illumina), and the scarce bioinformatic pipelines available, are limiting its widespread use. This study aimed to compare the quality, costs, rapidity and taxonomic resolution of Nanopore and Illumina sequencing. In addition, two marker genes were compared to assess target group amplification and benefits of a multi-marker approach.
We used mesocosm and field eDNA samples, together with mock communities of fish genomic DNA, to compare Illumina and Nanopore sequencing, using 12S ribosomal RNA and Cytochrome Oxidase subunit I (COI) mitochondrial genes. For each marker, a short fragment of 170-320 bp was targeted for Illumina, and a long fragment of 650 bp was targeted for Nanopore, with the long fragments encompassing the short ones.
Results showed comparable throughput and costs for the two platforms, with consistently lower quality scores but remarkably shorter processing time for Nanopore sequencing. The 12S markers were more taxon-specific in amplifying fish DNA compared to COI markers and produced a more accurate profile of the mock community across sequencing platforms. In addition, a multi-marker approach increased species richness in most samples compared to individual markers. Overall, this study will be highly informative for eDNA metabarcoding research, paving the route towards onsite eDNA analysis tools for augmented ecological monitoring.