Miss Anya Kardailsky1, Mr Benjamin Durán -Vinet2, OceanOmics division1, Dr Gert-Jan Jeunen3, Dr Allison K. Miller2, Dr Philipp E. Bayer1,4
1Minderoo Foundation, Perth, Australia, 2Anatomy Department, The University of Otago, Dunedin, New Zealand, 3Marine Science Department, The University of Otago, Dunedin, New Zealand, 4UWA Oceans Institute, The University of Western Australia, Perth, Australia
Biography:
Anya Kardailsky is a Research Analyst at the Minderoo Foundation in Perth, Australia, where she specialises in advancing aquatic monitoring techniques using CRISPR-Cas technologies and Oxford Nanopore sequencing. Her work builds on her Master’s research at the University of Otago, New Zealand, where she investigated CRISPR-Cas enrichment for environmental DNA (eDNA) analysis in freshwater ecosystems. Anya’s expertise spans molecular techniques, bioinformatics, and machine learning, with a keen focus on improving environmental monitoring methods.
Abstract:
Environmental DNA (eDNA) biomonitoring faces challenges due to biases towards certain species and the low taxonomic resolution of current metabarcoding approaches. Broader methods, such as short- and long read-based shotgun metagenomics, adaptive sampling, and CRISPR-Cas based upsampling or downsampling methods offer alternative venues.
In this talk, we will present findings from comparing five approaches to eDNA using the same eDNA samples aimed at improving eDNA sequencing efficiency and coverage for marine vertebrates. We explored: 1) metabarcoding using 12S and 16S assays targeting fish DNA; 2) shotgun sequencing using the Illumina NovaSeq platform; 3) CRISPR-Cas based depletion of common species from marine eDNA samples; 4) long-read shotgun sequencing using the Oxford Nanopore Technologies (ONT) PromethION platform; 5) adaptive sampling on the ONT platform removing common species.
We discuss read phenotypes and compare species-level accuracy and comprehensiveness across these technologies. Preliminary analysis of these results indicates promise in ONT’s adaptive sampling and CRISPR-Cas methods for improving target vertebrate coverage, though each approach offers potential for advancing eDNA monitoring.