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bioRxiv · 10.1101/2025.09.11.675722

Multigenerational Tracking of Reef-Building Corals Using CRISPR-Cas9induced Genetic Barcodes and eDNA Metabarcoding

Moonier, M. M.·Bay, L. K.·Sato, Y.·Mocellin, V.·Cleves, P.·Lister, R.·Thomas, L.
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Abstract

Widespread biodiversity loss driven by human activity has intensified global efforts to restore degraded ecosystems. Yet a key challenge remains: how to track restored individuals and their offspring over time and space to assess the true impact of restoration? This is especially pressing for coral reefs, which support a quarter of all marine species, are in severe decline globally, and are now the focus of growing restoration initiatives worldwide. Here, we demonstrate a novel approach that combines genome editing and environmental DNA (eDNA) monitoring to enable scalable, non-invasive tracking of individual corals and their offspring. Using CRISPR-Cas9, we introduced unique genetic barcodes into non-coding regions of the Acropora millepora genome. These barcodes - stable, heritable, and distributed across the genome - will allow for individual-level identification over multiple generations. We show that these barcodes can be reliably detected in surrounding seawater using eDNA metabarcoding, offering a powerful, non-destructive tool for tracking corals in situ. Together, this approach provides a proof-of-concept for precision monitoring of restoration outcomes, with broad applicability across species and ecosystems.

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Moonier, M. M., Bay, L. K., Sato, Y., Mocellin, V., Cleves, P., Lister, R., Thomas, L.. 2025-09-12. Multigenerational Tracking of Reef-Building Corals Using CRISPR-Cas9induced Genetic Barcodes and eDNA Metabarcoding. https://doi.org/10.1101/2025.09.11.675722

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