A universal coral-specific ITS2 primer set for eDNA-based coral diversity monitoring

Monitoring coral diversity is critical for assessing biodiversity trajectories and understanding the impacts of environmental change on reef ecosystems. Environmental DNA (eDNA) has emerged as a powerful tool for non-invasive biodiversity assessments, enabling the detection of diverse taxa through molecular techniques. The ribosomal ITS2 region is well suited for coral diversity studies owing to its high interspecific and intraspecific variability, which supports fine-scale taxonomic discrimination. However, the effectiveness of eDNA-based approaches hinges on the development of primers that are both universal, enabling amplification across a broad range of coral taxa, and specific, thereby minimizing non-target amplification. Here, we present a novel coral-specific ITS2 primer set (amplicon size: ca. 450 bp) designed for PCR amplification and subsequent Illumina-sequencing of the ITS2 region. The primer set was tested across diverse coral and non-coral taxa to evaluate its performance in terms of specificity and universality. This study demonstrates the utility of the primer set for eDNA-based coral monitoring, warranting the development of a comprehensive coral ITS2 reference dataset to enable reliable detection of coral taxonomic signatures from eDNA, advancing biodiversity research and conservation in coral reef ecosystems.

If you use these primers, please cite us :)

Colin, L., Mayer, K.-I., & Voolstra, C. R. (2026). A universal coral-specific ITS2 primer set for eDNA-based coral diversity monitoring. Zenodo. https://doi.org/10.5281/zenodo.18432041

Changes in v1.1: added primer sequences for the intermediate primer set.