A study conducted by Hinano Mizuno et al. has been published in the Methods in Ecology and Evolution.
Environmental DNA (eDNA) has emerged as a powerful tool for monitoring aquatic biodiversity without capturing organisms. In conservation and aquaculture, there is an increasing demand to assess genetic variation at the individual level. However, conventional eDNA approaches typically rely on short DNA fragments, limiting their ability to distinguish closely related species or resolve genetic variation at the individual level.
In this study, we developed a method to reconstruct complete mitochondrial genomes from aquatic eDNA using long-read sequencing (LRS). By optimizing filtration pore size and DNA extraction methods, we successfully recovered long DNA fragments exceeding 16 kb. Notably, full-length mitogenomes were reconstructed even from PCR-free datasets, reducing biases introduced during PCR amplification and demonstrating the feasibility of direct sequencing of native eDNA. We further showed that comparing reconstructed sequences enables the detection of genetic variation within the same species. This highlights the potential of eDNA-based approaches for high-resolution genetic analysis beyond species detection. This non-invasive technique opens new possibilities for genetic monitoring in conservation and aquaculture, enabling the assessment of genetic variation at the individual level without handling organisms. In the future, it could support applications in natural ecosystems to study population structure and biodiversity with unprecedented detail.
Title: Non-invasive Reconstruction of Complete Mitochondrial Genomes from Aquatic Environmental DNA Using PCR-free Long-read Sequencing
Authors: Mizuno, H., Tanaka, H., Furuta, Y., Muramoto, N.
Journal Name: Methods in Ecology and Evolution
Published: January 1, 2026
https://doi.org/10.1111/2041-210x.70209