How does the efficiency of Nanopore compare to Illumina sequencing in tracking the spread of aquatic invasive species?
Abstract
eDNA-based methods offer a non-invasive, easy-to-use approach for monitoring aquatic biodiversity, particularly for tracking invasive or cryptic species. While Illumina sequencing is commonly used, few studies have explored pairing eDNA sampling with Nanopore sequencing, a third-generation technology that allows for on-site sequencing but with a higher error rate. Here, we compared the performance of both technologies in detecting the invasive host-parasite complex Pseudorasbora parva-Sphaerothecum destruens. Water samples were collected from sites in Camargue and Corsica (Southern France), followed by DNA extraction, PCR amplification, and sequencing using either Illumina or Nanopore. Both technologies showed similar detection rates of P. parva, but only when Nanopore sequencing was performed under optimal conditions. However, for S. destruens, results varied: Illumina failed to detect the parasite, while Nanopore identified its DNA in multiple sites. We suggest that this discrepancy may be due to the different bioinformatic approaches used to process the reads and/or the higher error rate of Nanopore sequencing which could result in misassignments during species identification.
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BibTeX
@article{deremarque2026does,
title = {{How does the efficiency of Nanopore compare to Illumina sequencing in tracking the spread of aquatic invasive species?}},
author = {Théo Deremarque and Gozlan Rodolphe Elie and Ravo Ravaozafindrasoa and Giuliano Mucci and Lucie Delalex and Jean-Michel Foissy and Michaël Cagnant and Mathieu Clair and Justina Givens and Fabienne Justy and Alice Valentini and Delphine Nicolas and Pascal Contournet and Claire Tetrel and Marc Thibault and Marine Combe},
journal = {Water Biology and Security},
year = {2026},
month = sep,
doi = {10.1016/j.watbs.2025.100423},
url = {https://hal.science/hal-05764368v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - How does the efficiency of Nanopore compare to Illumina sequencing in tracking the spread of aquatic invasive species?
AU - Théo Deremarque
AU - Gozlan Rodolphe Elie
AU - Ravo Ravaozafindrasoa
AU - Giuliano Mucci
AU - Lucie Delalex
AU - Jean-Michel Foissy
AU - Michaël Cagnant
AU - Mathieu Clair
AU - Justina Givens
AU - Fabienne Justy
AU - Alice Valentini
AU - Delphine Nicolas
AU - Pascal Contournet
AU - Claire Tetrel
AU - Marc Thibault
AU - Marine Combe
PY - 2026
DA - 2026/09/25
JO - Water Biology and Security
DO - 10.1016/j.watbs.2025.100423
UR - https://hal.science/hal-05764368v1
AB - eDNA-based methods offer a non-invasive, easy-to-use approach for monitoring aquatic biodiversity, particularly for tracking invasive or cryptic species. While Illumina sequencing is commonly used, few studies have explored pairing eDNA sampling with Nanopore sequencing, a third-generation technology that allows for on-site sequencing but with a higher error rate. Here, we compared the performance of both technologies in detecting the invasive host-parasite complex Pseudorasbora parva-Sphaerothecum destruens. Water samples were collected from sites in Camargue and Corsica (Southern France), followed by DNA extraction, PCR amplification, and sequencing using either Illumina or Nanopore. Both technologies showed similar detection rates of P. parva, but only when Nanopore sequencing was performed under optimal conditions. However, for S. destruens, results varied: Illumina failed to detect the parasite, while Nanopore identified its DNA in multiple sites. We suggest that this discrepancy may be due to the different bioinformatic approaches used to process the reads and/or the higher error rate of Nanopore sequencing which could result in misassignments during species identification.
SN - 2772-7351
ER -