| Abstract | Traditional detection of aquatic invasive species via morphological identification is often time-
consuming and can require a high level of taxonomic expertise, leading to delayed mitigation
responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-
ased sequencing technology have been used to overcome these hindrances, but sample
processing is often lengthy. More recently, portable nanopore sequencing technology has
become available, which has the potential to make molecular detection of invasive species more
dely accessible and substantially decrease sample turnaround times. However, nanopore-
sequenced reads have a much higher error rate than those produced by Illumina platforms, which
s so far hindered the adoption of this technology. We provide a detailed laboratory protocol and
bioinformatic tools (msi package) to increase the reliability of nanopore sequencing to detect
vasive species, and we test its application using invasive bivalves while comparing it with
Illumina-based sequencing. We sampled water from sites with pre-existing bivalve occurrence
and abundance data, and contrasting bivalve communities, in Italy and Portugal. Samples were
extracted, amplified, and sequenced by the two platforms. The mean agreement between
sequencing methods was 69% and the difference between methods was non-significant. The lack
detections of some species at some sites could be explained by their known low abundances.
his is the first reported use of MinION to detect aquatic invasive species from eDNA samples. |
| Text | 466007 2022 10.1111/1755 0998.13610 Invasive MinION Nanopore MiSeq Illumina eDNA metabarcoding mussel Speeding up the detection of invasive bivalve species using environmental DNA a Nanopore and Illumina sequencing comparison Bastian Egeter, Joana Verissimo, Manuel Lopes Lima, Catia Chaves, Joana Pinto, Nicoletta Riccardi, Pedro Beja, Nuno A. Fonseca CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, InBIO Laboratorio Associado, Campus de Va rão, Universidade do Porto, 4485 661 Vairão, Portugal BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485 661 Vairão, Portugal Departamento de Biologia, Faculdade de Ciencias, Universidade do Porto, Porto, Portugal IUCN SSC Mollusc Specialist Group, c/o 219 Huntingdon Road, Cambridge, CB3 0DL U.K. CNR Water Research Institute, Verbania Pallanza VB , Italy CIBIO/InBIO, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal NatureMetrics, Bakeham Lane, Egham, Surrey, TW20 9TY, U. K. Traditional detection of aquatic invasive species via morphological identification is often time consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA eDNA detection approaches of multiple species using Illumina ased sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more dely accessible and substantially decrease sample turnaround times. However, nanopore sequenced reads have a much higher error rate than those produced by Illumina platforms, which s so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools msi package to increase the reliability of nanopore sequencing to detect vasive species, and we test its application using invasive bivalves while comparing it with Illumina based sequencing. We sampled water from sites with pre existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. Samples were extracted, amplified, and sequenced by the two platforms. The mean agreement between sequencing methods was 69% and the difference between methods was non significant. The lack detections of some species at some sites could be explained by their known low abundances. his is the first reported use of MinION to detect aquatic invasive species from eDNA samples. Preprint Speeding up the detection of invasive bivalve species using environmental DNA a Nanopore and Illumina sequencing comparison pdf preprint Egeter et al. 2022_eDNA.pdf Articolo in rivista Blackwell 1755 0998 Molecular ecology resources Online Molecular ecology resources Online Mol. ecol. resour. Online Molecular ecology resources Online nicolettarita.riccardi RICCARDI NICOLETTA RITA |
