Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison.
Illumina
MiSeq
MinION
eDNA
invasive
metabarcoding
mussel
nanopore
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Aug 2022
Aug 2022
Historique:
revised:
09
02
2022
received:
18
06
2020
accepted:
02
03
2022
pubmed:
20
3
2022
medline:
7
7
2022
entrez:
19
3
2022
Statut:
ppublish
Résumé
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-based 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 widely accessible and substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has 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 invasive 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 nonsignificant. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples.
Identifiants
pubmed: 35305077
doi: 10.1111/1755-0998.13610
doi:
Substances chimiques
DNA, Environmental
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2232-2247Subventions
Organisme : PORBIOTA
ID : POCI-01-0145-FEDER-022127
Organisme : Fundação para a Ciência e a Tecnologia
ID : SFRH/BD/133159/2017
Organisme : Fundação para a Ciência e a Tecnologia
ID : 2020.03608.CEECIND
Organisme : European Regional Development Fund (FEDER)
Organisme : EDP-Biodiversity Chair
Organisme : Horizon 2020 Framework Programme
ID : 668981
Informations de copyright
© 2022 John Wiley & Sons Ltd.
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