The topological nature of tag jumping in environmental DNA metabarcoding studies.
a-DNA
detection limits
e-DNA
false positive
index hopping
sample crosstalk
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Apr 2023
Apr 2023
Historique:
revised:
07
10
2022
received:
19
01
2022
accepted:
17
11
2022
pubmed:
9
12
2022
medline:
8
3
2023
entrez:
8
12
2022
Statut:
ppublish
Résumé
Metabarcoding of environmental DNA constitutes a state-of-the-art tool for environmental studies. One fundamental principle implicit in most metabarcoding studies is that individual sample amplicons can still be identified after being pooled with others-based on their unique combinations of tags-during the so-called demultiplexing step that follows sequencing. Nevertheless, it has been recognized that tags can sometimes be changed (i.e., tag jumping), which ultimately leads to sample crosstalk. Here, using four DNA metabarcoding data sets derived from the analysis of soils and sediments, we show that tag jumping follows very specific and systematic patterns. Specifically, we find a strong correlation between the number of reads in blank samples and their topological position in the tag matrix (described by vertical and horizontal vectors). This observed spatial pattern of artefactual sequences could be explained by polymerase activity, which leads to the exchange of the 3' tag of single stranded tagged sequences through the formation of heteroduplexes with mixed barcodes. Importantly, tag jumping substantially distorted our data sets-despite our use of methods suggested to minimize this error. We developed a topological model to estimate the noise based on the counts in our blanks, which suggested that 40%-80% of the taxa in our soil and sedimentary samples were likely false positives introduced through tag jumping. We highlight that the amount of false positive detections caused by tag jumping strongly biased our community analyses.
Identifiants
pubmed: 36479848
doi: 10.1111/1755-0998.13745
doi:
Substances chimiques
DNA, Environmental
0
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
621-631Subventions
Organisme : Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
ID : P2BEP2-188256
Organisme : Swedish research council
ID : 2017-04548
Informations de copyright
© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
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