Using Gap Visualization to Navigate Multivariate Metabarcode Data, Select Primer Pairs, and Enhance Reference Data Quality

ABSTRACT The success of amplicon sequencing studies of environmental DNA (eDNA) depends on the choice of primer pairs used to select taxa‐specific regions of DNA for amplification then sequencing to characterize sample composition. This paper presents practical methods to visualize the extent to whi...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Environmental DNA (Hoboken, N.J.) N.J.), 2024-11, Vol.6 (6), p.n/a
Hauptverfasser: Chua, Xin‐Yi, Ord, Louise, Bent, Stephen J., Lovell, David, McGrath, Annette
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung:ABSTRACT The success of amplicon sequencing studies of environmental DNA (eDNA) depends on the choice of primer pairs used to select taxa‐specific regions of DNA for amplification then sequencing to characterize sample composition. This paper presents practical methods to visualize the extent to which different primer pairs can differentiate taxonomic groups, enabling researchers to assess which primers might be best suited for a study or environment of interest. These methods can also be used to review taxonomic annotations in genomic reference sequence databases. We apply the concept of DNA barcoding gaps to metabarcoding of multiple species in environmental DNA to leverage reference data on the amplicon sequences of previously characterized specimens. Since reference data sets are large and complex, we provide a simple and intuitive method to navigate subsets of reference sequence data containing conflicting or ambiguous relationships between genomic information and taxonomic classification. We demonstrate how to use gap visualization and taxonomic segmentation in comparing how well different primer pairs discriminate species of interest, and in detecting anomalies in reference sequence annotation. We show how these visualization methods can enable amplicon survey study design and make fundamental molecular resources more accessible to a wider research audience beyond bioinformaticians and data scientists. We introduce the metabarcoding gap visualization and demonstrated how it can make comparisons of PCR primers rapidly comprehensible for researchers in the molecular ecology community. We use gap visualization to simultaneously interrogate multiple primer pairs and enhance reference data quality. This has significant impact for study design as selecting the right PCR primer pairs is imperative to obtain accurate representation of the surveyed ecosystem.
ISSN:2637-4943
2637-4943
DOI:10.1002/edn3.597