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Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance - PubMed

  • ️Tue Jan 01 2019

Review

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

Alexander M Piper et al. Gigascience. 2019.

Abstract

Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations. DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.

Keywords: alien species; bioinformatics; biosecurity; biosurveillance; controls; early detection; non-destructive; quality assurance; reference database; validation.

© The Author(s) 2019. Published by Oxford University Press.

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Figures

Figure 1:
Figure 1:

Metabarcoding in the literature. (A) Published articles obtained from Scopus, Crossref, and PubMed searches on 6 June 2019 for all metabarcoding studies, and those containing keywords in title or abstract relevant to invasive insect surveillance. (B) Sequencing platforms used in the above metabarcoding studies displayed as a proportion for each year.

Figure 2:
Figure 2:

Overview of common metabarcoding workflows for identification of trapped insect species

Figure 3:
Figure 3:

DNA barcodes in public reference databases. (A) Global distribution of all sufficiently annotated DNA barcode records from BOLD and GenBank for all barcode loci; records for all Insecta are displayed as a density map, while those species present on international pest lists are overlaid in red. (B) Distribution of records and unique species within major public databases for the 10 barcode markers with the most reference information for entire Insecta and for (C) Insecta species present on international pest lists.

Figure 4:
Figure 4:

Unique dual indexing overcomes issues of cross-contamination due to index-switching. (A) An amplified barcode locus with sequencing adapters attached; read locations and orientations are indicated for commonly used Illumina MiSeq platform. Reads 1 and 2 are designed to overlap to facilitate assembly into a consensus sequence. Both sequencing adapters incorporate a unique oligonucleotide index sequence to allow differentiation of multiplexed samples. Strategies for indexing include (B) combinatorial indexing, where indices on either end of the molecule are shared with other samples but the combination of the two is unique, and (C) unique dual indexing, where adapter indices at both ends of the molecule are completely unique to the sample.

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