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Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias

Citation

Clarke, LJ and Soubrier, J and Weyrich, LS and Cooper, A, Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias, Molecular Ecology Resources, 14, (6) pp. 1160-1170. ISSN 1755-098X (2014) [Refereed Article]

Copyright Statement

Copyright 2014 John Wiley & Sons Ltd

DOI: doi:10.1111/1755-0998.12265

Abstract

Studies of insect assemblages are suited to the simultaneous DNA-based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR-amplification bias, as well as sufficient sequence divergence to resolve species. We used in silico PCR to compare the taxonomic coverage and resolution of newly designed insect metabarcodes (targeting 16S) with that of existing markers [16S and cytochrome oxidase c subunit I (COI)] and then compared their efficiency in vitro. Existing metabarcoding primers amplified in silico <75% of insect species with complete mitochondrial genomes available, whereas new primers targeting 16S provided >90% coverage. Furthermore, metabarcodes targeting COI appeared to introduce taxonomic PCR-amplification bias, typically amplifying a greater percentage of Lepidoptera and Diptera species, while failing to amplify certain orders in silico. To test whether bias predicted in silico was observed in vitro, we created an artificial DNA blend containing equal amounts of DNA from 14 species, representing 11 insect orders and one arachnid. We PCR-amplified the blend using five primer sets, targeting either COI or 16S, with high-throughput amplicon sequencing yielding more than 6 million reads. In vitro results typically corresponded to in silico PCR predictions, with newly designed 16S primers detecting 11 insect taxa present, thus providing equivalent or better taxonomic coverage than COI metabarcodes. Our results demonstrate that in silico PCR is a useful tool for predicting taxonomic bias in mixed template PCR and that researchers should be wary of potential bias when selecting metabarcoding markers.

Item Details

Item Type:Refereed Article
Keywords:environmental DNA, insect, metabarcoding, PCR bias
Research Division:Biological Sciences
Research Group:Genetics
Research Field:Population, Ecological and Evolutionary Genetics
Objective Division:Environment
Objective Group:Ecosystem Assessment and Management
Objective Field:Ecosystem Assessment and Management not elsewhere classified
Author:Clarke, LJ (Dr Laurence Clarke)
ID Code:104022
Year Published:2014
Web of Science® Times Cited:64
Deposited By:CRC-Antarctic Climate & Ecosystems
Deposited On:2015-11-01
Last Modified:2018-03-17
Downloads:0

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