Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects
Top Cited Papers
Open Access
- 19 April 2016
- Vol. 4, e1966
- https://doi.org/10.7717/peerj.1966
Abstract
Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.Other Versions
Funding Information
- Kurt Eberhard Bode foundation
- Agence Nationale de la Recherche (ANR-13-ECOT-0002-01)
This publication has 36 references indexed in Scilit:
- Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplificationGigaScience, 2013
- Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator speciesFrontiers in Zoology, 2013
- Dispersal and gene flow in free-living marine nematodesFrontiers in Zoology, 2013
- A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contentsFrontiers in Zoology, 2013
- Environmental DNAMolecular Ecology, 2012
- ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysisNucleic Acids Research, 2011
- Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River BenthosPLOS ONE, 2011
- BLAST+: architecture and applicationsBMC Bioinformatics, 2009
- Towards a comprehensive barcode library for arctic life - Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, CanadaFrontiers in Zoology, 2009
- bold: The Barcode of Life Data System (http://www.barcodinglife.org)Molecular Ecology Notes, 2007