Validation of COI metabarcoding primers for terrestrial arthropods

Metabarcoding a Diverse Arthropod Mock Community

(2019) Thomas W. A. Braukmann et al.   Molecular Ecology Resources

Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater

(2019) G. A. C. Singer et al.   Scientific Reports

Non‐specific amplification compromises environmental DNA metabarcoding with COI

(2019) Rupert A. Collins et al.   Methods in Ecology and Evolution

Does Size Matter? An Experimental Evaluation of the Relative Abundance and Decay Rates of Aquatic Environmental DNA

(2018) Jonas Bylemans et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative

(2018) Josep Piñol et al.   MOLECULAR ECOLOGY

Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure

(2018) Kristine Bohmann et al.   Molecular Ecology Resources

Minimizing polymerase biases in metabarcoding

(2018) Ruth V. Nichols et al.   Molecular Ecology Resources

Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis

(2018) Maxime Galan et al.   Molecular Ecology Resources

The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota

(2018) Henrik Krehenwinkel et al.   PLoS One

Automated high throughput animal CO1 metabarcode classification

(2018) Teresita M. Porter et al.   Scientific Reports

Estimating intraspecific genetic diversity from community DNA metabarcoding data

(2018) Vasco Elbrecht et al.   PeerJ

DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers

(2018) Owen S. Wangensteen et al.   PeerJ

Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities

(2018) Guang K. Zhang et al.   Evolutionary Applications

Why the COI barcode should be the community DNA metabarcode for the metazoa

(2018) Carmelo Andújar et al.   MOLECULAR ECOLOGY

Comparison of environmental DNA and bulk-sample metabarcoding using highly degenerate cytochrome c oxidase I primers

(2018) Jan-Niklas Macher et al.   Molecular Ecology Resources

New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods

(2018) Daniel Marquina et al.   Molecular Ecology Resources

Over 2.5 million COI sequences in GenBank and growing

(2018) Teresita M. Porter et al.   PLoS One

Slippage of degenerate primers can cause variation in amplicon length

(2018) Vasco Elbrecht et al.   Scientific Reports

An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals

(2018) Michelle A. Jusino et al.   Molecular Ecology Resources

PCR cycles above routine numbers do not compromise high-throughput DNA barcoding results

(2017) J. Vierna et al.   GENOME

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill

(2017) Carmelo Andújar et al.   MOLECULAR ECOLOGY

Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

(2017) Henrik Krehenwinkel et al.   Scientific Reports

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

(2017) Laurence J. Clarke et al.   Ecology and Evolution

Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding

(2017) Matthieu Leray et al.   PeerJ

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Protist metabarcoding and environmental biomonitoring: Time for change

(2016) J. Pawlowski et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

PrimerMiner : an r package for development and in silico validation of DNA metabarcoding primers

(2016) Vasco Elbrecht et al.   Methods in Ecology and Evolution

The ecologist's field guide to sequence-based identification of biodiversity

(2016) Simon Creer et al.   Methods in Ecology and Evolution

Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects

(2016) Vasco Elbrecht et al.   PeerJ

The utility of DNA metabarcoding for studying the response of arthropod diversity and composition to land-use change in the tropics

(2016) Kingsly Chuo Beng et al.   Scientific Reports

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

DNA metabarcoding of insects and allies: an evaluation of primers and pipelines

(2015) G.-J. Brandon-Mong et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

The ecology of environmental DNA and implications for conservation genetics

(2015) Matthew A. Barnes et al.   CONSERVATION GENETICS

High-Throughput Sequencing Technologies

(2015) Jason A. Reuter et al.   MOLECULAR CELL

DNA barcodes from century-old type specimens using next-generation sequencing

(2015) Sean W. J. Prosser et al.   Molecular Ecology Resources

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

(2015) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Planetary boundaries: Guiding human development on a changing planet

(2015) W. Steffen et al.   SCIENCE

Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities

(2015) Dominique A. Cowart et al.   PLoS One

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

(2015) Vasco Elbrecht et al.   PLoS One

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing

(2015) Joel F. Gibson et al.   PLoS One

Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

(2015) Shadi Shokralla et al.   Scientific Reports

DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match

(2014) B. E. Deagle et al.   Biology Letters

Environmental metabarcodes for insects:in silicoPCR reveals potential for taxonomic bias

(2014) Laurence J. Clarke et al.   Molecular Ecology Resources

Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods

(2014) J. Piñol et al.   Molecular Ecology Resources

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith et al.   PLoS One

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics

(2014) J. Gibson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defaunation in the Anthropocene

(2014) R. Dirzo et al.   SCIENCE

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 contents

(2013) Matthieu Leray et al.   Frontiers in Zoology

Dispersal and gene flow in free-living marine nematodes

(2013) Sofie Derycke et al.   Frontiers in Zoology

Recovery of DNA barcodes from blackfly museum specimens (Diptera: Simuliidae) using primer sets that target a variety of sequence lengths

(2013) L. M. Hernández-Triana et al.   Molecular Ecology Resources

Redesign of PCR primers for mitochondrial cytochromecoxidase subunit I for marine invertebrates and application in all-taxa biotic surveys

(2013) J. Geller et al.   Molecular Ecology Resources

A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System

(2013) Sujeevan Ratnasingham et al.   PLoS One

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

(2012) Douglas W. Yu et al.   Methods in Ecology and Evolution

Plant and animal endemism in the eastern Andean slope: challenges to conservation

(2012) Jennifer J Swenson et al.   BMC ECOLOGY

Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

(2011) Mehrdad Hajibabaei et al.   PLoS One

Barcoding Bugs: DNA-Based Identification of the True Bugs (Insecta: Hemiptera: Heteroptera)

(2011) Doo-Sang Park et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces

(2010) MATT R. K. ZEALE et al.   Molecular Ecology Resources

Global threats to human water security and river biodiversity

(2010) C. J. Vörösmarty et al.   NATURE

Influence of DNA extraction methods, PCR inhibitors and quantification methods on real-time PCR assay of biotechnology-derived traits

(2009) Tigst Demeke et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS