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

Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples

(2018) Iliana Bista et al.   Molecular Ecology Resources

Instances of erroneous DNA barcoding of metazoan invertebrates: Are universal cox1 gene primers too “universal”?

(2018) Monika Mioduchowska et al.   PLoS One

Estimating intraspecific genetic diversity from community DNA metabarcoding data

(2018) Vasco Elbrecht et al.   PeerJ

The use of nemabiome metabarcoding to explore gastro-intestinal nematode species diversity and anthelmintic treatment effectiveness in beef calves

(2017) Russell W. Avramenko et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

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

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

(2017) Henrik Krehenwinkel et al.   Scientific Reports

Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

(2017) Michael Stat et al.   Scientific Reports

Connecting Earth observation to high-throughput biodiversity data

(2017) Alex Bush et al.   Nature Ecology & Evolution

A new primer set for DNA metabarcoding of soil Metazoa

(2016) E. Capra et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

A quantitative protocol for DNA metabarcoding of springtails (Collembola)

(2016) Seikoh Saitoh et al.   GENOME

Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae)

(2016) Axel Hausmann et al.   GENOME

A combined field survey and molecular identification protocol for comparing forest arthropod biodiversity across spatial scales

(2016) Brent C. Emerson et al.   Molecular Ecology Resources

Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil

(2016) Paula Arribas et al.   Methods in Ecology and Evolution

BarcodingR: an integrated r package for species identification using DNA barcodes

(2016) Ai-bing Zhang 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

SPINGO: a rapid species-classifier for microbial amplicon sequences

(2015) Guy Allard et al.   BMC BIOINFORMATICS

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

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

Performance of cytochrome c oxidase subunit I (COI), ribosomal DNA Large Subunit (LSU) and Internal Transcribed Spacer 2 (ITS2) in DNA barcoding of Collembola

(2015) Sten Anslan et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material

(2015) Austen C. Thomas et al.   Molecular Ecology Resources

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Evaluating a multigene environmental DNA approach for biodiversity assessment

(2015) Alexei J. Drummond et al.   GigaScience

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

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

Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator

(2014) Chenxue Yang et al.   ECOLOGICAL INDICATORS

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

DNA barcoding gap: reliable species identification over morphological and geographical scales

(2014) Klemen Čandek et al.   Molecular Ecology Resources

A metagenetic approach for revealing community structure of marine planktonic copepods

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

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

(2014) Douglas W Fadrosh et al.   Microbiome

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

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

GenBank

(2013) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation

(2013) Ricardo Ramirez-Gonzalez et al.   PLoS One

Whole-community DNA barcoding reveals a spatio-temporal continuum of biodiversity at species and genetic levels

(2013) Andrés Baselga et al.   Nature Communications

On the comparison of population-level estimates of haplotype and nucleotide diversity: a case study using the gene cox1 in animals

(2012) W P Goodall-Copestake et al.   HEREDITY

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

PCR Primers for Metazoan Mitochondrial 12S Ribosomal DNA Sequences

(2012) Ryuji J. Machida et al.   PLoS One

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

(2012) C. Q. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

(2011) N. PUILLANDRE et al.   MOLECULAR ECOLOGY

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

DNA Barcoding of Marine Metazoa

(2010) Ann Bucklin et al.   Annual Review of Marine Science

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

Second-generation environmental sequencing unmasks marine metazoan biodiversity

(2010) Vera G. Fonseca et al.   Nature Communications

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

(2009) M. Buée et al.   NEW PHYTOLOGIST

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS