High-Throughput Sequencing—The Key to Rapid Biodiversity Assessment of Marine Metazoa?

Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda

(2015) Shu Wu et al.   PLoS One

Morphometric and molecular identification of individual barnacle cyprids from wild plankton: an approach to detecting fouling and invasive barnacle species

(2013) Hsi-Nien Chen et al.   BIOFOULING

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

Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

(2013) Melissa E Carew et al.   Frontiers in Zoology

Evaluating the Accuracy of Morphological Identification of Larval Fishes by Applying DNA Barcoding

(2013) Hui-Ling Ko et al.   PLoS One

Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

(2013) Penelope K. Lindeque et al.   PLoS One

High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities

(2013) Aibin Zhan et al.   Methods in Ecology and Evolution

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

The Magnitude of Global Marine Species Diversity

(2012) Ward Appeltans et al.   CURRENT BIOLOGY

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing

(2012) DONALD J. BAIRD et al.   MOLECULAR ECOLOGY

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Evolution in the deep sea: Biological traits, ecology and phylogenetics of pelagic copepods

(2012) Silke Laakmann et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses

(2012) V. G. Fonseca et al.   NUCLEIC ACIDS RESEARCH

Molecular Systematic of Three Species of Oithona (Copepoda, Cyclopoida) from the Atlantic Ocean: Comparative Analysis Using 28S rDNA

(2012) Georgina D. Cepeda et al.   PLoS One

Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill

(2012) Holly M. Bik et al.   PLoS One

PCR Primers for Metazoan Mitochondrial 12S Ribosomal DNA Sequences

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

Distance and Character-Based Evaluation of the V4 Region of the 18S rRNA Gene for the Identification of Diatoms (Bacillariophyceae)

(2012) Ian A. Luddington et al.   PLoS One

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   PLoS One

PCR Primers for Metazoan Nuclear 18S and 28S 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

The golden age of DNA metasystematics

(2012) Mehrdad Hajibabaei   TRENDS IN GENETICS

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

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

Systematic exploration of error sources in pyrosequencing flowgram data

(2011) S. Balzer et al.   BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

(2011) André Gilles et al.   BMC GENOMICS

Nuclear 18S rDNA As A Species-Level Molecular Marker for Leucothoidae (Amphipoda)

(2011) Kristine N. White   JOURNAL OF CRUSTACEAN BIOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

(2011) HOLLY M. BIK et al.   MOLECULAR ECOLOGY

GenBank

(2011) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols

(2011) Jonas Zimmermann et al.   ORGANISMS DIVERSITY & EVOLUTION

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

(2011) Mehrdad Hajibabaei et al.   PLoS One

Pyrosequencing for Mini-Barcoding of Fresh and Old Museum Specimens

(2011) Shadi Shokralla et al.   PLoS One

Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments

(2011) Béatrice Lecroq et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes

(2010) Michael J Raupach et al.   Frontiers in Zoology

Short rDNA Barcodes for Species Identification in Foraminifera

(2010) JAN PAWLOWSKI et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

Dissimilarity of Species and Forms of Planktonic Neocalanus Copepods Using Mitochondrial COI, 12S, Nuclear ITS, and 28S Gene Sequences

(2010) Ryuji J. Machida et al.   PLoS One

Tantulocarida (Crustacea) from the Southern Ocean deep sea, and the description of three new species of Tantulacus Huys, Andersen & Kristensen, 1992

(2010) Inga Mohrbeck et al.   SYSTEMATIC PARASITOLOGY

Second-generation environmental sequencing unmasks marine metazoan biodiversity

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

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

(2010) Einat Hazkani-Covo et al.   PLoS Genetics

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Complete lack of mitochondrial divergence between two species of NE Atlantic marine intertidal gastropods

(2009) P. KEMPPAINEN et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

High GC Contents of Primer 5′-End Increases Reaction Efficiency in Polymerase Chain Reaction

(2009) Naoki Shinoda et al.   NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS

Gene flow and species delimitation

(2009) Rémy J. Petit et al.   TRENDS IN ECOLOGY & EVOLUTION

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS

THE FREQUENCY OF rDNA VARIANTS WITHIN INDIVIDUALS PROVIDES EVIDENCE OF POPULATION HISTORY AND GENE FLOW ACROSS A GRASSHOPPER HYBRID ZONE

(2008) Irene Keller et al.   EVOLUTION

Four years of DNA barcoding: Current advances and prospects

(2008) Lise Frézal et al.   INFECTION GENETICS AND EVOLUTION

Phylogenetic comparison of local length plasticity of the small subunit of nuclear rDNAs among all Hexapoda orders and the impact of hyper-length-variation on alignment

(2008) Qiang Xie et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified

(2008) H. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A species complex within the isopod genus Haploniscus (Crustacea: Malacostraca: Peracarida) from the Southern Ocean deep sea: a morphological and molecular approach

(2008) WIEBKE BRÖKELAND et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY