Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis

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

(2017) Benjamin J Callahan et al.   ISME Journal

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

FuzzyID2: A software package for large data set species identification via barcoding and metabarcoding using hidden Markov models and fuzzy set methods

(2017) Zhi-yong Shi et al.   Molecular Ecology Resources

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

(2017) Supratim Mukherjee et al.   NATURE BIOTECHNOLOGY

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Accuracy of microbial community diversity estimated by closed- and open-reference OTUs

(2017) Robert C. Edgar   PeerJ

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Biodiversity research requires more boots on the ground

(2017) Edward O. Wilson   Nature Ecology & Evolution

Connecting Earth observation to high-throughput biodiversity data

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

Zooplankton Community Profiling in a Eutrophic Freshwater Ecosystem-Lake Tai Basin by DNA Metabarcoding

(2017) Jianghua Yang et al.   Scientific Reports

DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient

(2017) Caroline E. Emilson et al.   Scientific Reports

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

(2016) Nhu H. Nguyen et al.   Fungal Ecology

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Telling plant species apart with DNA: from barcodes to genomes

(2016) Peter M. Hollingsworth et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas

(2016) Teresita M. Porter et al.   PLoS One

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

(2016) James L. O’Donnell et al.   PLoS One

Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers

(2016) Nicole A. Fahner et al.   PLoS One

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Are multi-omics enough?

(2016) Cristina Vilanova et al.   Nature Microbiology

$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples

(2015) Rudolf Meier et al.   CLADISTICS

ITS2 Database V: Twice as Much: Table 1.

(2015) Markus J. Ankenbrand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome skimming for next-generation biodiversity analysis

(2015) Steven Dodsworth   TRENDS IN PLANT SCIENCE

Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures

(2015) Stefan A. Boers et al.   Scientific Reports

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

(2015) Sarah L. Westcott et al.   PeerJ

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

(2015) Leho Tedersoo et al.   MycoKeys

Use of Droplet Digital PCR for Estimation of Fish Abundance and Biomass in Environmental DNA Surveys

(2015) Hideyuki Doi 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

A DNA Mini-Barcoding System for Authentication of Processed Fish Products

(2015) Shadi Shokralla et al.   Scientific Reports

Plant DNA barcoding: from gene to genome

(2014) Xiwen Li et al.   BIOLOGICAL REVIEWS

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

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

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

(2014) Jonas Zimmermann et al.   Molecular Ecology Resources

Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

(2014) Jan Pawlowski et al.   Molecular Ecology Resources

Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics

(2014) Min Tang et al.   NUCLEIC ACIDS RESEARCH

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

(2014) Robert Riley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array

(2014) Alison M. Devault et al.   Scientific Reports

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

The 3,000 rice genomes project: new opportunities and challenges for future rice research

(2014) Jia-Yang Li et al.   GigaScience

Biodiversity and evolutionary history: useful extensions of the PD phylogenetic diversity assessment framework

(2013) Daniel P. Faith   Annals of the New York Academy of Sciences

Unifying measures of biodiversity: understanding when richness and phylogenetic diversity should be congruent

(2013) Caroline M. Tucker et al.   DIVERSITY AND DISTRIBUTIONS

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

(2013)   JOURNAL OF HEREDITY

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

(2013)   JOURNAL OF HEREDITY

Extraction, amplification and detection of DNA in microfluidic chip-based assays

(2013) Jinbo Wu et al.   MICROCHIMICA ACTA

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Robust Detection of Rare Species Using Environmental DNA: The Importance of Primer Specificity

(2013) Taylor M. Wilcox et al.   PLoS One

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree

(2013) Hannah McPherson et al.   BMC ECOLOGY

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason et al.   ISME Journal

PCR inhibitors - occurrence, properties and removal

(2012) C. Schrader et al.   JOURNAL OF APPLIED MICROBIOLOGY

Application of metatranscriptomics to soil environments

(2012) Lilia C. Carvalhais et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

Bioinformatic challenges for DNA metabarcoding of plants and animals

(2012) ERIC COISSAC et al.   MOLECULAR ECOLOGY

Environmental DNA

(2012) PIERRE TABERLET 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

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Using the RDP Classifier to Predict Taxonomic Novelty and Reduce the Search Space for Finding Novel Organisms

(2012) Yemin Lan et al.   PLoS One

Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error

(2012) Teresita M. Porter et al.   PLoS One

Performance of Two Southern California Benthic Community Condition Indices Using Species Abundance and Presence-Only Data: Relevance to DNA Barcoding

(2012) J. Ananda Ranasinghe et al.   PLoS One

Arthropod Diversity in a Tropical Forest

(2012) Y. Basset et al.   SCIENCE

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

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

Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol

(2012) Mehrdad Hajibabaei et al.   BMC ECOLOGY

Biodiversity assessment: State-of-the-art techniques in phylogenomics and species identification

(2011) P. R. Steele et al.   AMERICAN JOURNAL OF BOTANY

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

(2011) Kuan-Liang Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring

(2011) Massimo Milan et al.   BMC GENOMICS

Targeted enrichment of genomic DNA regions for next-generation sequencing

(2011) F. Mertes et al.   Briefings in Functional Genomics

Impediments to taxonomy and users of taxonomy: accessibility and impact evaluation

(2011) Malte C. Ebach et al.   CLADISTICS

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

(2011) Thomas M. Gihring et al.   ENVIRONMENTAL MICROBIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality?

(2011) Bernard W. Sweeney et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

Monitoring endangered freshwater biodiversity using environmental DNA

(2011) PHILIP FRANCIS THOMSEN et al.   MOLECULAR ECOLOGY

Antibiotic resistance is ancient

(2011) Vanessa M. D’Costa et al.   NATURE

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?

(2011) Teresita M. Porter et al.   NEW PHYTOLOGIST

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

(2011) Mehrdad Hajibabaei et al.   PLoS One

Choosing and Using a Plant DNA Barcode

(2011) Peter M. Hollingsworth et al.   PLoS One

Persistence of Environmental DNA in Freshwater Ecosystems

(2011) Tony Dejean et al.   PLoS One

Microfluidics-Based Lab-on-Chip Systems in DNA-Based Biosensing: An Overview

(2011) Sabo Wada Dutse et al.   SENSORS

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences

(2011) David S. Hibbett et al.   Fungal Biology Reviews

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Comparative performances of DNA barcoding across insect orders

(2010) Massimiliano Virgilio et al.   BMC BIOINFORMATICS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

A microbial detection array (MDA) for viral and bacterial detection

(2010) Shea N Gardner et al.   BMC GENOMICS

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

QPCR: a tool for analysis of mitochondrial and nuclear DNA damage in ecotoxicology

(2010) Joel N. Meyer   ECOTOXICOLOGY

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Classification of Nucleotide Sequences Using Support Vector Machines

(2010) Tae-Kun Seo   JOURNAL OF MOLECULAR EVOLUTION

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

Assigning sequences to species in the absence of large interspecific differences

(2010) Melanie Lou et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

Chloroplast genome sequences from total DNA for plant identification

(2010) Catherine J. Nock et al.   PLANT BIOTECHNOLOGY JOURNAL

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

GenGIS: A geospatial information system for genomic data

(2009) D. H. Parks et al.   GENOME RESEARCH

The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework

(2009) Daniel Faith et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Microdroplet-based PCR enrichment for large-scale targeted sequencing

(2009) Ryan Tewhey et al.   NATURE BIOTECHNOLOGY

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Extracellular DNA in soil and sediment: fate and ecological relevance

(2008) G. Pietramellara et al.   BIOLOGY AND FERTILITY OF SOILS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology

(2008) Cindy J. Smith et al.   FEMS MICROBIOLOGY ECOLOGY

An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity

(2008) Martin Ryberg et al.   NEW PHYTOLOGIST

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library

(2008) Chaysavanh Manichanh et al.   NUCLEIC ACIDS RESEARCH

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Fast phylogenetic DNA barcoding

(2008) K. Munch et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

(2008) Tim Urich et al.   PLoS One

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

Preserving Accuracy in GenBank

(2008) M. I. Bidartondo   SCIENCE

Inferring Species Membership Using DNA Sequences with Back-Propagation Neural Networks

(2008) A. B. Zhang et al.   SYSTEMATIC BIOLOGY

Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics

(2008) Kasper Munch et al.   SYSTEMATIC BIOLOGY