Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest

(2013) Jennifer Kerekes et al.   MOLECULAR ECOLOGY

Adding unaligned sequences into an existing alignment using MAFFT and LAST

(2012) Kazutaka Katoh et al.   BIOINFORMATICS

Denoising PCR-amplified metagenome data

(2012) Michael J Rosen et al.   BMC BIOINFORMATICS

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?

(2012) Tor Carlsen et al.   Fungal Ecology

Comparison of ITS1 and ITS2 rDNA in 454 sequencing of hyperdiverse fungal communities

(2012) Anna L. Bazzicalupo et al.   Fungal Ecology

Estimation of fungal biomass in forest litter and soil

(2012) Petr Baldrian et al.   Fungal Ecology

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

(2012) Martin Hartmann et al.   ISME Journal

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

Fast, accurate error-correction of amplicon pyrosequences using Acacia

(2012) Lauren Bragg et al.   NATURE METHODS

Seasonal trends in the biomass and structure of bryophyte-associated fungal communities explored by 454 pyrosequencing

(2012) Marie L. Davey et al.   NEW PHYTOLOGIST

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

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

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

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples

(2012) Hirokazu Toju et al.   PLoS One

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

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

Sequencing our way towards understanding global eukaryotic biodiversity

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

Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

(2011) Johan Bengtsson et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

(2011) David Berry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

(2011) Xiaolin Hao et al.   BIOINFORMATICS

Systematic exploration of error sources in pyrosequencing flowgram data

(2011) S. Balzer et al.   BIOINFORMATICS

A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

(2011) David J Russell et al.   BMC BIOINFORMATICS

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

(2011) Surendra Kumar et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

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

Replication, lies and lesser-known truths regarding experimental design in environmental microbiology

(2011) Jay T. Lennon   ENVIRONMENTAL MICROBIOLOGY

Population genetics of ectomycorrhizal fungi: from current knowledge to emerging directions

(2011) Greg W. Douhan et al.   Fungal Biology

RNA reveals a succession of active fungi during the decay of Norway spruce logs

(2011) Tiina Rajala et al.   Fungal Ecology

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

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

(2011) Petr Baldrian et al.   ISME Journal

454-sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities

(2011) Ylva Lekberg et al.   JOURNAL OF ECOLOGY

Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences

(2011) ROMINA GAZIS et al.   MOLECULAR ECOLOGY

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

ITS-1 versus ITS-2 pyrosequencing: a comparison of fungal populations in truffle grounds

(2011) Antonietta Mello et al.   MYCOLOGIA

Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus

(2011) Daniel L. Lindner et al.   MYCOLOGIA

High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples

(2011) Håvard Kauserud et al.   MYCORRHIZA

Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities

(2011) R. Henrik Nilsson et al.   NEW PHYTOLOGIST

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

(2011) Leho Tedersoo et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Arbuscular Mycorrhiza: The Challenge to Understand the Genetics of the Fungal Partner

(2010) Ian R. Sanders et al.   Annual Review of Genetics

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

(2010) Dominik Begerow et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Interference with spectrophotometric analysis of nucleic acids and proteins by leaching of chemicals from plastic tubes

(2010) L. Lewis et al.   BIOTECHNIQUES

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

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

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

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

Replicate or lie

(2010) James I. Prosser   ENVIRONMENTAL MICROBIOLOGY

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Disruption of root carbon transport into forest humus stimulates fungal opportunists at the expense of mycorrhizal fungi

(2010) Björn D Lindahl et al.   ISME Journal

V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences

(2010) Martin Hartmann et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Yeast Pre-rRNA Processing and Modification Occur Cotranscriptionally

(2010) Martin Koš et al.   MOLECULAR CELL

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

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

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Spatial and temporal ecology of Scots pine ectomycorrhizas

(2010) Brian J. Pickles et al.   NEW PHYTOLOGIST

Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests

(2010) Håkan Wallander et al.   NEW PHYTOLOGIST

Insidious effects of sequencing errors on perceived diversity in molecular surveys

(2010) Ian A. Dickie   NEW PHYTOLOGIST

The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)

(2010) M. Öpik et al.   NEW PHYTOLOGIST

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

DNA barcoding of arbuscular mycorrhizal fungi

(2010) Herbert Stockinger et al.   NEW PHYTOLOGIST

Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets

(2010) Angélique Gobet et al.   NUCLEIC ACIDS RESEARCH

The Promise and Pitfalls of Sequence-Based Identification of Plant-Pathogenic Fungi and Oomycetes

(2010) Seogchan Kang et al.   PHYTOPATHOLOGY

Fungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil

(2010) Harald Kellner et al.   PLoS One

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

Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

(2009) Julie A. Huber et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

The ITS region as a target for characterization of fungal communities using emerging sequencing technologies

(2009) Rolf Henrik Nilsson et al.   FEMS MICROBIOLOGY LETTERS

ClassII peroxidase-encoding genes are present in a phylogenetically wide range of ectomycorrhizal fungi

(2009) Inga T M Bödeker et al.   ISME Journal

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

(2009) Micah Hamady et al.   ISME Journal

Strain-Dependent Variation in 18S Ribosomal DNA Copy Numbers in Aspergillus fumigatus

(2009) M. L. Herrera et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages

(2009) Leho Tedersoo et al.   MYCORRHIZA

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

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

(2009) M. Buée et al.   NEW PHYTOLOGIST

DNA-based species level detection ofGlomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi

(2009) Manuela Krüger et al.   NEW PHYTOLOGIST

Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperateQuercus macrocarpaphyllosphere

(2009) A. Jumpponen et al.   NEW PHYTOLOGIST

Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest

(2009) M. Öpik et al.   NEW PHYTOLOGIST

The ITS2 Database III—sequences and structures for phylogeny

(2009) Christian Koetschan et al.   NUCLEIC ACIDS RESEARCH

Evidence that chytrids dominate fungal communities in high-elevation soils

(2009) K. R. Freeman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temporal Changes in the Ectomycorrhizal Community in Two Soil Horizons of a Temperate Oak Forest

(2008) P.-E. Courty et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi

(2008) Jaikoo Lee et al.   FEMS MICROBIOLOGY ECOLOGY

Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

(2008) Richard Christen   MICROBES AND ENVIRONMENTS

Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide

(2008) Annette W. Coleman   MOLECULAR PHYLOGENETICS AND EVOLUTION

Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers

(2008) Leho Tedersoo et al.   NEW PHYTOLOGIST