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

PCR primers for assessing community structure of aquatic fungi including Chytridiomycota and Cryptomycota

(2015) Nobuyoshi Ishii et al.   Fungal Ecology

Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

(2015) Shawn P. Brown et al.   Fungal Ecology

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

(2015) Leho Tedersoo et al.   ISME Journal

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

(2015) R. Henrik Nilsson et al.   MICROBES AND ENVIRONMENTS

High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats

(2015) Jizhong Zhou et al.   mBio

Impact of primer choice on characterization of orchid mycorrhizal communities using 454 pyrosequencing

(2014) Michael Waud et al.   Molecular Ecology Resources

ITS1: a DNA barcode better than ITS2 in eukaryotes?

(2014) Xin-Cun Wang et al.   Molecular Ecology Resources

Temporal patterns of orchid mycorrhizal fungi in meadows and forests as revealed by 454 pyrosequencing

(2014) Jane Oja et al.   NEW PHYTOLOGIST

Global biogeography ofAlnus-associatedFrankiaactinobacteria

(2014) Sergei Põlme et al.   NEW PHYTOLOGIST

Comparison and Validation of Some ITS Primer Pairs Useful for Fungal Metabarcoding Studies

(2014) Michiel Op De Beeck et al.   PLoS One

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

LotuS: an efficient and user-friendly OTU processing pipeline

(2014) Falk Hildebrand et al.   Microbiome

A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning

(2013) D. Lee Taylor et al.   ECOLOGICAL MONOGRAPHS

Phylogenetic detection of novel Cryptomycota in an Iowa (United States) aquifer and from previously collected marine and freshwater targeted high-throughput sequencing sets

(2013) Joshua A. Livermore et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

ITS1 versus ITS2 as DNA metabarcodes for fungi

(2013) R. Blaalid et al.   Molecular Ecology Resources

Comparison of commonly used primer sets for evaluating arbuscular mycorrhizal fungal communities: Is there a universal solution?

(2013) Petr Kohout et al.   SOIL BIOLOGY & BIOCHEMISTRY

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

(2013) Johan Bengtsson-Palme et al.   Methods in Ecology and Evolution

Lineages of ectomycorrhizal fungi revisited: Foraging strategies and novel lineages revealed by sequences from belowground

(2013) Leho Tedersoo et al.   Fungal Biology Reviews

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

(2013) Xin Zhou et al.   GigaScience

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella 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

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Fungal Diversity Is Not Determined by Mineral and Chemical Differences in Serpentine Substrates

(2012) Stefania Daghino 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

Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets

(2012) Johan Bengtsson et al.   RESEARCH IN MICROBIOLOGY

The Fungi: 1, 2, 3 … 5.1 million species?

(2011) Meredith Blackwell   AMERICAN JOURNAL OF BOTANY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Multiple markers pyrosequencing reveals highly diverse and host-specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa

(2011) Yonathan Arfi et al.   FEMS MICROBIOLOGY ECOLOGY

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

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

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

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

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

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

Soil Microbial Community Responses to Multiple Experimental Climate Change Drivers

(2009) H. F. Castro et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

The merging of community ecology and phylogenetic biology

(2009) Jeannine Cavender-Bares et al.   ECOLOGY LETTERS

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

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

Windshield splatter analysis with the Galaxy metagenomic pipeline

(2009) S. Kosakovsky Pond et al.   GENOME RESEARCH

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

Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas

(2008) D. Lee Taylor et al.   NEW PHYTOLOGIST