Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi

Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics

(2014) James T. Monacell et al.   BIOINFORMATICS

Correction: Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2014) Susan M. Huse et al.   PLoS Genetics

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

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

Host Genotype Shapes the Foliar Fungal Microbiome of Balsam Poplar (Populus balsamifera)

(2013) Miklós Bálint et al.   PLoS One

Host and geographic structure of endophytic and endolichenic fungi at a continental scale

(2012) Jana M. U'Ren et al.   AMERICAN JOURNAL OF BOTANY

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

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

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

Amplicon-pyrosequencing-based detection of compositional shifts in bryophyte-associated fungal communities along an elevation gradient

(2012) Marie L. Davey et al.   MOLECULAR ECOLOGY

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

(2012) Hirokazu Toju et al.   PLoS One

Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape

(2012) N. B. Zimmerman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

A preliminary survey of lichen associated eukaryotes using pyrosequencing

(2011) Scott T. BATES et al.   LICHENOLOGIST

Culturing and direct PCR suggest prevalent host generalism among diverse fungal endophytes of tropical forest grasses

(2011) K. Lindsay Higgins et al.   MYCOLOGIA

Diverse Helotiales associated with the roots of three species of Arctic Ericaceae provide no evidence for host specificity

(2011) John F. Walker et al.   NEW PHYTOLOGIST

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Accessing the Soil Metagenome for Studies of Microbial Diversity

(2010) Tom O. Delmont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Exploring the evolutionary ecology of fungal endophytes in agricultural systems: using functional traits to reveal mechanisms in community processes

(2010) Megan Saunders et al.   Evolutionary Applications

An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology

(2010) R. Henrik Nilsson et al.   Fungal Ecology

Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores

(2010) Audra S Liggenstoffer et al.   ISME Journal

Differential effect of sample preservation methods on plant and arbuscular mycorrhizal fungal DNA

(2010) L.D. Bainard et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Community Analysis Reveals Close Affinities Between Endophytic and Endolichenic Fungi in Mosses and Lichens

(2010) Jana M. U’Ren et al.   MICROBIAL ECOLOGY

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

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

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

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

A hands-on overview of tissue preservation methods for molecular genetic analyses

(2010) Zoltán Tamás Nagy   ORGANISMS DIVERSITY & EVOLUTION

Identity, Diversity, and Molecular Phylogeny of the Endophytic Mycobiota in the Roots of Rare Wild Rice (Oryza granulate) from a Nature Reserve in Yunnan, China

(2009) Z.-l. Yuan 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

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Fungal-Fungal Associations Affect the Assembly of Endophyte Communities in Maize (Zea mays)

(2009) Jean J. Pan et al.   MICROBIAL ECOLOGY

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperateQuercus macrocarpaphyllosphere

(2009) A. Jumpponen et al.   NEW PHYTOLOGIST

Fungal endophytes: diversity and functional roles

(2009) R. J. Rodriguez et al.   NEW PHYTOLOGIST

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

(2009) Yijun Sun et al.   NUCLEIC ACIDS RESEARCH

A Phylogenetic Estimation of Trophic Transition Networks for Ascomycetous Fungi: Are Lichens Cradles of Symbiotrophic Fungal Diversification?

(2009) A. Elizabeth Arnold et al.   SYSTEMATIC BIOLOGY

Biogeographic and phylogenetic patterns in diversity of liverwort-associated endophytes

(2008) E. C. Davis et al.   AMERICAN JOURNAL OF BOTANY

Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs

(2008) Hege Vestheim et al.   Frontiers in Zoology

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

Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analysing fungal environmental samples

(2008) Jana M. U'Ren et al.  

High throughput tissue preparation for large-scale genotyping experiments

(2007) TRACEY A. BODO SLOTTA et al.   Molecular Ecology Resources