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

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Single-Nucleotide Polymorphisms and Other Mismatches Reduce Performance of Quantitative PCR Assays

(2013) S. Lefever et al.   CLINICAL CHEMISTRY

Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem

(2013) Shawn P. Brown et al.   FEMS MICROBIOLOGY ECOLOGY

Spatial variation in below-ground seed germination and divergent mycorrhizal associations correlate with spatial segregation of three co-occurring orchid species

(2013) Hans Jacquemyn et al.   JOURNAL OF ECOLOGY

ITS1 versus ITS2 as DNA metabarcodes for fungi

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

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

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

Repeated Evolution of Fungal Cultivar Specificity in Independently Evolved Ant-Plant-Fungus Symbioses

(2013) Rumsaïs Blatrix et al.   PLoS One

SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons

(2013) Shanlin Liu et al.   Methods in Ecology and Evolution

Phylogenetic and Microsatellite Markers for Tulasnella (Tulasnellaceae) Mycorrhizal Fungi Associated with Australian Orchids

(2013) Monica P. Ruibal et al.   Applications in Plant Sciences

Does mycorrhizal specificity affect orchid decline and rarity?

(2012) Bruno Cachapa Bailarote et al.   AMERICAN JOURNAL OF BOTANY

Novel High-Rank Phylogenetic Lineages within a Sulfur Spring (Zodletone Spring, Oklahoma), Revealed Using a Combined Pyrosequencing-Sanger Approach

(2012) Noha Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Pyrosequencing as a tool for the detection ofPhytophthoraspecies: error rate and risk of false Molecular Operational Taxonomic Units

(2012) A.M. Vettraino et al.   LETTERS IN APPLIED MICROBIOLOGY

The role of epiphytism in architecture and evolutionary constraint within mycorrhizal networks of tropical orchids

(2012) FLORENT MARTOS et al.   MOLECULAR ECOLOGY

Specificity and preference of mycorrhizal associations in two species of the genus Dendrobium (Orchidaceae)

(2012) Xiaoke Xing et al.   MYCORRHIZA

Fast, accurate error-correction of amplicon pyrosequences using Acacia

(2012) Lauren Bragg et al.   NATURE METHODS

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

(2012) Hirokazu Toju et al.   PLoS One

Variation in Mycorrhizal Associations with Tulasnelloid Fungi among Populations of Five Dactylorhiza Species

(2012) Hans Jacquemyn 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

Photosynthetic Mediterranean meadow orchids feature partial mycoheterotrophy and specific mycorrhizal associations

(2011) Mariangela Girlanda et al.   AMERICAN JOURNAL OF BOTANY

The Effects of Above- and Belowground Mutualisms on Orchid Speciation and Coexistence

(2011) Richard J. Waterman et al.   AMERICAN NATURALIST

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

(2011) William A. Walters et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

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

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

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

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

Nonrandom spatial structuring of orchids in a hybrid zone of three Orchis species

(2011) Hans Jacquemyn et al.   NEW PHYTOLOGIST

Analysis of network architecture reveals phylogenetic constraints on mycorrhizal specificity in the genus Orchis (Orchidaceae)

(2011) Hans Jacquemyn et al.   NEW PHYTOLOGIST

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

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Low specificity and nested subset structure characterize mycorrhizal associations in five closely related species of the genus Orchis

(2010) HANS JACQUEMYN et al.   MOLECULAR ECOLOGY

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

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

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

Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments

(2010) A. Jumpponen et al.   NEW PHYTOLOGIST

Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics

(2010) A. S. Amend et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Ectomycorrhizal Inocybe species associate with the mycoheterotrophic orchid Epipogium aphyllum but not its asexual propagules

(2009) Melanie Roy et al.   ANNALS OF BOTANY

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

Amplification of soil fungal community DNA using the ITS86F and ITS4 primers

(2009) Tony Vancov et al.   FEMS MICROBIOLOGY LETTERS

From extensive clone libraries to comprehensive DNA arrays for the efficient and simultaneous detection and identification of orchid mycorrhizal fungi

(2009) Bart Lievens et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

(2009) M. Buée 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

Mycorrhizal interactions of orchids colonizing Estonian mine tailings hills

(2008) Richard P. Shefferson et al.   AMERICAN JOURNAL OF BOTANY

New tools for discovering and characterizing microbial diversity

(2008) Erick Cardenas et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

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

Orchid mycorrhiza: implications of a mycophagous life style

(2008) Hanne N. Rasmussen et al.   OIKOS

Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

(2008) Anders F. Andersson et al.   PLoS One