PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens

A Sequel to Sanger: amplicon sequencing that scales

(2018) Paul D. N. Hebert et al.   BMC GENOMICS

Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK)

(2018) R. Henrik Nilsson et al.   MycoKeys

Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase

(2018) Daniel J. G. Lahr et al.   BIOTECHNIQUES

Clustering of circular consensus sequences: accurate error correction and assembly of single molecule real-time reads from multiplexed amplicon libraries

(2018) Felix Francis et al.   BMC BIOINFORMATICS

Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments

(2018) Felix Heeger et al.   Molecular Ecology Resources

Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

(2018) Sten Anslan et al.   MycoKeys

A quantitative SMRT cell sequencing method for ribosomal amplicons

(2017) Bethan M. Jones et al.   JOURNAL OF MICROBIOLOGICAL METHODS

PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data

(2017) Sten Anslan et al.   Molecular Ecology Resources

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

DNA barcoding and LC-MS metabolite profiling of the lichen-forming genus Melanelia: Specimen identification and discrimination focusing on Icelandic taxa

(2017) Maonian Xu et al.   PLoS One

Community Profiling of Fusarium in Combination with Other Plant-Associated Fungi in Different Crop Species Using SMRT Sequencing

(2017) Florian Walder et al.   Frontiers in Plant Science

Examining Sources of Error in PCR by Single-Molecule Sequencing

(2017) Vladimir Potapov et al.   PLoS One

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation

(2016) Kristiina Mark et al.   GENOME

Polymerase specific error rates and profiles identified by single molecule sequencing

(2016) Matthew S. Hestand et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

High-resolution community profiling of arbuscular mycorrhizal fungi

(2016) Klaus Schlaeppi et al.   NEW PHYTOLOGIST

Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches

(2016) Rebecca Yahr et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

(2016) Patrick D. Schloss et al.   PeerJ

Identification of Putative Coffee Rust Mycoparasites via Single-Molecule DNA Sequencing of Infected Pustules

(2015) Timothy Y. James et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A DNA barcoding approach for identification of hidden diversity in Parmeliaceae (Ascomycota):Parmelia sensu strictoas a case study

(2015) Pradeep K. Divakar et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 %

(2015) Alena K. Oliver et al.   Fungal Ecology

Next generation multilocus sequence typing (NGMLST) and the analytical software program MLSTEZ enable efficient, cost-effective, high-throughput, multilocus sequencing typing

(2015) Yuan Chen et al.   FUNGAL GENETICS AND BIOLOGY

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database—the quality controlled standard tool for routine identification of human and animal pathogenic fungi

(2015) Laszlo Irinyi et al.   MEDICAL MYCOLOGY

Initial colonization, community assembly and ecosystem function: fungal colonist traits and litter biochemistry mediate decay rate

(2015) Lauren C. Cline et al.   MOLECULAR ECOLOGY

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles

(2014) Katherine Kennedy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith et al.   PLoS One

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

(2014) C. L. Schoch et al.   Database-The Journal of Biological Databases and Curation

The Genera of Fungi: fixing the application of type species of generic names

(2014) Pedro W. Crous et al.   IMA Fungus

Multiple ITS Haplotypes in the Genome of the Lichenized Basidiomycete Cora inversa (Hygrophoraceae): Fact or Artifact?

(2013) Robert Lücking et al.   JOURNAL OF MOLECULAR EVOLUTION

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

DNA barcoding of brown Parmeliae (Parmeliaceae) species: a molecular approach for accurate specimen identification, emphasizing species in Greenland

(2013) Steven D. Leavitt et al.   ORGANISMS DIVERSITY & EVOLUTION

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform

(2013) Erin B Fichot et al.   Microbiome

DNA-based identification of lichen-forming fungi: can publicly available sequence databases aid in lichen diversity inventories of Mount Cameroon (West Africa)?

(2012) Elizabeth Ayuk OROCK et al.   LICHENOLOGIST

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

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

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

(2011) Antonietta Mello et al.   MYCOLOGIA

DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context

(2011) Laura J. Kelly et al.   NEW PHYTOLOGIST

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

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