Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi

Names of phytopathogenic fungi: a practical guide

(2021) Pedro W Crous et al.   PHYTOPATHOLOGY

High-throughput sequencing view on the magnitude of global fungal diversity

(2021) Petr Baldrian et al.   FUNGAL DIVERSITY

Single Strain High-Depth NGS Reveals High rDNA (ITS-LSU) Variability in the Four Prevalent Pathogenic Species of the Genus Candida

(2021) Claudia Colabella et al.   Microorganisms

Fungal taxonomy and sequence-based nomenclature

(2021) Robert Lücking et al.   Nature Microbiology

Black fungus and COVID-19: role of otorhinolaryngologists and audiologists

(2021) Aiza Fatima Raza et al.   EUROPEAN ARCHIVES OF OTO-RHINO-LARYNGOLOGY

Using High-Throughput Amplicon Sequencing to Evaluate Intragenomic Variation and Accuracy in Species Identification of Cordyceps Species

(2021) Soumitra Paloi et al.   Journal of Fungi

Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi

(2020) Michael Bradshaw et al.   BMC EVOLUTIONARY BIOLOGY

Intragenomic polymorphisms in the ITS region of high-quality genomes of the Hypoxylaceae (Xylariales, Ascomycota)

(2020) Marc Stadler et al.   MYCOLOGICAL PROGRESS

High quality genome sequences of thirteen Hypoxylaceae (Ascomycota) strengthen the phylogenetic family backbone and enable the discovery of new taxa

(2020) Daniel Wibberg et al.   FUNGAL DIVERSITY

Cryptic diversity of the genus Beauveria with a new species from Thailand

(2020) Artit Khonsanit et al.   MYCOLOGICAL PROGRESS

Threats Posed by the Fungal Kingdom to Humans, Wildlife, and Agriculture

(2020) Matthew C. Fisher et al.   mBio

Fungal species concepts in the genomics era

(2020) Jianping Xu   GENOME

The amazing potential of fungi: 50 ways we can exploit fungi industrially

(2019) Kevin D. Hyde et al.   FUNGAL DIVERSITY

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Fungal species boundaries in the genomics era

(2019) Daniel R. Matute et al.   FUNGAL GENETICS AND BIOLOGY

Population genomics revealed cryptic species within host-specific zombie-ant fungi (Ophiocordyceps unilateralis)

(2019) Noppol Kobmoo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Patterns of PCR Amplification Artifacts of the Fungal Barcode Marker in a Hybrid Mushroom

(2019) Jun-Liang Zhou et al.   Frontiers in Microbiology

A Sequel to Sanger: amplicon sequencing that scales

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

Can we use environmental DNA as holotypes?

(2018) Sinang Hongsanan et al.   FUNGAL DIVERSITY

Novel and interesting Ophiocordyceps spp. ( Ophiocordycipitaceae , Hypocreales ) with superficial perithecia from Thailand

(2018) J. Luangsa-ard et al.   STUDIES IN MYCOLOGY

Beauveria majiangensis, a new entomopathogenic fungus from Guizhou, China

(2018) WAN-HAO CHEN et al.   Phytotaxa

Removing contaminants from databases of draft genomes

(2018) Jennifer Lu et al.   PLoS Computational Biology

Birth-and-Death Evolution and Reticulation of ITS Segments of Metschnikowia andauensis and Metschnikowia fructicola rDNA Repeats

(2018) Matthias Sipiczki et al.   Frontiers in Microbiology

NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective

(2018) Claudia Colabella et al.   IMA Fungus

Utilization of Hybrid Assembly Approach to Determine the Genome of an Opportunistic Pathogenic Fungus, Candida albicans TIMM 1768

(2018) Suresh Panthee et al.   Genome Biology and Evolution

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

(2018) Felix Heeger et al.   Molecular Ecology Resources

Introducing ribosomal tandem repeat barcoding for fungi

(2018) Christian Wurzbacher et al.   Molecular Ecology Resources

Early Ongoing Speciation of Ogataea uvarum Sp. Nov. Within the Grape Ecosystem Revealed by the Internal Variability Among the rDNA Operon Repeats

(2018) Luca Roscini et al.   Frontiers in Microbiology

Genetic characterization, pathogenicity and benomyl susceptibility of Lecanicillium fungal isolates from Argentina

(2018) Romina G. Manfrino et al.   JOURNAL OF APPLIED ENTOMOLOGY

High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations

(2018) Leho Tedersoo et al.   Molecular Ecology Resources

Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation

(2018) D. Vu et al.   STUDIES IN MYCOLOGY

Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)

(2017) Bernard A. Dujon et al.   GENETICS

Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community

(2017) Huzefa A. Raja et al.   JOURNAL OF NATURAL PRODUCTS

Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates

(2017) H. Badouin et al.   MOLECULAR ECOLOGY

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

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

rRNA Pseudogenes in Filamentous Ascomycetes as Revealed by Genome Data

(2017) Yi Li et al.   G3-Genes Genomes Genetics

Mining the Volatilomes of Plant-Associated Microbiota for New Biocontrol Solutions

(2017) Aurélien Bailly et al.   Frontiers in Microbiology

Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)

(2017) Bernard A. Dujon et al.   GENETICS

High-throughput sequencing of multiple amplicons for barcoding and integrative taxonomy

(2017) Perrine Cruaud et al.   Scientific Reports

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

(2017) Francesca Giordano et al.   Scientific Reports

Searching Biomarkers in the Sequenced Genomes of Staphylococcus for their Rapid Identification

(2016) Ravi Kumar et al.   INDIAN JOURNAL OF MICROBIOLOGY

Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions ofRhizophagus irregularisandGigaspora margaritais high and isolate-dependent

(2016) Odile Thiéry et al.   MOLECULAR ECOLOGY

ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities

(2016) Anders Bjørnsgaard Aas et al.   Molecular Ecology Resources

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

Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens

(2016) Jie Chen et al.   PLoS One

No evidence for extensive horizontal gene transfer in the genome of the tardigradeHypsibius dujardini

(2016) Georgios Koutsovoulos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

(2016) Tom O. Delmont et al.   PeerJ

INC-Seq: accurate single molecule reads using nanopore sequencing

(2016) Chenhao Li et al.   GigaScience

Pitfalls of haplotype phasing from amplicon-based long-read sequencing

(2016) Thomas W. Laver et al.   Scientific Reports

Molecular analysis of fungal populations in patients with oral candidiasis using next-generation sequencing

(2016) Yumi Imabayashi et al.   Scientific Reports

Studying Genome Heterogeneity within the Arbuscular Mycorrhizal Fungal Cytoplasm

(2015) Eva Boon et al.   Genome Biology and Evolution

Genome Wide Analysis for Rapid Identification of Vibrio Species

(2015) Vipin Chandra Kalia et al.   INDIAN JOURNAL OF MICROBIOLOGY

A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus

(2015) Vipin Chandra Kalia et al.   INDIAN JOURNAL OF MICROBIOLOGY

Genome Wide Analysis for Searching Novel Markers to Rapidly Identify Clostridium Strains

(2015) Anay Kekre et al.   INDIAN JOURNAL OF MICROBIOLOGY

A nuclear ribosomal DNA pseudogene in triatomines opens a new research field of fundamental and applied implications in Chagas disease

(2015) María Angeles Zuriaga et al.   MEMORIAS DO INSTITUTO OSWALDO CRUZ

One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes

(2015) J.B. Stielow et al.   PERSOONIA

Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade

(2015) Thomas C. Boothby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Response to Comment on "Global diversity and geography of soil fungi"

(2015) L. Tedersoo et al.   SCIENCE

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

(2015) Leho Tedersoo et al.   MycoKeys

Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

(2015) Shadi Shokralla et al.   Scientific Reports

Genomic evidence for adaptation by gene duplication

(2014) Wenfeng Qian et al.   GENOME RESEARCH

Intraspecific and intragenomic variability of ITS rDNA sequences reveals taxonomic problems in Ceratocystis fimbriata sensu stricto

(2014) T.C. Harrington et al.   MYCOLOGIA

Ribosomal DNA Sequence Heterogeneity Reflects Intraspecies Phylogenies and Predicts Genome Structure in Two Contrasting Yeast Species

(2014) Claire West et al.   SYSTEMATIC BIOLOGY

The Candida Pathogenic Species Complex

(2014) S. A. Turner et al.   Cold Spring Harbor Perspectives in Medicine

Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus

(2014) Kui Lin et al.   PLoS Genetics

Analysis of plant microbe interactions in the era of next generation sequencing technologies

(2014) Claudia Knief   Frontiers in Plant Science

Unexpected cross-species contamination in genome sequencing projects

(2014) Samier Merchant et al.   PeerJ

Identification, molecular characterization, and evolution of group I introns at the expansion segment D11 of 28S rDNA in Rhizoctonia species

(2013) Dolores González   Fungal Biology

Evolutionary Mobility of the Ribosomal DNA Array in Yeasts

(2013) Estelle Proux-Wéra et al.   Genome Biology and Evolution

Non-concerted ITS evolution in fungi, as revealed from the important medicinal fungus Ophiocordyceps sinensis

(2013) Yi Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary consequences of putative intra-and interspecific hybridization in agaric fungi

(2013) Karen W. Hughes et al.   MYCOLOGIA

The ‘obligate diploid’ Candida albicans forms mating-competent haploids

(2013) Meleah A. Hickman et al.   NATURE

Metschnikowia Species Share a Pool of Diverse rRNA Genes Differing in Regions That Determine Hairpin-Loop Structures and Evolve by Reticulation

(2013) Matthias Sipiczki et al.   PLoS One

Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

(2013) Daniel L. Lindner et al.   Ecology and Evolution

Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

(2012) R. Henrik Nilsson et al.   Evolutionary 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

Species reassignment of Geotrichum bryndzae, Geotrichum phurueaensis, Geotrichum silvicola and Geotrichum vulgare based on phylogenetic analyses and mating compatibility

(2012) M. Groenewald et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Emerging fungal threats to animal, plant and ecosystem health

(2012) Matthew C. Fisher et al.   NATURE

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

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Limits of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences as species barcodes for Fungi

(2012) L. Kiss   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Genetic analyses place most Spanish isolates of Beauveria bassiana in a molecular group with word-wide distribution

(2011) Inmaculada Garrido-Jurado et al.   BMC MICROBIOLOGY

Regulation of ribosomal RNA gene copy number and its role in modulating genome integrity and evolutionary adaptability in yeast

(2011) Takehiko Kobayashi   CELLULAR AND MOLECULAR LIFE SCIENCES

The diversity of Terfezia desert truffles: new species and a highly variable species complex with intrasporocarpic nrDNA ITS heterogeneity

(2011) Gábor M. Kovács 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

Fungi—an unusual source for cosmetics

(2010) K. D. Hyde et al.   FUNGAL DIVERSITY

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

A reason for overlap peaks in direct sequencing of rRNA gene ITS in Pleurotus nebrodensis

(2009) Chenyang Huang et al.   FEMS MICROBIOLOGY LETTERS

Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing

(2009) S. A. James et al.   GENOME RESEARCH

Dioszegia antarctica sp. nov. and Dioszegia cryoxerica sp. nov., psychrophilic basidiomycetous yeasts from polar desert soils in Antarctica

(2009) L. B. Connell et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Detection of rDNA ITS polymorphism in Rhizoctonia solani AG 2-1 isolates

(2009) Joke Pannecoucque et al.   MYCOLOGIA

Putative natural hybrid between Puccinia lagenophorae and an unknown rust fungus on Senecio madagascariensis in KwaZulu-Natal, South Africa

(2009) Louise Morin et al.  

Purifying selection and birth-and-death evolution in the class II hydrophobin gene families of the ascomycete Trichoderma/Hypocrea

(2008) Christian P. Kubicek et al.   BMC EVOLUTIONARY BIOLOGY

Intragenomic Variation of Fungal Ribosomal Genes Is Higher than Previously Thought

(2008) U. K. Simon et al.   MOLECULAR BIOLOGY AND EVOLUTION