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

No abstract is available for this paper.

• Publication year

  2011

• Venue

  New Phytologist

• Publication date

  2011-11-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1111/j.1469-8137.2011.03838.xPMID 21806618
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

  2011cited by this paper
• Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences

  2011cited by this paper
• A bioinformatics pipeline for sequence-based analyses of fungal biodiversity.

  2011cited by this paper
• Where is the unseen fungal diversity hidden? A study of Mortierella reveals a large contribution of reference collections to the identification of fungal environmental sequences.

  2011cited by this paper
• Fungal diversity in deep-sea sediments – the presence of novel fungal groups

  2010cited by this paper
• Vertical distribution of fungal communities in tallgrass prairie soil

  2010cited by this paper
• The environmental clade LKM11 and Rozella form the deepest branching clade of fungi.

  2010cited by this paper
• Phylogenetic and ecological analyses of soil and sporocarp DNA sequences reveal high diversity and strong habitat partitioning in the boreal ectomycorrhizal genus Russula (Russulales; Basidiomycota).

  2010cited by this paper
• Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

  2010cited by this paper
• 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases.

  2010cited by this paper
• An open source chimera checker for the fungal ITS region

  2010cited by this paper
• Current state and perspectives of fungal DNA barcoding and rapid identification procedures

  2010cited by this paper
• The UNITE database for molecular identification of fungi--recent updates and future perspectives.

  2010cited by this paper
• Massively parallel 454‐sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites

  2010cited by this paper
• Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics

  2010influential reference
• ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

  2010cited by this paper
• The ITS region as a target for characterization of fungal communities using emerging sequencing technologies.

  2009cited by this paper
• The ITS2 Database III—sequences and structures for phylogeny

  2009cited by this paper
• 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity.

  2009cited by this paper
• Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers. (Russulales; Basidiomycota) in Alaska, based on soil and sporocarp DNA

  2009cited by this paper
• 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.

  2009cited by this paper
• The search for the fungal tree of life.

  2009cited by this paper
• Progress towards DNA barcoding of fungi

  2009cited by this paper
• A software pipeline for processing and identification of fungal ITS sequences

  2009cited by this paper
• Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere.

  2009cited by this paper
• How to know unknown fungi: the role of a herbarium.

  2009cited by this paper
• Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest.

  2009cited by this paper
• Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates.

  2009cited by this paper
• Preserving Accuracy in GenBank

  2008cited by this paper
• LSID Tester, a tool for testing Life Science Identifier resolution services

  2008cited by this paper
• Preserving accuracy in GenBank

  2008cited by this paper
• Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

  2008cited by this paper
• Statistical assignment of DNA sequences using Bayesian phylogenetics.

  2008cited by this paper
• Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life.

  2008cited by this paper
• Fruiting body and soil rDNA sampling detects complementary assemblage of Agaricomycotina (Basidiomycota, Fungi) in a hemlock‐dominated forest plot in southern Ontario

  2008cited by this paper
• Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR

  2007cited by this paper
• Short pyrosequencing reads suffice for accurate microbial community analysis

  2007cited by this paper
• MEGAN analysis of metagenomic data.

  2007cited by this paper
• Soil Fungal Communities Underneath Willow Canopies on a Primary Successional Glacier Forefront: rDNA Sequence Results Can Be Affected by Primer Selection and Chimeric Data

  2007cited by this paper
• Assembling The Fungal Tree of Life (AFTOL)

  2005cited by this paper
• Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples

  2005cited by this paper
• Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi

  2005cited by this paper
• Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases.

  2003cited by this paper
• BMC Bioinformatics BioMed Central

  2003cited by this paper
• Revisiting the rDNA sequence diversity of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica

  2003cited by this paper
• Seasonal Dynamics of Previously Unknown Fungal Lineages in Tundra Soils

  2003cited by this paper
• Ribosomal ITS sequences and plant phylogenetic inference.

  2003cited by this paper
• Extensive fungal diversity in plant roots.

  2002cited by this paper
• The Bioperl toolkit: Perl modules for the life sciences.

  2002cited by this paper
• The Closest BLAST Hit Is Often Not the Nearest Neighbor

  2001cited by this paper
• The magnitude of fungal diversity: the 1.5 million species estimate revisited * * Paper presented at

  2001cited by this paper
• Phylogenetic species recognition and species concepts in fungi.

  2000cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997cited by this paper
• Identifying microbial diversity in the natural environment: a molecular phylogenetic approach.

  1996cited by this paper
• Erratum: The ITS Region of Nuclear Ribosomal DNAZ: A Valuable Source of Evidence on Angiosperm Phylogeny

  1995cited by this paper
• Length variation in the internal transcribed spacer of ribosomal DNA in chanterelles

  1994cited by this paper
• ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts

  1993cited by this paper
• Fungal Molecular Systematics

  1991cited by this paper
• Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics

  1990cited by this paper

• Investigating fungal diversity through metabarcoding for environmental samples: assessment of ITS1 and ITS2 Illumina sequencing using multiple defined mock communities with different classification methods and reference databases

  2025cites this paper
• Biotechnological Potential of Endophytic Fungi Isolated From the Endangered Medicinal Plant Gloriosa superba.

  2025cites this paper
• Molecular Detection of Rust Fungus (Puccinia spp.) on Sugarcane using ITS region

  2025cites this paper
• Isolasi, Identifikasi dan Karakterisasi Jamur Pyricularia oryzae Penyebab Penyakit Blas pada Tanaman Padi di Kediri, Jawa Timur

  2024cites this paper
• Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing

  2024cites this paper
• Pathogenicity, Host Resistance, and Genetic Diversity of Fusarium Species under Controlled Conditions from Soybean in Canada

  2024cites this paper
• Adapted molecular methods to unravel the recalcitrant mycorrhizal associations of Aucoumea klaineana Pierre.

  2024cites this paper
• Association of Golovinomyces ambrosiae and Podosphaera xanthii in causing powdery mildew disease of Guizotia abyssinica L.f. Cass in India

  2023cites this paper
• AN ITS GENE-MEDIATED MOLECULAR DETECTION OF FUNGI ASSOCIATED WITH NATURAL AND ARTIFICIAL AGARWOOD FROM Aquilaria malaccensis

  2023cites this paper
• Cropping sequence affects the structure and diversity of pathogenic and non-pathogenic soil microbial communities

  2023cites this paper
• DNA Extraction and PCR Optimization for DNA Barcode Analysis of Commercially-Grown Coffee Varieties in Nepal

  2022cites this paper
• A poisoned apple: First insights into community assembly and networks of the fungal pathobiome of healthy-looking senescing leaves of temperate trees in mixed forest ecosystem

  2022cites this paper
• LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

  2021cites this paper
• Morpho‐molecular and mating‐type locus diversity of Ustilaginoidea virens: an incitant of false smut of rice from Southern parts of India

  2021cites this paper
• Beginners guide to bioinformatics for high throughput sequencing

  2020cites this paper
• Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

  2020cites this paper
• A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758)

  2020cites this paper
• DNA Barcoding of Fungi in the Forest Ecosystem of the Psunj and Papuk Mountains in Croatia

  2020cites this paper
• Morphological and molecular characterization of powdery mildew on watermelon plants in São Paulo state

  2019cites this paper
• Hyper production of carboxy methyl cellulase by Thermomyces dupontii utilizing physical and chemical mutagenesis

  2019cites this paper
• Environmental genomics of the Saccharomyces sensu stricto group

  2019cites this paper
• Molecular identification and antibacterial properties of an ericoid associated mycorrhizal fungus

  2019cites this paper
• Profile of microbial community of naturally fermented Sumbawa mare’s milk using next-generation sequencing

  2019cites this paper
• Introduction to Endophytic Fungi Associated with Lichens i.e. Endolichenic Fungi

  2019cites this paper
• Targeted metagenomics approach to capture the biodiversity of Saccharomyces genus in wild environments

  2019cites this paper
• Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them

  2018cites this paper
• Rapid Bioconversion of Rice Straw Using Cellulolytic Cultures for Improved and Sustainable Crop Productivity and Soil Fertility in Mwea, Kenya

  2018cites this paper
• Long-read DNA metabarcoding of ribosomal rRNA in the analysis of fungi from aquatic environments

  2018cites this paper
• eDNA IN ENVIRONMENTAL MONITORING

  2018cites this paper
• Isolation and characterization of aflatoxigenic Aspergillus spp. from maize of livestock feed from Bogor

  2018cites this paper
• Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis

  2018cites this paper
• Genetic diversity and aggressiveness of Fusarium species isolated from soybean in Alberta, Canada

  2018cites this paper
• Isolating and Identifying Fungal Endophytes from Roots of Rare Orchid Cypripedium arietinum in Grand Sable Dunes, Michigan

  2018cites this paper
• Identifikasi fungi endofit dari buah dan biji juwet (Syzygium cumini L.) skeels berdasarkan karakter morfologi dan analisis rDNA ITS (Internal Transcribed Spacer)

  2018cites this paper
• Removal of Heavy Metal Compounds from Industrial Wastes Using a Novel Locally-Isolated Vanrija sp . HMAT 2

  2017cites this paper
• Ciliate micrograzer dynamics of the New England Shelf

  2017cites this paper
• Forgotten fungi—the gut mycobiome in human health and disease

  2017cites this paper
• Exploring the Plant Microbiome Through Multi-omics Approaches

  2017cites this paper
• Evolution of Fungal Endophytes and Their Functional Transitions Between Endophytism and Saprotrophism

  2017cites this paper
• Supplement S3 - Detailed DNA metabarcoding methods

  2016cites this paper
• Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation.

  2016cites this paper
• Environmental DNA Barcode Sequence Capture: Targeted, PCR-free Sequence Capture for Biodiversity Analysis from Bulk Environmental Samples

  2016cites this paper
• Marine fungal community associated with standing plants of Spartina maritima (Curtis) Fernald

  2016cites this paper
• Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas

  2016cites this paper
• Rapid detection and identification of Stachybotrys and Chaetomium species using tissue PCR analysis.

  2016cites this paper
• Diversity of Suillus Fungi from Pine (Pinus merkusii) Stands at Various Locations in Bandung Area, Indonesia

  2016cites this paper
• A High-Level Fungal Diversity in the Intertidal Sediment of Chinese Seas Presents the Spatial Variation of Community Composition

  2016cites this paper
• Complexity in Mutualisms: Indirect Interactions With Multiple Parties

  2015cites this paper
• Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples - an example of saddle fungi.

  2015cites this paper
• 'Species Concept' in Microbial Taxonomy and Systematics

  2015cites this paper
• Why Nuclear Ribosomal Internal Transcribed Spacer (ITS) has been Selected asthe DNA Barcode for Fungi

  2015cites this paper
• Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order - Phaeomoniellales.

  2015cites this paper
• Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda

  2015cites this paper
• Heredity of zinc tolerance in Suillus luteus and impact of metal pollution on ectomycorrhizal fungal communities

  2014cites this paper
• The sooty moulds

  2014cites this paper
• Multiple ITS Copies Reveal Extensive Hybridization within Rheum (Polygonaceae), a Genus That Has Undergone Rapid Radiation

  2014cites this paper
• Identification accuracy and diversity reproducibility associated with internal transcribed spacer-based fungal taxonomic library preparation.

  2014cites this paper
• Multiple ITS Haplotypes in the Genome of the Lichenized Basidiomycete Cora inversa (Hygrophoraceae): Fact or Artifact?

  2014cites this paper
• Fungal High‐throughput Taxonomic Identification tool for use with Next‐Generation Sequencing (FHiTINGS)

  2014cites this paper
• Molecular Analysis of Colletotrichum Species in the Carposphere and Phyllosphere of Olive

  2014cites this paper
• Impact of primer choice on characterization of orchid mycorrhizal communities using 454 pyrosequencing

  2014cites this paper
• Comparison and Validation of Some ITS Primer Pairs Useful for Fungal Metabarcoding Studies

  2014cites this paper
• Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

  2014cites this paper
• Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods.

  2014cites this paper
• Tallgrass prairie soil fungal communities are resilient to climate change

  2014cites this paper
• A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning

  2014cites this paper
• Determinants of root‐associated fungal communities within Asteraceae in a semi‐arid grassland

  2014cites this paper
• MANCHA DE Cercospora EM Toona ciliata NO

  2014cites this paper
• Biological and physical characterization of aerosols generated in showers

  2014cites this paper
• Profiling of Fungal Communities Quantitative , Ultra-High-Throughput Spacer-Specific Primers Enables Improved Selection of Internal Transcribed

  2013cites this paper
• Comparison of ITS1 and ITS2 rDNA in 454 sequencing of hyperdiverse fungal communities

  2013cites this paper
• Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities

  2013cites this paper
• Ion Torrent PGM as Tool for Fungal Community Analysis: A Case Study of Endophytes in Eucalyptus grandis Reveals High Taxonomic Diversity

  2013cites this paper
• CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

  2013cites this paper
• From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition

  2013cites this paper
• Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error

  2012influential citation
• Fungal Diversity Is Not Determined by Mineral and Chemical Differences in Serpentine Substrates

  2012cites this paper
• CREST – Classification Resources for Environmental Sequence Tags

  2012influential citation
• Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

  2012cites this paper
• Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN

  2012cites this paper
• Communities of Arbuscular Mycorrhizal Fungi Detected in Forest Soil Are Spatially Heterogeneous but Do Not Vary throughout the Growing Season

  2012cites this paper
• RIBOSOMAL LARGE SUBUNIT AS A UNIVERSAL MOLECULAR MARKER FOR CANDIDA GALIS

  2012cites this paper
• Ectomycorrhizal Fungal Communities of Edible Ectomycorrhizal Mushrooms

  2012cites this paper
• Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

  2012cites this paper