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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

https://doi.org/10.1016/j.funeco.2010.05.002

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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inferred← citeshttps://doi.org/10.1111/1365-2664.12138openalex-snapshot

Decomposer communities in human‐impacted streams: species dominance rather than richness affects leaf decomposition

inferred← citeshttps://doi.org/10.1111/1365-2745.14298openalex-snapshot

Phorophyte preference of an epiphytic orchid ( Dendrobium wangliangii ) is independent of orchid mycorrhizal fungi that promote seed germination

inferred← citeshttps://doi.org/10.1111/1462-2920.12338openalex-snapshot

Identification accuracy and diversity reproducibility associated with internal transcribed spacer‐based fungal taxonomic library preparation

inferred← citeshttps://doi.org/10.1111/1462-2920.12894openalex-snapshot

Compartmentalized and contrasted response of ectomycorrhizal and soil fungal communities of S cots pine forests along elevation gradients in F rance and S pain

inferred← citeshttps://doi.org/10.1111/1462-2920.13026openalex-snapshot

Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter

inferred← citeshttps://doi.org/10.1111/1462-2920.13034openalex-snapshot

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems

inferred← citeshttps://doi.org/10.1111/1462-2920.15180openalex-snapshot

Major changes in grapevine wood microbiota are associated with the onset of esca, a devastating trunk disease

inferred← citeshttps://doi.org/10.1111/1574-6941.12046openalex-snapshot

Utilizing ITS1 and ITS2 to study environmental fungal diversity using pyrosequencing

inferred← citeshttps://doi.org/10.1111/1755-0998.12065openalex-snapshot

ITS 1 versus ITS 2 as DNA metabarcodes for fungi

inferred← citeshttps://doi.org/10.1111/1755-0998.12252openalex-snapshot

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

inferred← citeshttps://doi.org/10.1111/2041-210x.12073openalex-snapshot

Improved software detection and extraction of ITS1 and ITS 2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

inferred← citeshttps://doi.org/10.1111/efp.12515openalex-snapshot

Culture‐based methods using low‐temperature incubation revealed cold‐adapted fungal endophytes from semiarid forests

inferred← citeshttps://doi.org/10.1111/ele.13896openalex-snapshot

Temporal turnover of the soil microbiome composition is guild‐specific

inferred← citeshttps://doi.org/10.1111/geb.13772openalex-snapshot

The spatial patterns of community composition, their environmental drivers and their spatial scale dependence vary markedly between fungal ecological guilds

inferred← citeshttps://doi.org/10.1111/j.1096-0031.2011.00380.xopenalex-snapshot

Comprehensive taxon sampling reveals unaccounted diversity and morphological plasticity in a group of dimitic polypores (Polyporales, Basidiomycota)

inferred← citeshttps://doi.org/10.1111/j.1365-294x.2010.04898.xopenalex-snapshot

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

inferred← citeshttps://doi.org/10.1111/j.1365-294x.2012.05666.xopenalex-snapshot

Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules

inferred← citeshttps://doi.org/10.1111/j.1469-8137.2010.03373.xopenalex-snapshot

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

inferred← citeshttps://doi.org/10.1111/j.1469-8137.2011.03755.xopenalex-snapshot

Towards standardization of the description and publication of next‐generation sequencing datasets of fungal communities

inferred← citeshttps://doi.org/10.1111/j.1469-8137.2012.04284.xopenalex-snapshot

The composition of phyllosphere fungal assemblages of E uropean beech ( F agus sylvatica) varies significantly along an elevation gradient

inferred← citeshttps://doi.org/10.1111/j.1574-6941.2012.01314.xopenalex-snapshot

Structure and species composition of ectomycorrhizal fungal communities colonizing seedlings and adult trees of Pinus montezumae in Mexican neotropical forests

inferred← citeshttps://doi.org/10.1111/jbi.13802openalex-snapshot

Ectomycorrhizal fungal diversity predicted to substantially decline due to climate changes in North American Pinaceae forests

inferred← citeshttps://doi.org/10.1111/mec.12259openalex-snapshot

Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest

inferred← citeshttps://doi.org/10.1111/mec.12821openalex-snapshot

Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

inferred← citeshttps://doi.org/10.1111/mec.12854openalex-snapshot

Soil fungal communities of grasslands are environmentally structured at a regional scale in the A lps

inferred← citeshttps://doi.org/10.1111/mec.12947openalex-snapshot

Environmental drivers of ectomycorrhizal communities in Europe's temperate oak forests

inferred← citeshttps://doi.org/10.1111/mec.13018openalex-snapshot

Relocation, high‐latitude warming and host genetic identity shape the foliar fungal microbiome of poplars

inferred← citeshttps://doi.org/10.1111/mec.13051openalex-snapshot

Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield

inferred← citeshttps://doi.org/10.1111/nph.12532openalex-snapshot

Meta‐analysis of deep‐sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns

inferred← citeshttps://doi.org/10.1111/nph.13068openalex-snapshot

Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession

inferred← citeshttps://doi.org/10.1111/nph.13240openalex-snapshot

A continental view of pine‐associated ectomycorrhizal fungal spore banks: a quiescent functional guild with a strong biogeographic pattern

inferred← citeshttps://doi.org/10.1111/nph.14570openalex-snapshot

Investigating niche partitioning of ectomycorrhizal fungi in specialized rooting zones of the monodominant leguminous tree Dicymbe corymbosa

inferred← citeshttps://doi.org/10.1111/nph.15485openalex-snapshot

Removal of soil biota alters soil feedback effects on plant growth and defense chemistry

inferred← citeshttps://doi.org/10.1111/nph.17755openalex-snapshot

Warming drives a ‘hummockification’ of microbial communities associated with decomposing mycorrhizal fungal necromass in peatlands

inferred← citeshttps://doi.org/10.1111/nph.18109openalex-snapshot

Shift in tree species changes the belowground biota of boreal forests

inferred← citeshttps://doi.org/10.1111/nph.70012openalex-snapshot

Disentangling drivers behind fungal diversity gradients along altitude and latitude

inferred← citeshttps://doi.org/10.1111/nph.71523openalex-snapshot

Differential responses of fungal guilds to climatic effects mediated by changes in dominant vegetation

inferred← citeshttps://doi.org/10.1128/aem.01435-12openalex-snapshot

Pyrosequencing-Derived Bacterial, Archaeal, and Fungal Diversity of Spacecraft Hardware Destined for Mars

inferred← citeshttps://doi.org/10.1128/aem.02421-18openalex-snapshot

Superior Dispersal Ability Can Lead to Persistent Ecological Dominance throughout Succession

inferred← citeshttps://doi.org/10.1128/aem.03336-15openalex-snapshot

Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices

inferred← citeshttps://doi.org/10.1128/msystems.01017-20openalex-snapshot

Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood

inferred← citeshttps://doi.org/10.1139/cjb-2013-0239openalex-snapshot

Ectomycorrhizal fungal hyphae communities vary more along a pH and nitrogen gradient than between decayed wood and mineral soil microsites

inferred← citeshttps://doi.org/10.11646/phytotaxa.295.1.1openalex-snapshot

USING Next-Generation Sequencing (NGS) TO UNCOVER DIVERSITY OF WOOD-DECAYING FUNGI IN NEOTROPICAL ATLANTIC FORESTS

inferred← citeshttps://doi.org/10.1186/1471-2148-12-50openalex-snapshot

Selectivity by host plants affects the distribution of arbuscular mycorrhizal fungi: evidence from ITS rDNA sequence metadata

inferred← citeshttps://doi.org/10.1186/s12866-015-0538-xopenalex-snapshot

Lignocellulose-converting enzyme activity profiles correlate with molecular systematics and phylogeny grouping in the incoherent genus Phlebia (Polyporales, Basidiomycota)

inferred← citeshttps://doi.org/10.1186/s13104-016-2203-3openalex-snapshot

Mycofier: a new machine learning-based classifier for fungal ITS sequences

inferred← citeshttps://doi.org/10.1186/s40168-018-0589-yopenalex-snapshot

Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential

inferred← citeshttps://doi.org/10.1186/s40793-025-00730-5openalex-snapshot

Contrasting stability of fungal and bacterial communities during long-term decomposition of fungal necromass in Arctic tundra

inferred← citeshttps://doi.org/10.1186/s43008-020-00033-zopenalex-snapshot

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

inferred← citeshttps://doi.org/10.12688/f1000research.15704.1openalex-snapshot

ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis

inferred← citeshttps://doi.org/10.1371/journal.pone.0034847openalex-snapshot

Unravelling Soil Fungal Communities from Different Mediterranean Land-Use Backgrounds

inferred← citeshttps://doi.org/10.1371/journal.pone.0038040openalex-snapshot

Phylogenetic Analysis of a Spontaneous Cocoa Bean Fermentation Metagenome Reveals New Insights into Its Bacterial and Fungal Community Diversity

inferred← citeshttps://doi.org/10.1371/journal.pone.0053987openalex-snapshot

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

inferred← citeshttps://doi.org/10.1371/journal.pone.0062419openalex-snapshot

Filling Gaps in Biodiversity Knowledge for Macrofungi: Contributions and Assessment of an Herbarium Collection DNA Barcode Sequencing Project

inferred← citeshttps://doi.org/10.1371/journal.pone.0078295openalex-snapshot

Fungi at a Small Scale: Spatial Zonation of Fungal Assemblages around Single Trees

inferred← citeshttps://doi.org/10.1371/journal.pone.0100668openalex-snapshot

Leaf and Root-Associated Fungal Assemblages Do Not Follow Similar Elevational Diversity Patterns

inferred← citeshttps://doi.org/10.1371/journal.pone.0111525openalex-snapshot

The Impact of Selective-Logging and Forest Clearance for Oil Palm on Fungal Communities in Borneo

inferred← citeshttps://doi.org/10.1371/journal.pone.0142759openalex-snapshot

Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas

inferred← citeshttps://doi.org/10.1371/journal.pone.0164533openalex-snapshot

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat

inferred← citeshttps://doi.org/10.1371/journal.pone.0215024openalex-snapshot

Internal transcribed spacer 2 (ITS2) molecular morphometric analysis based species delimitation of foliar endophytic fungi from Aglaia elaeagnoidea, Flacourtia inermis and Premna serratifolia

inferred← citeshttps://doi.org/10.14214/sf.104openalex-snapshot

The effect of latitude, season and needle-age on the mycota of Scots pine (Pinus sylvestris) in Finland

inferred← citeshttps://doi.org/10.17638/03022579openalex-snapshot

Diversity and Roles of Mycorrhizal Fungi in the Bee Orchid Ophrys apifera

inferred← citeshttps://doi.org/10.20868/upm.thesis.69351openalex-snapshot

Papel funcional de los hongos endófitos del olmo común (Ulmus minor Mill.) en la resistencia al estrés biótico y abiótico

inferred← citeshttps://doi.org/10.2174/1874136301005010081openalex-snapshot

Molecular Identification of Fungi: Rationale, Philosophical Concerns, and the UNITE Database

inferred← citeshttps://doi.org/10.3389/fmicb.2015.01045openalex-snapshot

Relations of microbiome characteristics to edaphic properties of tropical soils from Trinidad

inferred← citeshttps://doi.org/10.3389/fmicb.2016.01976openalex-snapshot

Microbial Community Structure and Function of Soil Following Ecosystem Conversion from Native Forests to Teak Plantation Forests

inferred← citeshttps://doi.org/10.3389/fmicb.2017.01011openalex-snapshot

Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir

inferred← citeshttps://doi.org/10.3389/fmicb.2017.01127openalex-snapshot

Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes

inferred← citeshttps://doi.org/10.3389/fmicb.2017.02560openalex-snapshot

Host Specificity for Bacterial, Archaeal and Fungal Communities Determined for High- and Low-Microbial Abundance Sponge Species in Two Genera

inferred← citeshttps://doi.org/10.3389/fmicb.2018.00568openalex-snapshot

Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1168907openalex-snapshot

Pseudomonas sivasensis 2RO45 inoculation alters the taxonomic structure and functioning of the canola rhizosphere microbial community

inferred← citeshttps://doi.org/10.3389/fmicb.2024.1460330openalex-snapshot

The functions and factors governing fungal communities and diversity in agricultural waters: insights into the ecosystem services aquatic mycobiota provide

inferred← citeshttps://doi.org/10.3389/fpls.2023.1125942openalex-snapshot

Core endophytic mycobiome in Ulmus minor and its relation to Dutch elm disease resistance

inferred← citeshttps://doi.org/10.3390/f10030263openalex-snapshot

Host Phylogenetic Relatedness and Soil Nutrients Shape Ectomycorrhizal Community Composition in Native and Exotic Pine Plantations

inferred← citeshttps://doi.org/10.3390/jof6040190openalex-snapshot

Production of Fungal Mycelia in a Temperate Coniferous Forest Shows Distinct Seasonal Patterns

inferred← citeshttps://doi.org/10.3390/jof7070498openalex-snapshot

Impacts of Sodium Arsenite on Wood Microbiota of Esca-Diseased Grapevines

inferred← citeshttps://doi.org/10.3390/jof8070673openalex-snapshot

Factors Controlling Dead Wood Decomposition in an Old-Growth Temperate Forest in Central Europe

inferred← citeshttps://doi.org/10.3390/microorganisms9050896openalex-snapshot

The Impact of Pine Wood Nematode Infection on the Host Fungal Community

inferred← citeshttps://doi.org/10.3852/13-039openalex-snapshot

What is Antrodia sensu stricto?

inferred← citeshttps://doi.org/10.3852/14-293openalex-snapshot

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences

inferred← citeshttps://doi.org/10.3852/15-207openalex-snapshot

Quantifying the associations between fungal endophytes and biocontrol-induced herbivory of invasive purple loosestrife ( Lythrum salicaria L.)

inferred← citeshttps://doi.org/10.3897/mycokeys.10.5126openalex-snapshot

Cloning of ribosomal ITS PCR products creates frequent, non-random chimeric sequences – a test involving heterozygotes between Gymnopus dichrous taxa I and II

inferred← citeshttps://doi.org/10.3897/mycokeys.53.34761openalex-snapshot

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

inferred← citeshttps://doi.org/10.3897/mycokeys.86.77431openalex-snapshot

A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens

inferred← citeshttps://doi.org/10.4137/ebo.s6271openalex-snapshot

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

inferred← citeshttps://doi.org/10.5194/we-26-47-2026openalex-snapshot

Decoding fungal communities: ITS extraction matters more than ASVs vs. OTUs

inferred← citeshttps://doi.org/10.5772/23975openalex-snapshot

Fungal Diversity – An Overview

inferred← citeshttps://doi.org/10.5943/cream/9/1/20openalex-snapshot

Molecular characterization of fungal endophytes associated with medicinal plant, Ficus racemosa

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