ArticlePloS one2018
Evaluation of the ribosomal DNA internal transcribed spacer (ITS), specifically ITS1 and ITS2, for the analysis of fungal diversity by deep sequencing.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers, 1 of them a synthesis that pooled it.
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Who cites it
89 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Harnessing plant-microbe interactions: strategies for enhancing resilience and nutrient acquisition for sustainable agriculture.Frontiers in plant science · 2025Pooled it
- Development of a multiplex PCR assay for the authentication of six commercialFood chemistry. Molecular sciences · 2026Article
- Insights into fungal communities in some benchmark agricultural soils of Alberta, Canada.Microbiology (Reading, England) · 2026Article
- Limitations of Common Molecular Markers in Fungal Biodiversity Analysis and the Benefits of Their Synergistic Use.Molecular ecology resources · 2026Article
- Molecular identification with virulence gene profiles and in-vitro antifungal susceptibility of Candida species associated with subclinical mastitis in Anatolian buffaloes and dairy cows.Veterinary research communications · 2026Article
- Optimizing primer selection for microbial diversity studies in freshwater lakes: a comprehensive evaluation of 16S rRNA, 18S rRNA, and ITS gene regions.FEMS microbiology ecology · 2026Article
- The Medicinal MushroomJournal of fungi (Basel, Switzerland) · 2026Review
- Improved characterisation of coral-associated fungal communities using host DNA depletion and a novel ITS primer.ISME communications · 2026Article
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- Fungal dynamics and lignocellulose depolymerization in Pinus koraiensis: impact of longhorn beetle infestation.BMC microbiology · 2025Article
- Sclerotia-Mediated Soil Microbiome Modulation in Rice-Rapeseed Cropping Systems.Journal of fungi (Basel, Switzerland) · 2025Article
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- Exploring the Oral Microbiome: Understanding its Impact on the Development of Oral Squamous Cell Carcinoma.Current microbiology · 2025Review
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- Metabarcoding with Illumina and Oxford Nanopore Technologies provides complementary insights into tree seed mycobiota.Environmental microbiome · 2025Article
- Marine Mycobiomes Colonize Mediterranean Sponge Hosts in a Random Fashion.Microbial ecology · 2025Article
- Efficiency of the Coriolis µ Air Sampling Device for Fungal Contamination Analysis of Indoor Air: A Case Study.Pathogens (Basel, Switzerland) · 2025Article
- Protein Coding Low-CopyEcology and evolution · 2025Article
- Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch.Molecular ecology resources · 2025Article
29 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The nuclear ribosomal DNA internal transcribed spacer (ITS) has been widely used to assess the fungal composition in different environments by deep sequencing. To evaluate the ITS in the analysis of fungal diversity, comparisons of the clustering and taxonomy generated by sequencing with different portions of the whole fragment were conducted in this study. For a total of 83,120 full-length ITS sequences obtained from the UNITE database, it was found that, on average, ITS1 varied more than ITS2 within the kingdom Fungi; this variation included length and GC content variations and polymorphisms, with some polymorphisms specific to particular fungal groups. The taxonomic accuracy for ITS was higher than that for ITS1 or ITS2. The commonly used operational taxonomic unit (OTU) for evaluating fungal diversity and richness assigned several species to a single OTU even with clustering at 99.00% sequence similarity. The clustering and taxonomic capacities did not differ between ITS1 and ITS2. However, the OTU commonality between ITS1 and ITS2 was very low. To test this observation further, 219,741 pyrosequencing reads, including 39,840 full-length ITS sequences, were obtained from 10 soil samples and were clustered into OTUs. The pyrosequencing results agreed with the results of the in silico analysis. ITS1 might overestimate the fungal diversity and richness. Analyses using ITS, ITS1 and ITS2 yielded several different taxa, and the taxonomic preferences for ITS and ITS2 were similar. The results demonstrated that ITS2 alone might be a more suitable marker for revealing the operational taxonomic richness and taxonomy specifics of fungal communities when the full-length ITS is not available.
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