ArticleApplied and environmental microbiology2014
From genus to phylum: large-subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition.
Article in Applied and environmental microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed.
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- Molecular and ultrastructural morphological analyses of highly metamorphosed Aspergillus fumigatus on human formalin-fixed paraffin-embedded tissue.Medical molecular morphology · 2024Article
- Fine-scale characterization of the soybean rhizosphere microbiome via synthetic long reads and avidity sequencing.Environmental microbiome · 2024Article
- Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2.BMC bioinformatics · 2024Article
- Solitary Bees Host More Bacteria and Fungi on Their Cuticle than Social Bees.Microorganisms · 2023Article
- Fungal taxonomy: A puzzle with many missing piecesBiomedica : revista del Instituto Nacional de Salud · 2023Article
- Invasive pulmonary aspergillosis with candidiasis: usefulness of molecular and ultrastructural morphological analysis on FFPE tissue for invasive fungal infections.Medical molecular morphology · 2023Article
- Season, Vegetation Proximity and Building Age Shape the Indoor Fungal Communities' Composition at City-Scale.Journal of fungi (Basel, Switzerland) · 2022Article
- Fatty acid secretion by the white-rot fungus, Trametes versicolor.Journal of industrial microbiology & biotechnology · 2022Article
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- Using High-Throughput Amplicon Sequencing to Evaluate Intragenomic Variation and Accuracy in Species Identification ofJournal of fungi (Basel, Switzerland) · 2021Article
- Building of an Internal Transcribed Spacer (ITS) Gene Dataset to Support the Italian Health Service in Mushroom Identification.Foods (Basel, Switzerland) · 2021Article
- Simple Matching Using QIIME 2 and RDP Reveals Misidentified Sequences and an Underrepresentation of Fungi in Reference Datasets.Frontiers in genetics · 2021Article
- Microbial Communities Influence Soil Dissolved Organic Carbon Concentration by Altering Metabolite Composition.Frontiers in microbiology · 2021Article
- Endophytic Fungi as Potential Biological Control Agents against Grapevine Trunk Diseases in Alentejo Region.Biology · 2020Article
- The Mycobiota of the Deep Sea: What Omics Can Offer.Life (Basel, Switzerland) · 2020Review
- Ericoid mycorrhizal symbiosis: theoretical background and methods for its comprehensive investigation.Mycorrhiza · 2020Review
- Ectomycorrhizal community composition of organic and mineral soil horizons in silver fir (Abies alba Mill.) stands.Mycorrhiza · 2020Article
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4 authors.
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Abstract
We compared the classification accuracy of two sections of the fungal internal transcribed spacer (ITS) region, individually and combined, and the 5' section (about 600 bp) of the large-subunit rRNA (LSU), using a naive Bayesian classifier and BLASTN. A hand-curated ITS-LSU training set of 1,091 sequences and a larger training set of 8,967 ITS region sequences were used. Of the factors evaluated, database composition and quality had the largest effect on classification accuracy, followed by fragment size and use of a bootstrap cutoff to improve classification confidence. The naive Bayesian classifier and BLASTN gave similar results at higher taxonomic levels, but the classifier was faster and more accurate at the genus level when a bootstrap cutoff was used. All of the ITS and LSU sections performed well (>97.7% accuracy) at higher taxonomic ranks from kingdom to family, and differences between them were small at the genus level (within 0.66 to 1.23%). When full-length sequence sections were used, the LSU outperformed the ITS1 and ITS2 fragments at the genus level, but the ITS1 and ITS2 showed higher accuracy when smaller fragment sizes of the same length and a 50% bootstrap cutoff were used. In a comparison using the larger ITS training set, ITS1 and ITS2 had very similar accuracy classification for fragments between 100 and 200 bp. Collectively, the results show that any of the ITS or LSU sections we tested provided comparable classification accuracy to the genus level and underscore the need for larger and more diverse classification training sets.
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