ArticleEcology and evolution2013
Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi.
Article in Ecology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed.
- The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies.Molecular ecology resources · 2025Article
- Article
- Comparison of commonly used software pipelines for analyzing fungal metabarcoding data.BMC genomics · 2024Article
- Article
- Influence of scat ageing on the gut microbiome: how old is too old?BMC genomics · 2023Article
- A Custom Regional DNA Barcode Reference Library for Lichen-Forming Fungi of the Intermountain West, USA, Increases Successful Specimen Identification.Journal of fungi (Basel, Switzerland) · 2023Article
- Patterns in soil microbial diversity across Europe.Nature communications · 2023Article
- Spatial and Temporal Genetic Diversity and Population Structure of Hemileia vastatrix from Peruvian Coffee Plantations.The plant pathology journal · 2021Article
- TheFungal systematics and evolution · 2020Article
- Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi.BMC evolutionary biology · 2020Article
- Evaluating High-Throughput Sequencing Data of Microalgae Living in Melting Snow: Improvements and LimitationsFottea (Praha) · 2019Article
- Patterns of PCR Amplification Artifacts of the Fungal Barcode Marker in a Hybrid Mushroom.Frontiers in microbiology · 2019Article
- Mycobiome diversity: high-throughput sequencing and identification of fungi.Nature reviews. Microbiology · 2019Review
- Integrative taxonomy reveals hidden species within a common fungal parasite of ladybirds.Scientific reports · 2018Article
- Considerations and consequences of allowing DNA sequence data as types of fungal taxa.IMA fungus · 2018Article
- Article
- Formal description of sequence-based voucherlessIMA fungus · 2018Article
- Sequence-based nomenclature: a reply to ThinesIMA fungus · 2018Article
- Cryptic species diversity in polypores: theMycoKeys · 2018Article
- Birth-and-Death Evolution and Reticulation of ITS Segments ofFrontiers in microbiology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular investigations of environmental samples. In this study 454 amplicon pyrosequencing of the ITS1 region was applied to 99 phylogenetically diverse axenic single-spore cultures of fungi (Dikarya: Ascomycota and Basidiomycota) to investigate levels of intragenomic variation. Three species (one Basidiomycota and two Ascomycota), in addition to a positive control species known to contain ITS paralogs, displayed levels of molecular variation indicative of intragenomic variation; taxon inflation due to presumed intragenomic variation was ≈9%. Intragenomic variability in the ITS region appears to be widespread but relatively rare in fungi (≈3-5% of species investigated in this study), suggesting this problem may have minor impacts on species richness estimates relative to PCR and/or pyrosequencing errors. Our results indicate that 454 amplicon pyrosequencing represents a powerful tool for investigating levels of ITS intragenomic variability across taxa, which may be valuable for better understanding the fundamental mechanisms underlying concerted evolution of repetitive DNA regions.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.