ArticlePloS one2011
Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 59 citations in OpenAlex.
- Diverse, Cryptic, and Undescribed: Club and Coral Fungi in a Temperate Australian Forest.Journal of fungi (Basel, Switzerland) · 2025Article
- Next-generation sequencing applications in food science: fundamentals and recent advances.Frontiers in bioengineering and biotechnology · 2025Review
- Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera.Journal of fungi (Basel, Switzerland) · 2023Article
- DNA Metabarcoding Reveals Cryptic Diversity in Forest Soils on the Isolated Brazilian Trindade Island, South Atlantic.Microbial ecology · 2023Article
- Taxonomy and evolution ofComputational and structural biotechnology journal · 2018Review
- Article
- Effect of soil moisture on root-associated fungal communities of Erica dominans in Drakensberg mountains in South Africa.Mycorrhiza · 2017Article
- Improving taxonomic accuracy for fungi in public sequence databases: applying 'one name one species' in well-defined genera with Trichoderma/Hypocrea as a test case.Database : the journal of biological databases and curation · 2017Article
- Clavulina-Membranomyces is the most important lineage within the highly diverse ectomycorrhizal fungal community of Abies religiosa.Mycorrhiza · 2017Article
- A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts.Microbes and environments · 2015Article
- Ectomycorrhizal fungus diversity and community structure with natural and cultivated truffle hosts: applying lessons learned to future truffle culture.Mycorrhiza · 2014Review
- Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide.The New phytologist · 2013Review
- High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology.Applied and environmental microbiology · 2013Review
Corrections and comments
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Authors and funding
13 authors at 8 institutions in 8 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.
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