ArticleDatabase : the journal of biological databases and curation2017
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.
Article in Database : the journal of biological databases and curation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
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- Overview and limitations of database in global traditional medicines: A narrative review.Acta pharmacologica Sinica · 2025Review
- Volatile Organic Compounds Produced byMicroorganisms · 2024Article
- Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains.Systematic biology · 2024Article
- What are the 100 most cited fungal genera?Studies in mycology · 2024Article
- Next-generation fungal identification using target enrichment and Nanopore sequencing.BMC genomics · 2023Article
- Publicly Available and Validated DNA Reference Sequences Are Critical to Fungal Identification and Global Plant Protection Efforts: A Use-Case inPlant disease · 2022Article
- Customization of a DADA2-based pipeline for fungal internal transcribed spacer 1 (ITS1) amplicon data sets.JCI insight · 2022Article
- Comparative genome analysis reveals high-level drug resistance markers in a clinical isolate ofFrontiers in cellular and infection microbiology · 2022Article
- How to publish a new fungal species, or name, version 3.0.IMA fungus · 2021Article
- Towards Genomic Criteria for Delineating Fungal Species.Journal of fungi (Basel, Switzerland) · 2020Article
- MIST: a Multilocus Identification System forApplied and environmental microbiology · 2020Article
- Species Identification in Plant-Associated Prokaryotes and Fungi Using DNA.Phytobiomes journal · 2020Article
- Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?IMA fungus · 2020Article
- NCBI Taxonomy: a comprehensive update on curation, resources and tools.Database : the journal of biological databases and curation · 2020Review
- Characterization of genetic diversity on tropical Trichoderma germplasm by sequencing of rRNA internal transcribed spacers.BMC research notes · 2019Article
- Trichoderma biodiversity in major ecological systems of China.Journal of microbiology (Seoul, Korea) · 2019Article
- Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation.Studies in mycology · 2019Article
- New light on names and naming of dark taxa.MycoKeys · 2018Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National Center for Biotechnology Information (NCBI) is dedicated to the clear association between name, specimen and sequence data. This database is focused on sequences obtained from type material stored in public collections. While the initial ITS sequence curation effort together with numerous fungal taxonomy experts attempted to cover as many orders as possible, we extended our latest focus to the family and genus ranks. We focused on Trichoderma for several reasons, mainly because the asexual and sexual synonyms were well documented, and a list of proposed names and type material were recently proposed and published. In this case study the recent taxonomic information was applied to do a complete taxonomic audit for the genus Trichoderma in the NCBI Taxonomy database. A name status report is available here: https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi. As a result, the ITS RefSeq Targeted Loci database at NCBI has been augmented with more sequences from type and verified material from Trichoderma species. Additionally, to aid in the cross referencing of data from single loci and genomes we have collected a list of quality records of the RPB2 gene obtained from type material in GenBank that could help validate future submissions. During the process of curation misidentified genomes were discovered, and sequence records from type material were found hidden under previous classifications. Source metadata curation, although more cumbersome, proved to be useful as confirmation of the type material designation. Database URL:http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353
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