The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index.
High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples
Open accessAbstract
The kingdom Fungi is estimated to include 1.5 million or more species, playing key roles as decomposers, mutualists, and parasites in every biome on the earth. To comprehensively understand the diversity and ecology of this huge kingdom, DNA barcoding targeting the internal transcribed spacer (ITS) region of the nuclear ribosomal repeat has been regarded as a prerequisite procedure. By extensively surveying ITS sequences in public databases, we designed new ITS primers with improved coverage across diverse taxonomic groups of fungi compared to existing primers. An in silico analysis based on public sequence databases indicated that the newly designed primers matched 99% of ascomycete and basidiomycete ITS taxa (species, subspecies or varieties), causing little taxonomic bias toward either fungal group. Two of the newly designed primers could inhibit the amplification of plant sequences and would enable the selective investigation of fungal communities in mycorrhizal associations, soil, and other types of environmental samples. Optimal PCR conditions for the primers were explored in an in vitro investigation. The new primers developed in this study will provide a basis for ecological studies on the diversity and community structures of fungi in the era of massive DNA sequencing.
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Cites
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Cited by
Comparison and Validation of Some ITS Primer Pairs Useful for Fungal Metabarcoding Studies
Op De Beeck, M., Lievens, B., Busschaert, P., Declerck, S., Vangronsveld, J., & Colpaert, J. V. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097629 · Cited by 538
Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies
Zimmermann, J., Glöckner, G., Jahn, R., Enke, N., & Gemeinholzer, B. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12336 · Cited by 317
The potential role of marine fungi in plastic degradation – a review
Zeghal, E., Vaksmaa, A., Vielfaure, H., Boekhout, T., & Niemann, H. (2021) · Frontiers in Marine Science · doi:10.3389/fmars.2021.738877 · Cited by 155
Zhang, H., Du, H., & Xu, Y. (2021) · Applied and Environmental Microbiology · doi:10.1128/aem.02992-20 · Cited by 92
Entwistle, E. M., Zak, D. R., & Argiroff, W. A. (2018) · Ecological Monographs · doi:10.1002/ecm.1288 · Cited by 84
Metadata
- Authors
- Toju, H., Tanabe, A. S., Yamamoto, S., & Sato, H.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-07-12
- Volume
- 7
- Issue
- 7
- Pages
- e40863
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2101821016
- Cited by
- 1,256
- References
- 47
- FWCI
- 23.64
- Type
- journal article
- Language
- en
- Open access
- gold
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- Toju, H., Tanabe, A. S., Yamamoto, S., & Sato, H. (2012). High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples. PLoS ONE. https://doi.org/10.1371/journal.pone.0040863
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