The DOI matches its Crossref record; 35 of the 35 references it cites were found in a registry or an index.
A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts
Open accessAbstract
The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric-artificially joined-DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.
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Cites
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,826
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Edgar, R. C. (2013) · Nature Methods · doi:10.1038/nmeth.2604 · Cited by 16,707
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Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr381 · Cited by 15,114
Self-citationSchoch, C. L., Seifert, K. A., Huhndorf, S., Robert, V., Spouge, J. L., Levesque, C. A., Chen, W., Fungal Barcoding Consortium, Fungal Barcoding Consortium Author List, Bolchacova, E., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1117018109 · Cited by 5,120
Self-citationGlobal diversity and geography of soil fungi
Tedersoo, L., Bahram, M., Põlme, S., Kõljalg, U., Yorou, N. S., Wijesundera, R., Ruiz, L. V., Vasco-Palacios, A. M., Thu, P. Q., Suija, A., et al. (2014) · Science · doi:10.1126/science.1256688 · Cited by 3,702
Self-citationTowards a unified paradigm for sequence‐based identification of fungi
Kõljalg, U., Nilsson, R. H., Abarenkov, K., Tedersoo, L., Taylor, A. F. S., Bahram, M., Bates, S. T., Bruns, T. D., Bengtsson‐Palme, J., Callaghan, T. M., et al. (2013) · Molecular Ecology · doi:10.1111/mec.12481 · Cited by 3,586
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The UNITE database for molecular identification of fungi – recent updates and future perspectives
Abarenkov, K., Henrik Nilsson, R., Larsson, K., Alexander, I. J., Eberhardt, U., Erland, S., Høiland, K., Kjøller, R., Larsson, E., Pennanen, T., et al. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2009.03160.x · Cited by 1,927
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Cited by
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1189 · Cited by 6,357
“Results from this curation effort have been used and cited by various publications (42) (43) (44) (45) (46) and have aided additional efforts at validating subsets of reference sequences, e.g. medically significant species (47) .”
MethodMicrobial Interkingdom Interactions in Roots Promote Arabidopsis Survival
Durán, P., Thiergart, T., Garrido-Oter, R., Agler, M., Kemen, E., Schulze-Lefert, P., & Hacquard, S. (2018) · Cell · doi:10.1016/j.cell.2018.10.020 · Cited by 1,037
Tedersoo, L., Anslan, S., Bahram, M., Põlme, S., Riit, T., Liiv, I., Kõljalg, U., Kisand, V., Nilsson, H., Hildebrand, F., et al. (2015) · MycoKeys · doi:10.3897/mycokeys.10.4852 · Cited by 583
Self-citationAccuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences
Edgar, R. C. (2018) · PeerJ · doi:10.7717/peerj.4652 · Cited by 319
Self-citationPauvert, C., Buée, M., Laval, V., Edel-Hermann, V., Fauchery, L., Gautier, A., Lesur, I., Vallance, J., & Vacher, C. (2019) · Fungal Ecology · doi:10.1016/j.funeco.2019.03.005 · Cited by 253
Metadata
- Authors
- Nilsson, R. H., Tedersoo, L., Ryberg, M., Kristiansson, E., Hartmann, M., Unterseher, M., Porter, T. M., Bengtsson-Palme, J., Walker, D. M., de Sousa, F., Gamper, H. A., Larsson, E., Larsson, K.-H., Kõljalg, U., Edgar, R. C., & Abarenkov, K.
- Venue
- Microbes and environments
- Published
- 2015
- Volume
- 30
- Issue
- 2
- Pages
- 145-150
- ISSN
- 1342-6311 (ISSN-L)
- 1347-4405
- OpenAlex
- W1975182819
- Cited by
- 271
- References
- 35
- FWCI
- 31.12
- Type
- journal article
- Language
- en
- Open access
- diamond
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- Nilsson, R. H., Tedersoo, L., Ryberg, M., Kristiansson, E., Hartmann, M., Unterseher, M., Porter, T. M., Bengtsson-Palme, J., Walker, D. M., de Sousa, F., Gamper, H. A., Larsson, E., Larsson, K.-H., Kõljalg, U., Edgar, R. C., & Abarenkov, K. (2015). A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts. Microbes and environments. https://doi.org/10.1264/jsme2.me14121
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Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
