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Träfflista för sökning "hsv:(LANTBRUKSVETENSKAPER) hsv:(Veterinärmedicin) hsv:(Patobiologi) ;lar1:(cth);pers:(Ryberg Martin 1976)"

Search: hsv:(LANTBRUKSVETENSKAPER) hsv:(Veterinärmedicin) hsv:(Patobiologi) > Chalmers University of Technology > Ryberg Martin 1976

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  • Nilsson, R. Henrik, 1976, et al. (author)
  • A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts
  • 2015
  • In: Microbes and Environments. - 1342-6311 .- 1347-4405. ; 30:2, s. 145-150
  • Journal article (peer-reviewed)abstract
    • 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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2.
  • Nilsson, R. Henrik, 1976, et al. (author)
  • Top 50 most wanted fungi
  • 2016
  • In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 12, s. 29-40
  • Journal article (peer-reviewed)abstract
    • Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond “Fungi”. There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more.
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