Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

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Bengtsson-Palme J., Ryberg M., Hartmann M., Branco S., Wang Z., Godhe A., ...More

METHODS IN ECOLOGY AND EVOLUTION, vol.4, no.10, pp.914-919, 2013 (SCI-Expanded) identifier identifier

  • Publication Type: Article / Article
  • Volume: 4 Issue: 10
  • Publication Date: 2013
  • Doi Number: 10.1111/2041-210x.12073
  • Journal Name: METHODS IN ECOLOGY AND EVOLUTION
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Page Numbers: pp.914-919
  • Istanbul University Affiliated: No

Abstract

The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases.