Authors
Johan Bengtsson‐Palme, Martin Ryberg, Martin Hartmann, Sara Branco, Zheng Wang, Anna Godhe, Pierre De Wit, Marisol Sánchez‐García, Ingo Ebersberger, Filipe de Sousa, Anthony Amend, Ari Jumpponen, Martin Unterseher, Erik Kristiansson, Kessy Abarenkov, Yann JK Bertrand, Kemal Sanli, K Martin Eriksson, Unni Vik, Vilmar Veldre, R Henrik Nilsson
Publication date
2013/10
Journal
Methods in ecology and evolution
Volume
4
Issue
10
Pages
914-919
Description
- 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.
- We introduce ITSx, a Perl‐based software tool to extract ITS1, 5.8S and ITS2 – as well as full‐length ITS sequences – from both Sanger and high‐throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants …
Scholar articles
J Bengtsson‐Palme, M Ryberg, M Hartmann, S Branco… - Methods in ecology and evolution, 2013