Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
Artikel i vetenskaplig tidskrift, 2013
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, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences.
ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines.
ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
ribosomal DNA
next-generation sequencing
molecular ecology
Fungi
Perl
Författare
Johan Bengtsson Palme
Göteborgs universitet
Martin Ryberg
Uppsala universitet
Martin Hartmann
Forschungsanstalt Agroscope Reckenholz-Tanikon
Eidgenossische Forschungsanstalt fur Wald, Schnee Und Landschaft Eth-Bereichs
Sara Branco
University of California
Zheng Wang
Yale University
Anna Godhe
Göteborgs universitet
Pierre De Wit
Göteborgs universitet
Marisol Sánchez-García
University of Tennessee
Ingo Ebersberger
Johann Wolfgang Goethe Universität Frankfurt am Main
Filipe de Sousa
Göteborgs universitet
Anthony S. Amend
University of Hawaii
Ari Jumpponen
Kansas State University
Martin Unterseher
Universität Greifswald
Erik Kristiansson
Göteborgs universitet
Chalmers, Matematiska vetenskaper, Matematisk statistik
Kessy Abarenkov
Tartu Ülikool
Yann Bertrand
Göteborgs universitet
Kemal Sanli
Göteborgs universitet
Martin Eriksson
Chalmers, Sjöfart och marin teknik
Unni Vik
Universitetet i Oslo
Vilmar Veldre
R. Henrik Nilsson
Göteborgs universitet
Methods in Ecology and Evolution
2041210x (eISSN)
Vol. 4 10 914-919Ämneskategorier
Botanik
Biologisk systematik
Markvetenskap
Miljö- och naturvårdsvetenskap
Ekologi
Mikrobiologi
Bioinformatik (beräkningsbiologi)
Mikrobiologi inom det medicinska området
Bioinformatik och systembiologi
Zoologi
Datavetenskap (datalogi)
DOI
10.1111/2041-210X.12073