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

By Johan Bengtsson-Palme, Martin Ryberg, Martin Hartmann, S. Branco, Z. Wang, Anna Godhe, P. Wit, M. Sánchez-García, Ingo Ebersberger, F. Sousa and 11 more. 2013

1,206 citations recorded by the source corpus.

Subfields: Cell Biology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/0a6ebee57b105f162b101468fac2fc00d97ea4ee

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Citations in the corpus

Biological, physicochemical and plant health responses in lettuce and strawberry in soil or peat amended with biochar (2016, positive): “ITSx v.1.0.11 was used to extract the ITS2 sequences (Bengtsson-Palme et al., 2013).”
Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi (2015, neutral): “ITS1 and ITS2 sequences were processed in ITSx 1.0.9 (Bengtsson-Palme et al. 2013) to remove flanking 18S, 5.8S and 28S rRNA gene fragments.”
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications (2018, methodology): “Public fungal ITS sequences are sourced from the INDSC and subjected to a range of quality control measures, including processing with ITSx (16) and UCHIME (17) in an attempt to reject non-ITS and chimeric sequences.”
The “Plastisphere” of Biodegradable Plastics Is Characterized by Specific Microbial Taxa of Alpine and Arctic Soils (2020, methodology): “The OTU centroid sequences were then filtered for the presence of ribosomal signatures using Metaxa2 (Bengtsson-Palme et al., 2015) or ITSx (Bengtsson-Palme et al., 2013).”
Improving ITS sequence data for identification of plant pathogenic fungi (2014, background): “It has been the subject of several annotation efforts (Tedersoo et al. 2011; Bengtsson-Palme et al. 2013; Kõljalg et al. 2013), but these have in part been biased towards basidiomycetes and mycorrhizal fungi.”
metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data (2015, methodology): “Additionally, its software design has carried over into specialized packages for other barcoding regions, such as the ITS region in eukaryotes (Bengtsson-Palme et al. 2013b).”
Assembly of seed-associated microbial communities within and across successive plant generations (2017, methodology): “The variable ITS1 regions of the fungal internal transcribed spacer were extracted with the Perl-based software ITSx 1.0.4 (Bengtsson-Palme et al. 2013).”
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi (2014, methodology): “DNA barcoding and standards for GenBank submissions The ITSx script (46) has been a helpful and time-saving tool in curating the ITS records.”