A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

Microbes and Environments
R Henrik NilssonKessy Abarenkov

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-b...Continue Reading

References

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Citations

Feb 3, 2016·FEMS Microbiology Ecology·Beat FreyMartin Hartmann
May 5, 2016·Yeast·Kyria L Boundy-MillsBenedetta Turchetti
Aug 24, 2016·Genome Génome / Conseil National De Recherches Canada·Kristiina MarkChristoph Scheidegger
Aug 17, 2016·Proteomics·Johan Bengtsson-PalmeKaisa Thorell
Apr 14, 2017·Canadian Journal of Microbiology·Gavin KernaghanAmanda Griffin
Jul 5, 2017·The Laryngoscope·Yi Chen ZhaoAlkis James Psaltis
May 17, 2018·PloS One·Allison S Quan, Michael B Eisen
Mar 11, 2018·Scientific Reports·Teresita M Porter, Mehrdad Hajibabaei
Dec 19, 2016·IMA Fungus·Michael A CastellanoTerry W Henkel
Jul 25, 2019·Environmental Microbiology·Lluvia Vargas-GastélumMeritxell Riquelme
Jan 22, 2020·Veterinary Dermatology·Charles W BradleyChristine L Cain
Mar 30, 2020·Applied and Environmental Microbiology·Elizabeth C SternhagenLaura Aldrich-Wolfe
Jun 1, 2018·The ISME Journal·Cheolwoon WooNaomichi Yamamoto
Jan 1, 2018·Mycological Progress·Elisa BanchiLucia Muggia
May 30, 2019·Frontiers in Microbiology·Valentina Hurtado-McCormickJustin Robert Seymour
Apr 25, 2018·Frontiers in Microbiology·Ruibo SunBinbin Liu

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Methods Mentioned

BETA
PCR

Software Mentioned

BLAST
USEARCH
UPARSE
UCHIME
Perl
ITSx
UNITE
R
INSDC

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