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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MARC

Bengtsson-Palme, Johan,1985Gothenburg University,Göteborgs universitet,Institutionen för neurovetenskap och fysiologi, sektionen för fysiologi,Institute of Neuroscience and Physiology, Department of Physiology (author)

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

Article/chapterEnglish2013

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2013

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LIBRIS-ID:oai:research.chalmers.se:5e2b7184-a284-4ed1-9fe5-1ef9ce360f85
https://research.chalmers.se/publication/180760URI
https://doi.org/10.1111/2041-210X.12073DOI
https://gup.ub.gu.se/publication/180760URI
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-210224URI

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Language:English
Summary in:English

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Subject category:art swepub-publicationtype
Subject category:ref swepub-contenttype

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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.

Subject headings and genre

NATURVETENSKAP Biologi Botanik hsv//swe
NATURAL SCIENCES Biological Sciences Botany hsv//eng
NATURVETENSKAP Biologi Biologisk systematik hsv//swe
NATURAL SCIENCES Biological Sciences Biological Systematics hsv//eng
LANTBRUKSVETENSKAPER Lantbruksvetenskap, skogsbruk och fiske Markvetenskap hsv//swe
AGRICULTURAL SCIENCES Agriculture, Forestry and Fisheries Soil Science hsv//eng
LANTBRUKSVETENSKAPER Annan lantbruksvetenskap Miljö- och naturvårdsvetenskap hsv//swe
AGRICULTURAL SCIENCES Other Agricultural Sciences Environmental Sciences related to Agriculture and Land-use hsv//eng
NATURVETENSKAP Biologi Ekologi hsv//swe
NATURAL SCIENCES Biological Sciences Ecology hsv//eng
NATURVETENSKAP Biologi Mikrobiologi hsv//swe
NATURAL SCIENCES Biological Sciences Microbiology hsv//eng
NATURVETENSKAP Data- och informationsvetenskap Bioinformatik hsv//swe
NATURAL SCIENCES Computer and Information Sciences Bioinformatics hsv//eng
MEDICIN OCH HÄLSOVETENSKAP Medicinska och farmaceutiska grundvetenskaper Mikrobiologi inom det medicinska området hsv//swe
MEDICAL AND HEALTH SCIENCES Basic Medicine Microbiology in the medical area hsv//eng
NATURVETENSKAP Biologi Bioinformatik och systembiologi hsv//swe
NATURAL SCIENCES Biological Sciences Bioinformatics and Systems Biology hsv//eng
NATURVETENSKAP Biologi Zoologi hsv//swe
NATURAL SCIENCES Biological Sciences Zoology hsv//eng
NATURVETENSKAP Data- och informationsvetenskap Datavetenskap hsv//swe
NATURAL SCIENCES Computer and Information Sciences Computer Sciences hsv//eng
molecular ecology
next-generation sequencing
Perl
Fungi
ribosomal DNA
Fungi
molecular ecology
next-generation sequencing
Perl
ribosomal DNA

Added entries (persons, corporate bodies, meetings, titles ...)

Ryberg, Martin,1976Uppsala universitet,Systematisk biologi(Swepub:uu)marry118 (author)
Hartmann, MartinEidgenossische Forschungsanstalt fur Wald, Schnee Und Landschaft Eth-Bereichs,Forschungsanstalt Agroscope Reckenholz-Tanikon (author)
Branco, SaraUniversity of California (author)
Wang, Zheng,1980Yale University(Swepub:cth)wzheng (author)
Godhe, Anna,1967Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences(Swepub:gu)xgodan (author)
De Wit, Pierre,1978Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences(Swepub:gu)xdewpi (author)
Sánchez-García, MarisolUniversity of Tennessee (author)
Ebersberger, IngoJohann Wolfgang Goethe Universität Frankfurt am Main,Goethe University Frankfurt (author)
Sousa, Filipe de,1982Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences(Swepub:gu)xdesfi (author)
Amend, Anthony S.University of Hawaii (author)
Jumpponen, AriKansas State University (author)
Unterseher, MartinUniversität Greifswald,University of Greifswald (author)
Kristiansson, Erik,1978Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper, matematisk statistik,Department of Mathematical Sciences, Mathematical Statistics(Swepub:gu)xkrier (author)
Abarenkov, KessyTartu Ülikool,University of Tartu (author)
Bertrand, YannGothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences(Swepub:gu)xberya (author)
Sanli, Kemal,1986Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences(Swepub:gu)xsanlk (author)
Eriksson, Martin,1970Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)marte (author)
Vik, UnniUniversitetet i Oslo,University of Oslo (author)
Veldre, Vilmar (author)
Nilsson, R. Henrik,1976Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences(Swepub:gu)xnihen (author)
Göteborgs universitetInstitutionen för neurovetenskap och fysiologi, sektionen för fysiologi (creator_code:org_t)

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In:Methods in Ecology and Evolution4:10, s. 914-9192041-210X

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Botany

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Biological Syste ...

AGRICULTURAL SCIENCES: AGRICULTURAL SCI ...; and Agriculture Fore ...; and Soil Science

AGRICULTURAL SCIENCES: AGRICULTURAL SCI ...; and Other Agricultur ...; and Environmental Sc ...

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Ecology

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Microbiology

NATURAL SCIENCES: NATURAL SCIENCES; and Computer and Inf ...; and Bioinformatics

MEDICAL AND HEALTH SCIENCES: MEDICAL AND HEAL ...; and Basic Medicine; and Microbiology in ...

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Zoology

NATURAL SCIENCES: NATURAL SCIENCES; and Computer and Inf ...; and Computer Science ...

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