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Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of ITS sequences of mycorrhizal fungi

Tedersoo, Leho (author)
Abarenkov, Kessy (author)
Nilsson, R. Henrik, 1976 (author)
Gothenburg University,Göteborgs universitet,Institutionen för växt- och miljövetenskaper,Department of Plant and Environmental Sciences,Göteborgs Universitet
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Schüssler, Arthur (author)
Grelet, Gwen-Aëlle (author)
Kohout, Petr (author)
Oja, Jane (author)
Bonito, Gregory M. (author)
Veldre, Vilmar (author)
Jairus, Teele (author)
Ryberg, Martin, 1976 (author)
University of Tennessee
Larsson, Karl-Henrik, 1948 (author)
Kõljalg, Urmas (author)
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 (creator_code:org_t)
2011-09-15
2011
English.
In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:9
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  • Journal article (peer-reviewed)
Abstract Subject headings
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  • Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

Subject headings

NATURVETENSKAP  -- Biologi -- Biologisk systematik (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Biological Systematics (hsv//eng)
NATURVETENSKAP  -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
NATURVETENSKAP  -- Biologi -- Ekologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Ecology (hsv//eng)
LANTBRUKSVETENSKAPER  -- Lantbruksvetenskap, skogsbruk och fiske -- Markvetenskap (hsv//swe)
AGRICULTURAL SCIENCES  -- Agriculture, Forestry and Fisheries -- Soil Science (hsv//eng)
NATURVETENSKAP  -- Biologi -- Zoologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Zoology (hsv//eng)
NATURVETENSKAP  -- Biologi -- Mikrobiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Microbiology (hsv//eng)

Keyword

High-throughput sequencing; environmental sampling; fungi; barcoding; soil; mycorrhiza

Publication and Content Type

ref (subject category)
art (subject category)

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