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Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

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 a...

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Autores principales: Tedersoo, Leho, Abarenkov, Kessy, Nilsson, R. Henrik, Schüssler, Arthur, Grelet, Gwen-Aëlle, Kohout, Petr, Oja, Jane, Bonito, Gregory M., Veldre, Vilmar, Jairus, Teele, Ryberg, Martin, Larsson, Karl-Henrik, Kõljalg, Urmas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174234/
https://www.ncbi.nlm.nih.gov/pubmed/21949797
http://dx.doi.org/10.1371/journal.pone.0024940
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author Tedersoo, Leho
Abarenkov, Kessy
Nilsson, R. Henrik
Schüssler, Arthur
Grelet, Gwen-Aëlle
Kohout, Petr
Oja, Jane
Bonito, Gregory M.
Veldre, Vilmar
Jairus, Teele
Ryberg, Martin
Larsson, Karl-Henrik
Kõljalg, Urmas
author_facet Tedersoo, Leho
Abarenkov, Kessy
Nilsson, R. Henrik
Schüssler, Arthur
Grelet, Gwen-Aëlle
Kohout, Petr
Oja, Jane
Bonito, Gregory M.
Veldre, Vilmar
Jairus, Teele
Ryberg, Martin
Larsson, Karl-Henrik
Kõljalg, Urmas
author_sort Tedersoo, Leho
collection PubMed
description 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.
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spelling pubmed-31742342011-09-26 Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi Tedersoo, Leho Abarenkov, Kessy Nilsson, R. Henrik Schüssler, Arthur Grelet, Gwen-Aëlle Kohout, Petr Oja, Jane Bonito, Gregory M. Veldre, Vilmar Jairus, Teele Ryberg, Martin Larsson, Karl-Henrik Kõljalg, Urmas PLoS One Research Article 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. Public Library of Science 2011-09-15 /pmc/articles/PMC3174234/ /pubmed/21949797 http://dx.doi.org/10.1371/journal.pone.0024940 Text en Tedersoo et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Tedersoo, Leho
Abarenkov, Kessy
Nilsson, R. Henrik
Schüssler, Arthur
Grelet, Gwen-Aëlle
Kohout, Petr
Oja, Jane
Bonito, Gregory M.
Veldre, Vilmar
Jairus, Teele
Ryberg, Martin
Larsson, Karl-Henrik
Kõljalg, Urmas
Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi
title Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi
title_full Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi
title_fullStr Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi
title_full_unstemmed Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi
title_short Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi
title_sort tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174234/
https://www.ncbi.nlm.nih.gov/pubmed/21949797
http://dx.doi.org/10.1371/journal.pone.0024940
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