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:	Leho Tedersoo, Kessy Abarenkov, R Henrik Nilsson, Arthur Schüssler, Gwen-Aëlle Grelet, Petr Kohout, Jane Oja, Gregory M Bonito, Vilmar Veldre, Teele Jairus, Martin Ryberg, Karl-Henrik Larsson, Urmas Kõljalg
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6505976ecd50480f939e4efbe47ab144
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spelling	oai:doaj.org-article:6505976ecd50480f939e4efbe47ab1442021-11-04T06:08:27ZTidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.1932-620310.1371/journal.pone.0024940https://doaj.org/article/6505976ecd50480f939e4efbe47ab1442011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21949797/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Sequence 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.Leho TedersooKessy AbarenkovR Henrik NilssonArthur SchüsslerGwen-Aëlle GreletPetr KohoutJane OjaGregory M BonitoVilmar VeldreTeele JairusMartin RybergKarl-Henrik LarssonUrmas KõljalgPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 9, p e24940 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Leho Tedersoo Kessy Abarenkov R Henrik Nilsson Arthur Schüssler Gwen-Aëlle Grelet Petr Kohout Jane Oja Gregory M Bonito Vilmar Veldre Teele Jairus Martin Ryberg Karl-Henrik Larsson Urmas Kõljalg Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.
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.
format	article
author	Leho Tedersoo Kessy Abarenkov R Henrik Nilsson Arthur Schüssler Gwen-Aëlle Grelet Petr Kohout Jane Oja Gregory M Bonito Vilmar Veldre Teele Jairus Martin Ryberg Karl-Henrik Larsson Urmas Kõljalg
author_facet	Leho Tedersoo Kessy Abarenkov R Henrik Nilsson Arthur Schüssler Gwen-Aëlle Grelet Petr Kohout Jane Oja Gregory M Bonito Vilmar Veldre Teele Jairus Martin Ryberg Karl-Henrik Larsson Urmas Kõljalg
author_sort	Leho Tedersoo
title	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_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_sort	tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/6505976ecd50480f939e4efbe47ab144
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Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

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