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

Artikel i vetenskaplig tidskrift
Författare 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
Publicerad i PLoS ONE
Volym 6
Nummer/häfte 9
Sidor e24940
ISSN 1932-6203
Publiceringsår 2011
Publicerad vid Institutionen för växt- och miljövetenskaper
Sidor e24940
Språk en
Länkar dx.plos.org/10.1371/journal.pone.00...
Ämnesord High-throughput sequencing; environmental sampling; fungi; barcoding; soil; mycorrhiza
Ämneskategorier Mikrobiologi, Morfologi, Bioinformatik och systembiologi, Terrestrisk ekologi, Biologisk systematik, Markbiologi

Sammanfattning

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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