title: Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.
abstract: 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.
authors.affiliation: Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia. leho.tedersoo@ut.ee
authors.forename: Leho
authors.initials: L
authors.lastname: Tedersoo
authors.forename: Kessy
authors.initials: K
authors.lastname: Abarenkov
authors.forename: R Henrik
authors.initials: RH
authors.lastname: Nilsson
authors.forename: Arthur
authors.initials: A
authors.lastname: Schüssler
authors.forename: Gwen-Aëlle
authors.initials: GA
authors.lastname: Grelet
authors.forename: Petr
authors.initials: P
authors.lastname: Kohout
authors.forename: Jane
authors.initials: J
authors.lastname: Oja
authors.forename: Gregory M
authors.initials: GM
authors.lastname: Bonito
authors.forename: Vilmar
authors.initials: V
authors.lastname: Veldre
authors.forename: Teele
authors.initials: T
authors.lastname: Jairus
authors.forename: Martin
authors.initials: M
authors.lastname: Ryberg
authors.forename: Karl-Henrik
authors.initials: KH
authors.lastname: Larsson
authors.forename: Urmas
authors.initials: U
authors.lastname: Kõljalg
mesh_terms: D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D030561:Databases, Nucleic Acid; D004463:Ecology; D005843:Geography; D007391:International Cooperation; D020407:Internet; D038821:Mycorrhizae / Q000235:genetics*; D018517:Plant Roots / Q000235:genetics; D012407:rRNA Operon / Q000235:genetics*
chemical_list: D021903:DNA, Ribosomal Spacer