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Statements

Subject Item
n2:RIV%2F67985939%3A_____%2F11%3A00369201%21RIV13-AV0-67985939
rdf:type
n5:Vysledek skos:Concept
dcterms: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. 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.
dcterms:title
Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi
skos:prefLabel
Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi
skos:notation
RIV/67985939:_____/11:00369201!RIV13-AV0-67985939
n5:predkladatel
n12:ico%3A67985939
n3:aktivita
n4:Z n4:I
n3:aktivity
I, Z(AV0Z60050516)
n3:cisloPeriodika
9
n3:dodaniDat
n7:2013
n3:domaciTvurceVysledku
n8:2602253
n3:druhVysledku
n9:J
n3:duvernostUdaju
n18:S
n3:entitaPredkladatele
n13:predkladatel
n3:idSjednocenehoVysledku
235330
n3:idVysledku
RIV/67985939:_____/11:00369201
n3:jazykVysledku
n10:eng
n3:klicovaSlova
mycorrhizal fungi; databases; ITS
n3:klicoveSlovo
n11:databases n11:mycorrhizal%20fungi n11:ITS
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[70F51510D24E]
n3:nazevZdroje
PLoS ONE
n3:obor
n15:EF
n3:pocetDomacichTvurcuVysledku
1
n3:pocetTvurcuVysledku
13
n3:rokUplatneniVysledku
n7:2011
n3:svazekPeriodika
6
n3:tvurceVysledku
Tedersoo, L. Nilsson, R. H. Köljalg, U. Grelet, G.-A. Kohout, Petr Ryberg, M. Abarenkov, K. Jairus, T. Larssosn, K.-H. Veldre, V. Schüssler, A. Bonito, G. M. Oja, J.
n3:wos
000295041700079
n3:zamer
n16:AV0Z60050516
s:issn
1932-6203
s:numberOfPages
7
n17:doi
10.1371/journal.pone.0024940