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UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi

Koljalg, U; Larsson, K H; Abarenkov, K; Nilsson, R H; Alexander, IJ; Eberhardt, U; Erland, Susanne LU ; Höiland, K; Kjöller, R and Larsson, E, et al. (2005) In New Phytologist 166(3). p.1063-1068
Abstract
Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity... (More)
Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity using BLAST n, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a BLAST search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. The UNITE database is accessible through the URLhttp://unite.zbi.ee. (Less)
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type
Contribution to journal
publication status
published
subject
in
New Phytologist
volume
166
issue
3
pages
1063 - 1068
publisher
Wiley-Blackwell
external identifiers
  • pmid:15869663
  • wos:000228750700032
  • scopus:19344366809
ISSN
1469-8137
DOI
10.1111/j.1469-8137.2005.01376.x
language
English
LU publication?
yes
id
f3d3f141-ed75-4622-a53b-c94ed354d5a5 (old id 146804)
date added to LUP
2007-06-29 11:28:04
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2017-11-19 03:27:20
@article{f3d3f141-ed75-4622-a53b-c94ed354d5a5,
  abstract     = {Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity using BLAST n, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a BLAST search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. The UNITE database is accessible through the URLhttp://unite.zbi.ee.},
  author       = {Koljalg, U and Larsson, K H and Abarenkov, K and Nilsson, R H and Alexander, IJ and Eberhardt, U and Erland, Susanne and Höiland, K and Kjöller, R and Larsson, E and Pennanen, T and Sen, R and Taylor, A F S and Tedersoo, L and Vrålstad, T and Ursing, B M},
  issn         = {1469-8137},
  language     = {eng},
  number       = {3},
  pages        = {1063--1068},
  publisher    = {Wiley-Blackwell},
  series       = {New Phytologist},
  title        = {UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi},
  url          = {http://dx.doi.org/10.1111/j.1469-8137.2005.01376.x},
  volume       = {166},
  year         = {2005},
}