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

U Koljalg; K H Larsson; K Abarenkov; R H Nilsson; IJ Alexander; U Eberhardt; Susanne Erland; K Höiland; R Kjöller; E Larsson; T Pennanen; R Sen; A F S Taylor; L Tedersoo; T Vrålstad; B M Ursing

doi:10.1111/j.1469-8137.2005.01376.x

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

U Koljalg, K H Larsson, K Abarenkov, R H Nilsson, IJ Alexander, U Eberhardt, Susanne Erland, K Höiland, R Kjöller, E Larsson, T Pennanen, R Sen, A F S Taylor, L Tedersoo, T Vrålstad, B M Ursing

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	1063-1068
Journal	New Phytologist
Volume	166
Issue number	3
DOIs	https://doi.org/10.1111/j.1469-8137.2005.01376.x
Publication status	Published - 2005

Bibliographical note

The information about affiliations in this record was updated in December 2015.
The record was previously connected to the following departments: Microbial Ecology (Closed 2011) (011008001)

Subject classification (UKÄ)

Ecology

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10.1111/j.1469-8137.2005.01376.x

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Koljalg, U., Larsson, K. H., Abarenkov, K., Nilsson, R. H., Alexander, IJ., Eberhardt, U., Erland, S., Höiland, K., Kjöller, R., Larsson, E., Pennanen, T., Sen, R., Taylor, A. F. S., Tedersoo, L., Vrålstad, T., & Ursing, B. M. (2005). UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytologist, 166(3), 1063-1068. https://doi.org/10.1111/j.1469-8137.2005.01376.x

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

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 = "U Koljalg and Larsson, {K H} and K Abarenkov and Nilsson, {R H} and IJ Alexander and U Eberhardt and Susanne Erland and K H{\"o}iland and R Kj{\"o}ller and E Larsson and T Pennanen and R Sen and Taylor, {A F S} and L Tedersoo and T Vr{\aa}lstad and Ursing, {B M}",

note = "The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Microbial Ecology (Closed 2011) (011008001)",

year = "2005",

doi = "10.1111/j.1469-8137.2005.01376.x",

language = "English",

volume = "166",

pages = "1063--1068",

journal = "New Phytologist",

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Koljalg, U, Larsson, KH, Abarenkov, K, Nilsson, RH, Alexander, IJ, Eberhardt, U, Erland, S, Höiland, K, Kjöller, R, Larsson, E, Pennanen, T, Sen, R, Taylor, AFS, Tedersoo, L, Vrålstad, T & Ursing, BM 2005, 'UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi', New Phytologist, vol. 166, no. 3, pp. 1063-1068. https://doi.org/10.1111/j.1469-8137.2005.01376.x

TY - JOUR

T1 - UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi

AU - Koljalg, U

AU - Larsson, K H

AU - Abarenkov, K

AU - Nilsson, R H

AU - Alexander, IJ

AU - Eberhardt, U

AU - Erland, Susanne

AU - Höiland, K

AU - Kjöller, R

AU - Larsson, E

AU - Pennanen, T

AU - Sen, R

AU - Taylor, A F S

AU - Tedersoo, L

AU - Vrålstad, T

AU - Ursing, B M

N1 - The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Microbial Ecology (Closed 2011) (011008001)

PY - 2005

Y1 - 2005

N2 - 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.

AB - 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.

U2 - 10.1111/j.1469-8137.2005.01376.x

DO - 10.1111/j.1469-8137.2005.01376.x

M3 - Article

C2 - 15869663

SN - 1469-8137

VL - 166

SP - 1063

EP - 1068

JO - New Phytologist

JF - New Phytologist

IS - 3

ER -

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

Abstract

Bibliographical note

Subject classification (UKÄ)

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