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

Ian James Alexander, U. Koljalg

Research output: Contribution to journalArticle

469 Citations (Scopus)

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 languageEnglish
Pages (from-to)1063-1068
Number of pages5
JournalNew Phytologist
Volume166
DOIs
Publication statusPublished - 2005

Keywords

  • DNA taxonomy
  • ectomycorrhiza
  • fungi
  • molecular identification
  • sequence database
  • UNITE
  • PHYLOGENETIC ANALYSIS
  • DNA BARCODES
  • DIVERSITY
  • MICROARRAYS
  • FORESTS
  • PROFILE

Cite this

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. / Alexander, Ian James; Koljalg, U.

In: New Phytologist, Vol. 166, 2005, p. 1063-1068.

Research output: Contribution to journalArticle

@article{84fe7f6c614e447e96b211741df1003f,
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.",
keywords = "DNA taxonomy, ectomycorrhiza, fungi, molecular identification, sequence database, UNITE, PHYLOGENETIC ANALYSIS, DNA BARCODES, DIVERSITY, MICROARRAYS, FORESTS, PROFILE",
author = "Alexander, {Ian James} and U. Koljalg",
year = "2005",
doi = "10.1111/j.1469-8137.2005.01376.x",
language = "English",
volume = "166",
pages = "1063--1068",
journal = "New Phytologist",
issn = "0028-646X",
publisher = "Wiley/Blackwell (10.1111)",

}

TY - JOUR

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

AU - Alexander, Ian James

AU - Koljalg, U.

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.

KW - DNA taxonomy

KW - ectomycorrhiza

KW - fungi

KW - molecular identification

KW - sequence database

KW - UNITE

KW - PHYLOGENETIC ANALYSIS

KW - DNA BARCODES

KW - DIVERSITY

KW - MICROARRAYS

KW - FORESTS

KW - PROFILE

U2 - 10.1111/j.1469-8137.2005.01376.x

DO - 10.1111/j.1469-8137.2005.01376.x

M3 - Article

VL - 166

SP - 1063

EP - 1068

JO - New Phytologist

JF - New Phytologist

SN - 0028-646X

ER -