Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

Unified system for the DNA based fungal species linked to the classification

General information

Description: In this sysytem, 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.
Year founded: 2011
Last update: 2017
Version: 7.2
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: Estonia
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: University of Tartu
Address: Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
City: Tartu
Province/State:
Country/Region: Estonia
Contact name (PI/Team): Tedersoo L
Contact email (PI/Helpdesk): leho.tedersoo@ut.ee

Related Database

Record metadata

Created on: 2018-01-28
Curated by:
Fatima Batool [2018-12-27]
姜 美叶 [2018-03-07]

Ranking

All databases:
2360/4499 (47.566%)
Gene genome and annotation:
713/1199 (40.617%)
Phylogeny and homology:
100/189 (47.619%)
2360
Total Rank
18
Citations
2.25
z-index

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Publications

21949797
Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi. [PMID: 21949797]
Leho Tedersoo, Kessy Abarenkov, R Henrik Nilsson, Arthur Schüssler, Gwen-Aëlle Grelet, Petr Kohout, Jane Oja, Gregory M Bonito, Vilmar Veldre, Teele Jairus, Martin Ryberg, Karl-Henrik Larsson, Urmas Kõljalg,

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.

PLoS One. 2011:6(9) | 18 Citations (from Europe PMC, 2019-12-14)