Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences
• Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed PROTAX-fungi, a general tool for taxonomic placement of fungal ITS sequences, and implemented it into the PlutoF platform of the UNITE database fo...
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Data Archiving and Networked Services (DANS)
2019
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Online Access: | https://doi.org/10.5061/dryad.9dr6j0c |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::632335ffad8f34430a935e073df16eaf 2023-05-15T15:11:10+02:00 Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences Abarenkov, Kessy Somervuo, Panu Nilsson, R. Henrik Kirk, Paul M. Huotari, Tea Abrego, Nerea Ovaskainen, Otso 2019-05-29 https://doi.org/10.5061/dryad.9dr6j0c undefined unknown Data Archiving and Networked Services (DANS) http://dx.doi.org/10.5061/dryad.9dr6j0c https://dx.doi.org/10.5061/dryad.9dr6j0c lic_creative-commons oai:easy.dans.knaw.nl:easy-dataset:113368 10.5061/dryad.9dr6j0c oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:113368 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 Life sciences medicine and health care altitudinal gradient root-associated fungi mycorrhizal fungi Arctic Greenland Zackenberg envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2019 fttriple https://doi.org/10.5061/dryad.9dr6j0c 2023-01-22T17:22:53Z • Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed PROTAX-fungi, a general tool for taxonomic placement of fungal ITS sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. • PROTAX-fungi outperformed the SINTAX and RDB classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence database coverage. • With empirical data on root- and wood-associated fungi, PROTAX-fungi identified reliably (with at least 90% identification probability) the majority of sequences to the order level but only ca. one fifth of them to the species level, reflecting the current limited coverage of the databases. • When applied to examine the internal consistencies of the Index Fungorum and UNITE databases, PROTAX-fungi revealed inconsistencies in the taxonomy database as well as mislabelling and sequence quality problems in the reference database. The according improvements were implemented in both databases. • PROTAX-fungi provides a robust tool for performing statistically reliable identifications of fungi in spite of the incompleteness of extant reference sequence databases and unresolved taxonomic relationships. Root-associated fungi from GreenlandFungal ITS2 sequence data of root-associated fungi from Greenland in fasta format. DNA extracted from different plant species roots collected along the altitudinal gradient of Aucella mountain in the Zackenberg valley.root-associated fungi from Greenland.fas Dataset Arctic Greenland Zackenberg Unknown Arctic Greenland |
institution |
Open Polar |
collection |
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fttriple |
language |
unknown |
topic |
Life sciences medicine and health care altitudinal gradient root-associated fungi mycorrhizal fungi Arctic Greenland Zackenberg envir geo |
spellingShingle |
Life sciences medicine and health care altitudinal gradient root-associated fungi mycorrhizal fungi Arctic Greenland Zackenberg envir geo Abarenkov, Kessy Somervuo, Panu Nilsson, R. Henrik Kirk, Paul M. Huotari, Tea Abrego, Nerea Ovaskainen, Otso Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences |
topic_facet |
Life sciences medicine and health care altitudinal gradient root-associated fungi mycorrhizal fungi Arctic Greenland Zackenberg envir geo |
description |
• Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed PROTAX-fungi, a general tool for taxonomic placement of fungal ITS sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. • PROTAX-fungi outperformed the SINTAX and RDB classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence database coverage. • With empirical data on root- and wood-associated fungi, PROTAX-fungi identified reliably (with at least 90% identification probability) the majority of sequences to the order level but only ca. one fifth of them to the species level, reflecting the current limited coverage of the databases. • When applied to examine the internal consistencies of the Index Fungorum and UNITE databases, PROTAX-fungi revealed inconsistencies in the taxonomy database as well as mislabelling and sequence quality problems in the reference database. The according improvements were implemented in both databases. • PROTAX-fungi provides a robust tool for performing statistically reliable identifications of fungi in spite of the incompleteness of extant reference sequence databases and unresolved taxonomic relationships. Root-associated fungi from GreenlandFungal ITS2 sequence data of root-associated fungi from Greenland in fasta format. DNA extracted from different plant species roots collected along the altitudinal gradient of Aucella mountain in the Zackenberg valley.root-associated fungi from Greenland.fas |
format |
Dataset |
author |
Abarenkov, Kessy Somervuo, Panu Nilsson, R. Henrik Kirk, Paul M. Huotari, Tea Abrego, Nerea Ovaskainen, Otso |
author_facet |
Abarenkov, Kessy Somervuo, Panu Nilsson, R. Henrik Kirk, Paul M. Huotari, Tea Abrego, Nerea Ovaskainen, Otso |
author_sort |
Abarenkov, Kessy |
title |
Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences |
title_short |
Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences |
title_full |
Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences |
title_fullStr |
Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences |
title_full_unstemmed |
Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences |
title_sort |
data from: protax-fungi: a web-based tool for probabilistic taxonomic placement of fungal its sequences |
publisher |
Data Archiving and Networked Services (DANS) |
publishDate |
2019 |
url |
https://doi.org/10.5061/dryad.9dr6j0c |
geographic |
Arctic Greenland |
geographic_facet |
Arctic Greenland |
genre |
Arctic Greenland Zackenberg |
genre_facet |
Arctic Greenland Zackenberg |
op_source |
oai:easy.dans.knaw.nl:easy-dataset:113368 10.5061/dryad.9dr6j0c oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:113368 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 |
op_relation |
http://dx.doi.org/10.5061/dryad.9dr6j0c https://dx.doi.org/10.5061/dryad.9dr6j0c |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.9dr6j0c |
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1766342075323777024 |