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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ftzenodo:oai:zenodo.org:4947703 2024-09-15T18:09:31+00:00 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 unknown Zenodo https://doi.org/10.1111/nph.15301 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.9dr6j0c oai:zenodo.org:4947703 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode altitudinal gradient root-associated fungi mycorrhizal fungi info:eu-repo/semantics/other 2019 ftzenodo https://doi.org/10.5061/dryad.9dr6j0c10.1111/nph.15301 2024-07-27T02:47:32Z • 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 Greenland Fungal 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 Other/Unknown Material Greenland Zackenberg Zenodo |
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topic |
altitudinal gradient root-associated fungi mycorrhizal fungi |
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altitudinal gradient root-associated fungi mycorrhizal fungi 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 |
altitudinal gradient root-associated fungi mycorrhizal fungi |
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 Greenland Fungal 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 |
Other/Unknown Material |
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 |
Zenodo |
publishDate |
2019 |
url |
https://doi.org/10.5061/dryad.9dr6j0c |
genre |
Greenland Zackenberg |
genre_facet |
Greenland Zackenberg |
op_relation |
https://doi.org/10.1111/nph.15301 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.9dr6j0c oai:zenodo.org:4947703 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.9dr6j0c10.1111/nph.15301 |
_version_ |
1810447085971963904 |