Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK)
Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi – whether transient visitors or more persistent residents – may hold clues to the rising levels of human allergies and other medical and building-related health problems...
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doaj-24742f9a5dc846b9ab04dc9308387dfd2020-11-24T22:08:57ZengPensoft PublishersMycoKeys1314-40571314-40492018-01-0128658210.3897/mycokeys.28.2088720887Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK)R. Henrik Nilsson0Andy F. S. Taylor1Rachel I. Adams2Christiane Baschien3Johan Bengtsson-Palme4Patrik Cangren5Claudia Coleine6Heide-Marie Daniel7Sydney I. Glassman8Yuuri Hirooka9Laszlo Irinyi10Reda Iršėnaitė11Pedro M. Martin-Sanchez12Wieland Meyer13Seung-Yoon Oh14Jose Paulo Sampaio15Keith A. Seifert16Frantisek Sklenář17Dirk Stubbe18Sung-Oui Suh19Richard Summerbell20Sten Svantesson21Martin Unterseher22Cobus M. Visagie23Michael Weiss24Joyce HC Woudenberg25Christian Wurzbacher26Silke Van den Wyngaert27Neriman Yilmaz28Andrey Yurkov29Urmas Kõljalg30Kessy Abarenkov31Gothenburg Global Biodiversity CentreUniversity of AberdeenUniversity of CaliforniaLeibniz Institute DSMZ-German Collection of Microorganisms and Cell CulturesUniversity of GothenburgUniversity of GothenburgUniversity of CaliforniaUniversité catholique de LouvainUniversity of CaliforniaHosei UniversityUniversity of SydneyNature Research CentreBundesanstalt für Materialforschung und -prüfungWestmead Institute for Medical ResearchSeoul National UniversityUniversidade Nova de LisboaOttawa Research and Development Centre, Agriculture & Agri-Food CanadaInstitute of Microbiology, Academy of Sciences of the Czech RepublicScientific Institute of Public HealthAmerican Type Culture Collection (ATCC)University of TorontoUniversity of GothenburgEvangelisches Schulzentrum MartinschuleUniversity of OttawaSteinbeis-InnovationszentrumWesterdijk Fungal Biodiversity InstituteGothenburg Global Biodiversity CentreLeibniz-Institute of Freshwater Ecology and Inland FisheriesOttawa Research and Development Centre, Agriculture & Agri-Food CanadaLeibniz Institute DSMZ-German Collection of Microorganisms and Cell CulturesUniversity of TartuUniversity of Tartu Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi – whether transient visitors or more persistent residents – may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions – such as country and host/substrate of collection – are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10–11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes – including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences – were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment. https://mycokeys.pensoft.net/articles.php?id=20887 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
R. Henrik Nilsson Andy F. S. Taylor Rachel I. Adams Christiane Baschien Johan Bengtsson-Palme Patrik Cangren Claudia Coleine Heide-Marie Daniel Sydney I. Glassman Yuuri Hirooka Laszlo Irinyi Reda Iršėnaitė Pedro M. Martin-Sanchez Wieland Meyer Seung-Yoon Oh Jose Paulo Sampaio Keith A. Seifert Frantisek Sklenář Dirk Stubbe Sung-Oui Suh Richard Summerbell Sten Svantesson Martin Unterseher Cobus M. Visagie Michael Weiss Joyce HC Woudenberg Christian Wurzbacher Silke Van den Wyngaert Neriman Yilmaz Andrey Yurkov Urmas Kõljalg Kessy Abarenkov |
spellingShingle |
R. Henrik Nilsson Andy F. S. Taylor Rachel I. Adams Christiane Baschien Johan Bengtsson-Palme Patrik Cangren Claudia Coleine Heide-Marie Daniel Sydney I. Glassman Yuuri Hirooka Laszlo Irinyi Reda Iršėnaitė Pedro M. Martin-Sanchez Wieland Meyer Seung-Yoon Oh Jose Paulo Sampaio Keith A. Seifert Frantisek Sklenář Dirk Stubbe Sung-Oui Suh Richard Summerbell Sten Svantesson Martin Unterseher Cobus M. Visagie Michael Weiss Joyce HC Woudenberg Christian Wurzbacher Silke Van den Wyngaert Neriman Yilmaz Andrey Yurkov Urmas Kõljalg Kessy Abarenkov Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK) MycoKeys |
author_facet |
R. Henrik Nilsson Andy F. S. Taylor Rachel I. Adams Christiane Baschien Johan Bengtsson-Palme Patrik Cangren Claudia Coleine Heide-Marie Daniel Sydney I. Glassman Yuuri Hirooka Laszlo Irinyi Reda Iršėnaitė Pedro M. Martin-Sanchez Wieland Meyer Seung-Yoon Oh Jose Paulo Sampaio Keith A. Seifert Frantisek Sklenář Dirk Stubbe Sung-Oui Suh Richard Summerbell Sten Svantesson Martin Unterseher Cobus M. Visagie Michael Weiss Joyce HC Woudenberg Christian Wurzbacher Silke Van den Wyngaert Neriman Yilmaz Andrey Yurkov Urmas Kõljalg Kessy Abarenkov |
author_sort |
R. Henrik Nilsson |
title |
Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK) |
title_short |
Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK) |
title_full |
Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK) |
title_fullStr |
Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK) |
title_full_unstemmed |
Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK) |
title_sort |
taxonomic annotation of public fungal its sequences from the built environment – a report from an april 10–11, 2017 workshop (aberdeen, uk) |
publisher |
Pensoft Publishers |
series |
MycoKeys |
issn |
1314-4057 1314-4049 |
publishDate |
2018-01-01 |
description |
Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi – whether transient visitors or more persistent residents – may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions – such as country and host/substrate of collection – are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10–11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes – including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences – were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.
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url |
https://mycokeys.pensoft.net/articles.php?id=20887 |
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