Fungal Diversity

, Volume 67, Issue 1, pp 11–19

Improving ITS sequence data for identification of plant pathogenic fungi

  • R. Henrik Nilsson
  • Kevin D. Hyde
  • Julia Pawłowska
  • Martin Ryberg
  • Leho Tedersoo
  • Anders Bjørnsgard Aas
  • Siti A. Alias
  • Artur Alves
  • Cajsa Lisa Anderson
  • Alexandre Antonelli
  • A. Elizabeth Arnold
  • Barbara Bahnmann
  • Mohammad Bahram
  • Johan Bengtsson-Palme
  • Anna Berlin
  • Sara Branco
  • Putarak Chomnunti
  • Asha Dissanayake
  • Rein Drenkhan
  • Hanna Friberg
  • Tobias Guldberg Frøslev
  • Bettina Halwachs
  • Martin Hartmann
  • Beatrice Henricot
  • Ruvishika Jayawardena
  • Ari Jumpponen
  • Håvard Kauserud
  • Sonja Koskela
  • Tomasz Kulik
  • Kare Liimatainen
  • Björn D. Lindahl
  • Daniel Lindner
  • Jian-Kui Liu
  • Sajeewa Maharachchikumbura
  • Dimuthu Manamgoda
  • Svante Martinsson
  • Maria Alice Neves
  • Tuula Niskanen
  • Stephan Nylinder
  • Olinto Liparini Pereira
  • Danilo Batista Pinho
  • Teresita M. Porter
  • Valentin Queloz
  • Taavi Riit
  • Marisol Sánchez-García
  • Filipe de Sousa
  • Emil Stefańczyk
  • Mariusz Tadych
  • Susumu Takamatsu
  • Qing Tian
  • Dhanushka Udayanga
  • Martin Unterseher
  • Zheng Wang
  • Saowanee Wikee
  • Jiye Yan
  • Ellen Larsson
  • Karl-Henrik Larsson
  • Urmas Kõljalg
  • Kessy Abarenkov
Article

DOI: 10.1007/s13225-014-0291-8

Cite this article as:
Nilsson, R.H., Hyde, K.D., Pawłowska, J. et al. Fungal Diversity (2014) 67: 11. doi:10.1007/s13225-014-0291-8

Summary

Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.

Keywords

Phytopathogenic fungi Molecular identification ITS Taxonomy Annotation 

Supplementary material

13225_2014_291_MOESM1_ESM.pdf (33 kb)
Supplementary Item 1The 39 journals screened for ITS sequences from type specimens/ex-type cultures of fungi described (or re-typified) during the period 2000–2012 (variously and as applicable). The time coverage of the journal is indicated. Only papers whose title suggested that one or more new species were described (or that one or more species were re-typified) were examined. In some few cases, individual articles were not clear on whether a sequence actually came from the type specimen or not, and we hope that ongoing efforts to standardize what data to provide (and how to provide them) when describing new species in a molecular context will be successful. (PDF 32 kb)
13225_2014_291_MOESM2_ESM.pdf (2.9 mb)
Supplementary Item 2Screenshots showing examples of how the user can interact with, and modify, the public fungal ITS sequences in UNITE. The processes illustrated include taxonomic re-annotation, addition of ecological and geographical metadata, annotation of basic sequence properties, and association of sequences with voucher specimens/cultures. Structured INSDC searches as well as browsing among species hypotheses are also shown. A manual for the PlutoF sequence management environment is available at http://unite.ut.ee/temp/plutof2/files/PlutoF_2.5_Manual_small.pdf (PDF 2956 kb)

Copyright information

© Mushroom Research Foundation 2014

Authors and Affiliations

  • R. Henrik Nilsson
    • 1
  • Kevin D. Hyde
    • 2
    • 3
  • Julia Pawłowska
    • 4
  • Martin Ryberg
    • 5
  • Leho Tedersoo
    • 6
  • Anders Bjørnsgard Aas
    • 7
  • Siti A. Alias
    • 8
  • Artur Alves
    • 9
  • Cajsa Lisa Anderson
    • 1
  • Alexandre Antonelli
    • 1
  • A. Elizabeth Arnold
    • 10
  • Barbara Bahnmann
    • 11
  • Mohammad Bahram
    • 6
  • Johan Bengtsson-Palme
    • 12
  • Anna Berlin
    • 13
  • Sara Branco
    • 14
  • Putarak Chomnunti
    • 3
  • Asha Dissanayake
    • 2
    • 3
    • 15
  • Rein Drenkhan
    • 16
  • Hanna Friberg
    • 13
  • Tobias Guldberg Frøslev
    • 17
  • Bettina Halwachs
    • 18
    • 19
  • Martin Hartmann
    • 20
    • 21
  • Beatrice Henricot
    • 22
  • Ruvishika Jayawardena
    • 2
    • 3
    • 15
  • Ari Jumpponen
    • 23
  • Håvard Kauserud
    • 7
  • Sonja Koskela
    • 24
  • Tomasz Kulik
    • 25
  • Kare Liimatainen
    • 26
  • Björn D. Lindahl
    • 13
  • Daniel Lindner
    • 27
  • Jian-Kui Liu
    • 2
    • 3
  • Sajeewa Maharachchikumbura
    • 2
    • 3
  • Dimuthu Manamgoda
    • 2
    • 3
  • Svante Martinsson
    • 1
  • Maria Alice Neves
    • 28
  • Tuula Niskanen
    • 26
  • Stephan Nylinder
    • 29
  • Olinto Liparini Pereira
    • 30
  • Danilo Batista Pinho
    • 30
  • Teresita M. Porter
    • 31
  • Valentin Queloz
    • 32
  • Taavi Riit
    • 6
  • Marisol Sánchez-García
    • 33
  • Filipe de Sousa
    • 1
  • Emil Stefańczyk
    • 34
  • Mariusz Tadych
    • 35
  • Susumu Takamatsu
    • 36
  • Qing Tian
    • 2
    • 3
  • Dhanushka Udayanga
    • 2
    • 3
  • Martin Unterseher
    • 37
  • Zheng Wang
    • 38
  • Saowanee Wikee
    • 3
  • Jiye Yan
    • 15
  • Ellen Larsson
    • 1
  • Karl-Henrik Larsson
    • 39
  • Urmas Kõljalg
    • 6
    • 40
  • Kessy Abarenkov
    • 40
  1. 1.Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
  2. 2.Institute of Excellence in Fungal ResearchMae Fah Luang UniversityChiang RaiThailand
  3. 3.School of ScienceMae Fah Luang UniversityChiang RaiThailand
  4. 4.Department of Plant Systematics and Geography, Faculty of BiologyUniversity of WarsawWarsawPoland
  5. 5.Department of Organismal BiologyUppsala UniversityUppsalaSweden
  6. 6.Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
  7. 7.Microbial Evolution Research GroupUniversity of OsloOsloNorway
  8. 8.Institute of Biological SciencesUniversity of MalayaKuala LumpurMalaysia
  9. 9.Department of Biology, CESAMUniversity of AveiroAveiroPortugal
  10. 10.School of Plant SciencesThe University of ArizonaTucsonUSA
  11. 11.Laboratory of Environmental MicrobiologyInstitute of Microbiology ASCRPrague 4Czech Republic
  12. 12.Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska AcademyUniversity of GothenburgGöteborgSweden
  13. 13.Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
  14. 14.University of California at BerkeleyBerkeleyUSA
  15. 15.Institute of Plant and Environment ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijingChina
  16. 16.Institute of Forestry and Rural EngineeringEstonian University of Life SciencesTartuEstonia
  17. 17.Natural History Museum of DenmarkKøbenhavn KDenmark
  18. 18.Institute for Genomics and BioinformaticsGraz University of TechnologyGrazAustria
  19. 19.Core Facility BioinformaticsAustrian Centre of Industrial BiotechnologyGrazAustria
  20. 20.Forest Soils and BiogeochemistrySwiss Federal Research Institute WSLBirmensdorfSwitzerland
  21. 21.Molecular EcologyInstitute for Sustainability Sciences, AgroscopeZurichSwitzerland
  22. 22.Plant PathologyThe Royal Horticultural Society, WisleyWokingUK
  23. 23.Division of BiologyKansas State UniversityManhattanUSA
  24. 24.Metapopulation Research Group, Department of BiosciencesUniversity of HelsinkiHelsinkiFinland
  25. 25.Department of Diagnostics and Plant PathophysiologyUniversity of Warmia and Mazury in OlsztynOlsztynPoland
  26. 26.Plant Biology, Department of BiosciencesUniversity of HelsinkiHelsinkiFinland
  27. 27.US Forest Service, Northern Research StationCenter for Forest Mycology ResearchMadisonUSA
  28. 28.Departamento Botânica, PPG Biologia de Fungos, Algas e PlantasUniversidade Federal de Santa CatarinaFlorianópolisBrazil
  29. 29.Department of BotanySwedish Natural History MuseumStockholmSweden
  30. 30.Departamento de FitopatologiaUniversidade Federal de ViçosaViçosaBrazil
  31. 31.Department of BiologyMcMaster UniversityHamiltonCanada
  32. 32.ETH Zürich, Institute for Integrative BiologyZürichSwitzerland
  33. 33.Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleUSA
  34. 34.Plant Breeding and Acclimatization Institute-National Research InstituteMłochów Research CentreMłochówPoland
  35. 35.Department of Plant Biology and Pathology, School of Environmental and Biological SciencesRutgers, The State University of New JerseyNew BrunswickUSA
  36. 36.Laboratory of Plant Pathology, Faculty of BioresourcesMie UniversityTsu-cityJapan
  37. 37.Institute of Botany and Landscape EcologyErnst-Moritz-Arndt UniversityGreifswaldGermany
  38. 38.Biostatistics DepartmentYale School of Public HealthNew HavenUSA
  39. 39.Natural History MuseumBlindernNorway
  40. 40.Natural History MuseumUniversity of TartuTartuEstonia

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