Skip to main content

Advertisement

SpringerLink
Log in

Improving ITS sequence data for identification of plant pathogenic fungi

  • Published:
Fungal Diversity Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Abarenkov K, Nilsson RH, Larsson K-H, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T, Sen R, Taylor AFS, Tedersoo L, Ursing BM, Vrålstad T, Liimatainen K, Peintner U, Kõljalg U (2010a) The UNITE database for molecular identification of fungi - recent updates and future perspectives. New Phytol 186:281–285

    Article  PubMed  Google Scholar 

  • Abarenkov K, Tedersoo L, Nilsson RH, Vellak K, Saar I, Veldre V, Parmasto E, Prous M, Aan A, Ots M, Kurina O, Ostonen I, Jõgeva J, Halapuu S, Põldmaa K, Toots M, Truu J, Larsson K-H, Kõljalg U (2010b) PlutoF - a web-based workbench for ecological and taxonomic research, with an online implementation for fungal ITS sequences. Evol Bioinform 6:189–196

    Google Scholar 

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Barnes I, Crous PW, Wingfield BD, Wingfield MJ (2004) Multigene phylogenies reveal that red band needle blight is caused by two distinct species of Dothistroma, D. septosporum and D. pini. Stud Mycol 50:551–565

  • Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Wegener Parfrey L, Stajich JE (2013) Meeting report: fungal ITS workshop (October 2012). Stand Genomic Sci 8:118–123

    Article  PubMed  PubMed Central  Google Scholar 

  • Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger M, de Sousa F, Amend A, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson MK, Vik U, Veldre V, Nilsson RH (2013) Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol 4:914–919

    Google Scholar 

  • Bidartondo M, Bruns TD, Blackwell M et al (2008) Preserving accuracy in GenBank. Science 319:5870

    Article  Google Scholar 

  • Britton KO, Liebhold AM (2013) One world, many pathogens! New Phytol 197:9–10

    Article  PubMed  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Cunha KCD, Sutton DA, Fothergill AW, Gené GJ, Cano J, Madrid H, Hoog SD, Crous PW, Guarro J (2013) In vitro antifungal susceptibility and molecular identity of 99 clinical isolates of the opportunistic fungal genus Curvularia. Diagn Microbiol Infect Dis 76:168–174

    Article  PubMed  Google Scholar 

  • Dean R, Van Kan JA, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J, Foster GD (2012) The top 10 fungal pathogens in molecular plant pathology. Mol Plant Pathol 13:414–430

    Article  PubMed  Google Scholar 

  • Delaye L, García-Guzmán G, Heil M (2013) Endophytes versus biotrophic and necrotrophic pathogens – are fungal lifestyles evolutionarily stable traits? Fungal Divers 60:125–135

    Article  Google Scholar 

  • Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ (2012) Emerging fungal threats to animal, plant and ecosystem health. Nature 484:186–194

    Article  PubMed  CAS  Google Scholar 

  • Gauthier G, Keller N (2013) Crossover fungal pathogens: the biology and pathogenesis of fungi capable of crossing kingdoms to infect plants and humans. Fungal Genet Biol 61:146–57

    Article  PubMed  CAS  Google Scholar 

  • Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, Gillevet PM (2010) Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog 6:e1000713

    Article  PubMed  PubMed Central  Google Scholar 

  • Heath TA, Hedtke SM, Hillis DM (2008) Taxon sampling and the accuracy of phylogenetic analyses. J Syst Evol 46:239–257

    Google Scholar 

  • Hibbett DS, Ohman A, Glotzer D, Nuhn M, Kirk P, Nilsson RH (2011) Progress in molecular and morphological taxon discovery in fungi and options for formal classification of environmental sequences. Fungal Biol Rev 25:38–47

    Article  Google Scholar 

  • Hyde KD, Udayanga D, Manamgoda DS, Tedersoo L, Larsson E, Abarenkov K, Bertrand YJK, Oxelman B, Hartmann M, Kauserud H, Ryberg M, Kristiansson E, Nilsson RH (2013) Incorporating molecular data in fungal systematics: a guide for aspiring researchers. Curr Res Environ Appl Mycol 3:1–32

    Google Scholar 

  • Kang S, Mansfield MAM, Park B, Geiser DM, Ivors KL, Coffey MD, Grünwald NJ, Martin FN, Lévesque CA, Blair JE (2010) The promise and pitfalls of sequence-based identification of plant pathogenic fungi and oomycetes. Phytopathology 100:732–737

    Article  PubMed  Google Scholar 

  • Ko Ko TWK, Stephenson SL, Bahkali AH, Hyde KD (2011) From morphology to molecular biology: can we use sequence data to identify fungal endophytes? Fungal Divers 50:113–120

    Article  Google Scholar 

  • Kõljalg U, Nilsson RH, Abarenkov K et al (2013) Towards a unified paradigm for sequence-based identification of Fungi. Mol Ecol 22:5271–5277

    Article  PubMed  Google Scholar 

  • Kowalski T, Holdenrieder O (2009) The teleomorph of Chalara fraxinea, the causal agent of ash dieback. For Pathol 39:304–308

    Article  Google Scholar 

  • La Duc MT, Vaishampayan P, Nilsson RH, Torok T, Venkateswaran K (2012) Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars. Appl Environ Microbiol 78:5912–5922

    Article  PubMed  PubMed Central  Google Scholar 

  • Lanzén A, Jørgensen SL, Huson DH, Gorfer M, Grindhaug SH, Jonassen I, Øvreås L, Urich T (2012) CREST – classification resources for environmental sequence tags. PLoS One 7:e49334

    Article  PubMed  PubMed Central  Google Scholar 

  • Maharachchikumbura SSN, Guo LD, Cai L, Chukeatirote E, Wu WP, Sun X, Crous PW, Bhat DJ, McKenzie EHC, Bahkali AH, Hyde KD (2012) A multi-locus backbone tree for Pestalotiopsis, with a polyphasic characterization of 14 new species. Fungal Divers 56:95–129

    Article  Google Scholar 

  • Manamgoda DS, Cai L, McKenzie EHC, Crous PW, Madrid H, Chukeatirote E, Shivas RG, Tan YP, Hyde KD (2012) A phylogenetic and taxonomic re-evaluation of the Bipolaris, Cochliobolus, Curvularia complex. Fungal Divers 56:131–144

  • Nakamura Y, Cochrane G, Karsch-Mizrachi I (2013) The international nucleotide sequence database collaboration. Nucleic Acids Res 41:D21–D24

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Nilsson RH, Ryberg M, Sjökvist E, Abarenkov K (2011) Rethinking taxon sampling in the light of environmental sequencing. Cladistics 27:197–203

    Article  Google Scholar 

  • Nilsson RH, Tedersoo L, Abarenkov K, Ryberg M, Kristiansson E, Hartmann M, Schoch CL, Nylander JAA, Bergsten J, Porter TM, Jumpponen A, Vaishampayan P, Ovaskainen O, Hallenberg N, Bengtsson-Palme J, Eriksson KM, Larsson K-H, Larsson E (2012) Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys 4:37–63

    Article  Google Scholar 

  • Pautasso M (2013) Fungal under-representation is (slowly) diminishing in the life sciences. Fungal Ecol 6:129–135

    Article  Google Scholar 

  • Pennisi E (2008) “Proposal to ‘wikify’ GenBank meets stiff resistance”. Science 319:1598–1599

    Article  PubMed  CAS  Google Scholar 

  • Queloz V, Grunig CR, Berndt R, Kowalski T, Sieber TN, Holdenrieder O (2011) Cryptic speciation in Hymenoscyphus albidus. For Pathol 41:133–142

    Article  Google Scholar 

  • Robbertse B, Schoch CL, Robert V et al. (2014) Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database, in press

  • Rossman AY, Palm-Hernández ME (2008) Systematics of plant pathogenic fungi: why it matters. Plant Dis 10:1376–1386

    Article  Google Scholar 

  • Ryberg M, Kristiansson E, Sjökvist E, Nilsson RH (2009) An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity. New Phytol 181:471–477

    Article  PubMed  CAS  Google Scholar 

  • Samerpitak K, Van der Linde E, Choi HJ, Gerrits van den Ende AHG, Machouart M, Gueidan C, de Hoog GS (2014) Taxonomy of Ochroconis, a genus including opportunistic pathogens on humans and animals. Fungal Divers 65:89–126. doi:10.1007/s13225-013-0253-6

  • Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Schoch CL, Seifert KA, Huhndorf S et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci U S A 109:6241–6246

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Seifert K, Rossman AY (2010) How to describe a new fungal species. IMA Fungus 1:109–116

    Article  PubMed  PubMed Central  Google Scholar 

  • Sharma G, Kumar N, Weir BS, Hyde KD, Shenoy BD (2013) Apmat gene can resolve Colletotrichum species: a case study with Mangifera indica. Fungal Divers 61:117–138

    Article  Google Scholar 

  • Shenoy BD, Rajesh J, Hyde KD (2007) Impact of DNA sequence-data on the taxonomy of anamorphic fungi. Fungal Divers 26:1–54

    Google Scholar 

  • Stajich JE, Berbee ML, Blackwell M, Hibbett DS, James TY, Spatafora JW, Taylor JW (2009) The fungi. Curr Biol 19:R840–R845

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Tedersoo L, Abarenkov K, Nilsson RH, Schussler A, Grelet G-A, Kohout P, Oja J, Bonito GM, Veldre V, Jairus T, Ryberg M, Larsson K-H, Kõljalg U (2011) Tidying up international nucleotide sequence databases: ecological, geographical, and sequence quality annotation of ITS sequences of mycorrhizal fungi. PLoS One 6:e24940

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Udayanga D, Liu XX, Crous PW, McKenzie EHC, Chukeatirote E, Hyde KD (2012) A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis). Fungal Divers 56:157–171

    Article  Google Scholar 

  • Unterseher M, Peršoh D, Schnittler M (2013) Leaf-inhabiting endophytic fungi of European Beech (Fagus sylvatica L.) co-occur in leaf litter but are rare on decaying wood of the same host. Fungal Divers 60:43–54

    Article  Google Scholar 

  • U’Ren JM, Dalling JW, Gallery RE, Maddison DR, Davis EC, Gibson CM, Arnold EA (2009) Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analyzing fungal environmental samples. Mycol Res 113:432–449

    Article  PubMed  Google Scholar 

  • Woudenberg JHC, Groenewald JZ, Binder M, Crous PW (2013) Alternaria redefined. Stud Mycol 75:171–212

    Article  PubMed  CAS  PubMed Central  Google Scholar 

Download references

Acknowledgments

RHN acknowledges financial support from Swedish Research Council of Environment, Agricultural Sciences, and Spatial Planning (FORMAS, 215-2011-498). ArA acknowledges financial support from European Funds through COMPETE and by National Funds through the Portuguese Foundation for Science and Technology (FCT) within projects PTDC/AGR-FOR/3807/2012 - FCOMP-01-0124-FEDER-027979 and PEst-C/MAR/LA0017/2013. SB is supported by National Science Foundation Grant DBI 1046115. The Austrian Centre of Industrial Biotechnology (ACIB) contribution (BH) was supported by FFG, BMWFJ, BMVIT, ZIT, Zukunftsstiftung Tirol, and Land Steiermark within the Austrian COMET program FFG Grant 824186. Financial support to JP was partially provided by the Polish Ministry of Science and Higher Education (MNiSW), grant no. NN303_548839. OLP acknowledges financial support from FAPEMIG and CNPq. TMP was funded by the Government of Canada through Genome Canada and the Ontario Genomics Institute through the Biomonitoring 2.0 project (OGI-050). The GenBank staff is acknowledged for helpful discussions and data sharing. The NEFOM network is acknowledged for infrastructural support. The authors have no conflict of interests to report.

Author information

Authors and Affiliations

  1. Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden

    R. Henrik Nilsson, Cajsa Lisa Anderson, Alexandre Antonelli, Svante Martinsson, Filipe de Sousa & Ellen Larsson

  2. Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand

    Kevin D. Hyde, Asha Dissanayake, Ruvishika Jayawardena, Jian-Kui Liu, Sajeewa Maharachchikumbura, Dimuthu Manamgoda, Qing Tian & Dhanushka Udayanga

  3. School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand

    Kevin D. Hyde, Putarak Chomnunti, Asha Dissanayake, Ruvishika Jayawardena, Jian-Kui Liu, Sajeewa Maharachchikumbura, Dimuthu Manamgoda, Qing Tian, Dhanushka Udayanga & Saowanee Wikee

  4. Department of Plant Systematics and Geography, Faculty of Biology, University of Warsaw, Al. Ujazdowskie 4, 00-478, Warsaw, Poland

    Julia Pawłowska

  5. Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden

    Martin Ryberg

  6. Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia

    Leho Tedersoo, Mohammad Bahram, Taavi Riit & Urmas Kõljalg

  7. Microbial Evolution Research Group, University of Oslo, Blindernveien 31, 0371, Oslo, Norway

    Anders Bjørnsgard Aas & Håvard Kauserud

  8. Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia

    Siti A. Alias

  9. Department of Biology, CESAM, University of Aveiro, 3810-193, Aveiro, Portugal

    Artur Alves

  10. School of Plant Sciences, The University of Arizona, 1140 E South Campus Drive, Forbes 303, Tucson, AZ, 85721, USA

    A. Elizabeth Arnold

  11. Laboratory of Environmental Microbiology, Institute of Microbiology ASCR, Vídeňská 1083, 14220, Prague 4, Czech Republic

    Barbara Bahnmann

  12. Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, 413 46, Göteborg, Sweden

    Johan Bengtsson-Palme

  13. Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07, Uppsala, Sweden

    Anna Berlin, Hanna Friberg & Björn D. Lindahl

  14. University of California at Berkeley, 321 Koshland Hall University of California, Berkeley, CA, 94720-3102, USA

    Sara Branco

  15. Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China

    Asha Dissanayake, Ruvishika Jayawardena & Jiye Yan

  16. Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Kreutzwaldi, 5, 51014, Tartu, Estonia

    Rein Drenkhan

  17. Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, København K, Denmark

    Tobias Guldberg Frøslev

  18. Institute for Genomics and Bioinformatics, Graz University of Technology, 8010, Graz, Austria

    Bettina Halwachs

  19. Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology, 8010, Graz, Austria

    Bettina Halwachs

  20. Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Zuercherstrasse 111, 8903, Birmensdorf, Switzerland

    Martin Hartmann

  21. Molecular Ecology, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland

    Martin Hartmann

  22. Plant Pathology, The Royal Horticultural Society, Wisley, Woking, Surrey, GU23 6QB, UK

    Beatrice Henricot

  23. Division of Biology, Kansas State University, Manhattan, KS, 66506, USA

    Ari Jumpponen

  24. Metapopulation Research Group, Department of Biosciences, University of Helsinki, PO Box 65, 00014, Helsinki, Finland

    Sonja Koskela

  25. Department of Diagnostics and Plant Pathophysiology, University of Warmia and Mazury in Olsztyn, Plac Lodzki 5, Olsztyn, 10-957, Poland

    Tomasz Kulik

  26. Plant Biology, Department of Biosciences, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland

    Kare Liimatainen & Tuula Niskanen

  27. US Forest Service, Northern Research Station, Center for Forest Mycology Research, One Gifford Pinchot Drive, Madison, WI, USA

    Daniel Lindner

  28. Departamento Botânica, PPG Biologia de Fungos, Algas e Plantas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil

    Maria Alice Neves

  29. Department of Botany, Swedish Natural History Museum, Svante Arrhenius väg 7, 10405, Stockholm, Sweden

    Stephan Nylinder

  30. Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil

    Olinto Liparini Pereira & Danilo Batista Pinho

  31. Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada

    Teresita M. Porter

  32. ETH Zürich, Institute for Integrative Biology, CHN G 68.3, Universitätsstrasse 16, 8092, Zürich, Switzerland

    Valentin Queloz

  33. Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996-1610, USA

    Marisol Sánchez-García

  34. Plant Breeding and Acclimatization Institute-National Research Institute, Młochów Research Centre, Platanowa 19, 05831, Młochów, Poland

    Emil Stefańczyk

  35. Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 59 Dudley Rd., New Brunswick, NJ, 08901, USA

    Mariusz Tadych

  36. Laboratory of Plant Pathology, Faculty of Bioresources, Mie University, 1577 Kurima-Machiya, Tsu-city, 514-8507, Japan

    Susumu Takamatsu

  37. Institute of Botany and Landscape Ecology, Ernst-Moritz-Arndt University, Soldmannstr. 15, 17487, Greifswald, Germany

    Martin Unterseher

  38. Biostatistics Department, Yale School of Public Health, New Haven, CT, 06520, USA

    Zheng Wang

  39. Natural History Museum, P.O. Box 1172, Blindern, 0318, Oslo, Norway

    Karl-Henrik Larsson

  40. Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia

    Urmas Kõljalg & Kessy Abarenkov

Authors
  1. R. Henrik Nilsson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kevin D. Hyde
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Julia Pawłowska
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Martin Ryberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Leho Tedersoo
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Anders Bjørnsgard Aas
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Siti A. Alias
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Artur Alves
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Cajsa Lisa Anderson
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Alexandre Antonelli
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. A. Elizabeth Arnold
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Barbara Bahnmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Mohammad Bahram
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Johan Bengtsson-Palme
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Anna Berlin
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Sara Branco
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Putarak Chomnunti
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Asha Dissanayake
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Rein Drenkhan
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Hanna Friberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Tobias Guldberg Frøslev
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. Bettina Halwachs
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. Martin Hartmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  24. Beatrice Henricot
    View author publications

    You can also search for this author in PubMed Google Scholar

  25. Ruvishika Jayawardena
    View author publications

    You can also search for this author in PubMed Google Scholar

  26. Ari Jumpponen
    View author publications

    You can also search for this author in PubMed Google Scholar

  27. Håvard Kauserud
    View author publications

    You can also search for this author in PubMed Google Scholar

  28. Sonja Koskela
    View author publications

    You can also search for this author in PubMed Google Scholar

  29. Tomasz Kulik
    View author publications

    You can also search for this author in PubMed Google Scholar

  30. Kare Liimatainen
    View author publications

    You can also search for this author in PubMed Google Scholar

  31. Björn D. Lindahl
    View author publications

    You can also search for this author in PubMed Google Scholar

  32. Daniel Lindner
    View author publications

    You can also search for this author in PubMed Google Scholar

  33. Jian-Kui Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  34. Sajeewa Maharachchikumbura
    View author publications

    You can also search for this author in PubMed Google Scholar

  35. Dimuthu Manamgoda
    View author publications

    You can also search for this author in PubMed Google Scholar

  36. Svante Martinsson
    View author publications

    You can also search for this author in PubMed Google Scholar

  37. Maria Alice Neves
    View author publications

    You can also search for this author in PubMed Google Scholar

  38. Tuula Niskanen
    View author publications

    You can also search for this author in PubMed Google Scholar

  39. Stephan Nylinder
    View author publications

    You can also search for this author in PubMed Google Scholar

  40. Olinto Liparini Pereira
    View author publications

    You can also search for this author in PubMed Google Scholar

  41. Danilo Batista Pinho
    View author publications

    You can also search for this author in PubMed Google Scholar

  42. Teresita M. Porter
    View author publications

    You can also search for this author in PubMed Google Scholar

  43. Valentin Queloz
    View author publications

    You can also search for this author in PubMed Google Scholar

  44. Taavi Riit
    View author publications

    You can also search for this author in PubMed Google Scholar

  45. Marisol Sánchez-García
    View author publications

    You can also search for this author in PubMed Google Scholar

  46. Filipe de Sousa
    View author publications

    You can also search for this author in PubMed Google Scholar

  47. Emil Stefańczyk
    View author publications

    You can also search for this author in PubMed Google Scholar

  48. Mariusz Tadych
    View author publications

    You can also search for this author in PubMed Google Scholar

  49. Susumu Takamatsu
    View author publications

    You can also search for this author in PubMed Google Scholar

  50. Qing Tian
    View author publications

    You can also search for this author in PubMed Google Scholar

  51. Dhanushka Udayanga
    View author publications

    You can also search for this author in PubMed Google Scholar

  52. Martin Unterseher
    View author publications

    You can also search for this author in PubMed Google Scholar

  53. Zheng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  54. Saowanee Wikee
    View author publications

    You can also search for this author in PubMed Google Scholar

  55. Jiye Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  56. Ellen Larsson
    View author publications

    You can also search for this author in PubMed Google Scholar

  57. Karl-Henrik Larsson
    View author publications

    You can also search for this author in PubMed Google Scholar

  58. Urmas Kõljalg
    View author publications

    You can also search for this author in PubMed Google Scholar

  59. Kessy Abarenkov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kessy Abarenkov.

Additional information

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 and Jy Yan contributed equally to the project and are listed in alphabetical order.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Item 1

The 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)

Supplementary Item 2

Screenshots 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)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Nilsson, R.H., Hyde, K.D., Pawłowska, J. et al. Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Diversity 67, 11–19 (2014). https://doi.org/10.1007/s13225-014-0291-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13225-014-0291-8

Keywords

Search

Navigation