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Fungal taxonomy and sequence-based nomenclature



The identification and proper naming of microfungi, in particular plant, animal and human pathogens, remains challenging. Molecular identification is becoming the default approach for many fungal groups, and environmental metabarcoding is contributing an increasing amount of sequence data documenting fungal diversity on a global scale. This includes lineages represented only by sequence data. At present, these taxa cannot be formally described under the current nomenclature rules. By considering approaches used in bacterial taxonomy, we propose solutions for the nomenclature of taxa known only from sequences to facilitate consistent reporting and communication in the literature and public sequence repositories.

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Fig. 1: Fungal diversity.
Fig. 2: Timeline of important events in fungal taxonomy and nomenclature.
Fig. 3: Visualization of new lineages.


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Work by C.L.S. and B.R. was supported by the Intramural Research Program of the National Library of Medicine at the National Institutes of Health in Bethesda, Maryland, USA. D.M.G. received support through the National Science Foundation (NSF) grant DEB-1655980 and Project 4655 of the Pennsylvania State Agricultural Experiment Station. E.M. acknowledges CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil) and FACEPE (Fundação de Amparo à Ciência e Tecnologia de Pernambuco, Brazil). K.D.H. thanks the Thailand Research Fund, grant RDG6130001, entitled “Impact of Climate Change on Fungal Diversity and Biogeography in the Greater Mekong Subregion”. The USDA Hatch project 1010662 is acknowledged for support to M.C.A. M.Ö. was supported by the European Regional Development Fund (Centre of Excellence EcolChange). M.T. acknowledges LOEWE for funding in the framework of the Centre for Translational Biodiversity Genomics (TBG) and the German Science Foundation. N.Z. acknowledges the NSF of the United States (DEB-1452971). P.R.J. was supported through the Manaaki Whenua Biota Portfolio with funding from the Science and Innovation Group of the New Zealand Ministry of Business, Innovation and Employment. R.J. thanks the University of Mauritius for research support. We thank S. Redhead for nomenclatural advice. R. Sanders provided the update for the fungal ITS data in the SRA.

Author information




The present manuscript was first discussed among members of the ICTF. Based on contributions from this initial discussion, a first version of the manuscript was drafted by R.L., C.L.S., M.C.A., B.R. and A.N.M. This version was distributed among the ICTF and to selected colleagues outside the ICTF, and all comments were recorded and incorporated. Based on these initial comments, lead and co-authorship was determined, additional co-authors then including T.A., H.A.A., G.C., P.W.C., I.S.D., D.M.G., D.L.H., K.D.H., L.I., R.J., P.R.J., P.M.K., E.M., T.W.M., W.M., M.Ö., V.R., M.S., M.T., D.V., A.M.Y. and N.Z. The revised draft was circulated two more times among all authors for additional comments before submission. After the first review, H.R.N. was invited as an additional co-author to provide specific input regarding dark taxa and the role of the UNITE database in the proposed alternatives for dark taxa nomenclature. Apart from contributing generally to the manuscript, D.L.H. and T.W.M. revised the nomenclatural details included in Box 1 and Fig. 1. B.R. and D.V. also assisted in technical aspects regarding the SRA and Fig. 3. P.W.C., R.L., W.M., M.T. and A.M.Y. organized the photographs used in Fig. 2 from their working groups. The final draft was approved by all authors.

Corresponding author

Correspondence to Conrad L. Schoch.

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Peer review information Nature Microbiology thanks Michaela Lackner, Emma Steenkamp and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

References for the timeline events depicted in Fig. 2.

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Lücking, R., Aime, M.C., Robbertse, B. et al. Fungal taxonomy and sequence-based nomenclature. Nat Microbiol 6, 540–548 (2021).

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Further reading

  • How to publish a new fungal species, or name, version 3.0

    • M. Catherine Aime
    • , Andrew N. Miller
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    • , Konstanze Bensch
    • , Lei Cai
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    • , Kevin D. Hyde
    • , Paul M. Kirk
    • , Robert Lücking
    • , Tom W. May
    • , Elaine Malosso
    • , Scott A. Redhead
    • , Amy Y. Rossman
    • , Marc Stadler
    • , Marco Thines
    • , Andrey M. Yurkov
    • , Ning Zhang
    •  & Conrad L. Schoch

    IMA Fungus (2021)


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