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

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          Abstract

          It is now a decade since The International Commission on the Taxonomy of Fungi (ICTF) produced an overview of requirements and best practices for describing a new fungal species. In the meantime the International Code of Nomenclature for algae, fungi, and plants (ICNafp) has changed from its former name (the International Code of Botanical Nomenclature) and introduced new formal requirements for valid publication of species scientific names, including the separation of provisions specific to Fungi and organisms treated as fungi in a new Chapter F. Equally transformative have been changes in the data collection, data dissemination, and analytical tools available to mycologists. This paper provides an updated and expanded discussion of current publication requirements along with best practices for the description of new fungal species and publication of new names and for improving accessibility of their associated metadata that have developed over the last 10 years. Additionally, we provide: (1) model papers for different fungal groups and circumstances; (2) a checklist to simplify meeting ( i) the requirements of the ICNafp to ensure the effective, valid and legitimate publication of names of new taxa, and ( ii) minimally accepted standards for description; and, (3) templates for preparing standardized species descriptions.

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          The FAIR Guiding Principles for scientific data management and stewardship

          There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.
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            Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.

            Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
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              NCBI Taxonomy: a comprehensive update on curation, resources and tools

              The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration. Since the last review of this resource in 2012, it has undergone several improvements. Most notable is the shift from a single SQL database to a series of linked databases tied to a framework of data called NameBank. This means that relations among data elements can be adjusted in more detail, resulting in expanded annotation of synonyms, the ability to flag names with specific nomenclatural properties, enhanced tracking of publications tied to names and improved annotation of scientific authorities and types. Additionally, practices utilized by NCBI Taxonomy curators specific to major taxonomic groups are described, terms peculiar to NCBI Taxonomy are explained, external resources are acknowledged and updates to tools and other resources are documented. Database URL: https://www.ncbi.nlm.nih.gov/taxonomy
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                Author and article information

                Contributors
                maime@purdue.edu
                amiller7@illinois.edu
                taoki@affrc.go.jp
                k.bensch@mycobank.org
                cail@im.ac.cn
                p.crous@wi.knaw.nl
                d.hawksworth@kew.org
                kdhyde3@gmail.com
                P.Kirk@kew.org
                r.luecking@bgbm.org
                Tom.May@rbg.vic.gov.au
                elainemalosso@yahoo.com.br
                scott.redhead@canada.ca
                amydianer@yahoo.com
                Marc.Stadler@helmholtz-hzi.de
                m.thines@thines-lab.eu
                ayu@dsmz.de
                ningz@rutgers.edu
                schoch2@ncbi.nlm.nih.gov
                Journal
                IMA Fungus
                IMA Fungus
                IMA Fungus
                BioMed Central (London )
                2210-6340
                2210-6359
                3 May 2021
                3 May 2021
                2021
                : 12
                : 11
                Affiliations
                [1 ]GRID grid.169077.e, ISNI 0000 0004 1937 2197, Department of Botany and Plant Pathology, , Purdue University, ; West Lafayette, IN 47907 USA
                [2 ]GRID grid.35403.31, ISNI 0000 0004 1936 9991, Illinois Natural History Survey, , University of Illinois Urbana-Champaign, ; Champaign, IL 61820 USA
                [3 ]GRID grid.507752.2, Genetic Resources Center, National Agriculture and Food Research Organization, ; 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
                [4 ]GRID grid.418704.e, ISNI 0000 0004 0368 8584, Westerdijk Fungal Biodiversity Institute, ; Uppsalalaan 8, 3584CT Utrecht, the Netherlands
                [5 ]GRID grid.9227.e, ISNI 0000000119573309, State Key Laboratory of Mycology, Institute of Microbiology, , Chinese Academy of Sciences, ; NO.1 Beichen West Road, Chaoyang District, Beijing, 100101 China
                [6 ]GRID grid.4903.e, ISNI 0000 0001 2097 4353, Comparative Plant and Fungal Biology, , Royal Botanic Gardens, Kew, ; Surrey, TW9 3DS UK
                [7 ]GRID grid.35937.3b, ISNI 0000 0001 2270 9879, Department of Life Sciences, , The Natural History Museum, ; Cromwell Road, London, SW7 5BD UK
                [8 ]GRID grid.464353.3, ISNI 0000 0000 9888 756X, Jilin Agricultural University, ; Changchun, 130118 Jilin Province China
                [9 ]GRID grid.411554.0, ISNI 0000 0001 0180 5757, Center of Excellence in Fungal Research, , Mae Fah Luang University, ; Chiang Rai, 57100 Thailand
                [10 ]Biodiversity Informatics & Spatial Analysis, Royal Botanic Garden Kew, Richmond, London, TW9 3AE UK
                [11 ]GRID grid.14095.39, ISNI 0000 0000 9116 4836, Botanischer Garten und Botanisches Museum, , Freie Universität Berlin, ; Königin-Luise-Str. 6-8, 14195 Berlin, Germany
                [12 ]Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
                [13 ]GRID grid.411227.3, ISNI 0000 0001 0670 7996, Departamento de Micologia, Centro de Biociências, , Universidade Federal de Pernambuco, ; Recife, PE 50740-600 Brazil
                [14 ]GRID grid.55614.33, ISNI 0000 0001 1302 4958, Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, ; Ottawa, Ontario K1A 0C6 Canada
                [15 ]GRID grid.4391.f, ISNI 0000 0001 2112 1969, Botany and Plant Pathology Department, , Oregon State University, ; Corvallis, OR 97333 USA
                [16 ]GRID grid.7490.a, ISNI 0000 0001 2238 295X, Department Microbial Drugs, , Helmholtz Centre for Infection Research, ; Inhoffenstrasse 7, 38124 Braunschweig, Germany
                [17 ]GRID grid.7839.5, ISNI 0000 0004 1936 9721, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, , Goethe University, ; Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
                [18 ]GRID grid.507705.0, Senckenberg Biodiversity and Climate Research Centre, ; Senckenberganlage 25, 60325 Frankfurt am Main, Germany
                [19 ]GRID grid.420081.f, ISNI 0000 0000 9247 8466, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, ; Braunschweig, Germany
                [20 ]GRID grid.430387.b, ISNI 0000 0004 1936 8796, Department of Plant Biology, , Rutgers University, ; New Brunswick, NJ 08901 USA
                [21 ]GRID grid.419234.9, ISNI 0000 0004 0604 5429, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, ; 45 Center Drive, Bethesda, MD 20892 USA
                Author information
                http://orcid.org/0000-0001-8742-6685
                Article
                63
                10.1186/s43008-021-00063-1
                8091500
                33934723
                18af5d9a-3c42-40c3-9946-659786310125
                © The Author(s) 2021

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 13 December 2020
                : 8 April 2021
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000199, U.S. Department of Agriculture;
                Award ID: 1010662
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000092, U.S. National Library of Medicine;
                Award ID: Intramural Research Program
                Award Recipient :
                Funded by: German Science Foundation
                Funded by: LOEWE initiative of the Government of Hesse
                Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: DEB 1452971
                Award Recipient :
                Categories
                Nomenclature
                Custom metadata
                © The Author(s) 2021

                Plant science & Botany
                data repositories,dual nomenclature,fair principles,legitimate publication,new combinations,taxonomic best practices,typification,valid publication

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