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Abarenkov K, Nilsson RH, Larsson KH, Taylor AS, May T, Frøslev TG, Pawlowska J, Lindahl B, Põldmaa K, Truong C, Vu D, Hosoya T, Niskanen T, Piirmann T, Ivanov F, Zirk A, Peterson M, Cheeke T, Ishigami Y, Jansson A, Jeppesen T, Kristiansson E, Mikryukov V, Miller J, Oono R, Ossandon F, Paupério J, Saar I, Schigel D, Suija A, Tedersoo L, Kõljalg U. The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered. Nucleic Acids Res 2024; 52:D791-D797. [PMID: 37953409 PMCID: PMC10767974 DOI: 10.1093/nar/gkad1039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023] Open
Abstract
UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.
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Affiliation(s)
- Kessy Abarenkov
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 453, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 453, 405 30 Göteborg, Sweden
| | - Karl-Henrik Larsson
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 453, 405 30 Göteborg, Sweden
- Natural History Museum, University of Oslo, Box 1172 Blindern, 0318 Oslo, Norway
| | - Andy F S Taylor
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
| | - Tom W May
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, VIC 3004, Australia
| | - Tobias Guldberg Frøslev
- Global Biodiversity Information Facility (GBIF), Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, ul. Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Björn Lindahl
- Swedish University of Agricultural Sciences, Department of Soil and Environment, Box 7014, SE-750 07 Uppsala, Sweden
| | - Kadri Põldmaa
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Camille Truong
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, VIC 3004, Australia
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, The Netherlands
| | | | - Tuula Niskanen
- Botany Unit, Finnish Museum of Natural History, P.O.Box 7, 00014 University of Helsinki, Finland
| | - Timo Piirmann
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Filipp Ivanov
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Allan Zirk
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Marko Peterson
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Tanya E Cheeke
- School of Biological Sciences, Washington State University, 2710 Crimson Way, Richland, WA 9935, USA
| | - Yui Ishigami
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Arnold Tobias Jansson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 453, 405 30 Göteborg, Sweden
| | - Thomas Stjernegaard Jeppesen
- Global Biodiversity Information Facility (GBIF), Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Vladimir Mikryukov
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Joseph T Miller
- Global Biodiversity Information Facility (GBIF), Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Ryoko Oono
- Department of Ecology, Evolution, and Marine Biology, University of California at Santa Barbara, USA
| | | | - Joana Paupério
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Irja Saar
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Dmitry Schigel
- Global Biodiversity Information Facility (GBIF), Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Ave Suija
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
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Suija A, McMullin R, Lõhmus P. A phylogenetic assessment of a fungicolous lineage in Coniocybomycetes: Chaenotricha, a new genus of Trichaptum-inhabiting species. Fungal Syst Evol 2023; 12:255-269. [PMID: 38455956 PMCID: PMC10918626 DOI: 10.3114/fuse.2023.12.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/02/2023] [Indexed: 03/09/2024] Open
Abstract
The globally distributed genus Trichaptum is one of the most species-rich among polypores in terms of hosting other fungi. Among Trichaptum-associates, there is a group of mazaediate lichenized fungi (Coniocybomycetes, Ascomycota) that previously had an uncertain phylogenetic position. DNA sequences - mitochondrial small subunit (mtSSU), nuclear large subunit rDNA (nuLSU), and internal transcribed spacer (ITS) - were obtained from 29 specimens collected from Europe and North America. Maximum likelihood and Bayesian inference analyses of these three gene loci were used to infer phylogenetic position and relationships among lineages. Statistical tests were used to find which phenotypical characteristics distinguish species. The molecular sequence data provide evidence that the fungicolous specimens form a distinct lineage within Coniocybomycetes sister to the combined clade of Chaenotheca s. lat. and Sclerophora. Considering its phylogenetic placement and strict specialization, we describe a new genus - Chaenotricha. This fungicolous lineage contains three species based on molecular characteristics. Morphological characters mostly overlap except for spore size and stalk length of apothecia. We provide a new combination, Chaenotricha obscura, for the only previously described species for which we designate an epitype, and introduce a new species - Chaenotricha cilians. The third lineage remains undescribed because of a small sample size, which did not allow us to clearly delineate species boundaries. Citation: Suija A, McMullin RT, Lõhmus P (2023). A phylogenetic assessment of a fungicolous lineage in Coniocybomycetes: Chaenotricha, a new genus of Trichaptum-inhabiting species. Fungal Systematics and Evolution 12: 255-269. doi: 10.3114/fuse.2023.12.13.
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Affiliation(s)
- A. Suija
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2 (Oecologicum), EE50409 Tartu, Estonia
- Mycological collections, Natural History Museum and Botanical Garden, University of Tartu, Vanemuise 46, EE50410, Tartu, Estonia
| | - R.T. McMullin
- Research and Collections, Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, Ontario K1P 6P4, Canada
| | - P. Lõhmus
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2 (Oecologicum), EE50409 Tartu, Estonia
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Hongsanan S, Hyde KD, Phookamsak R, Wanasinghe DN, McKenzie EHC, Sarma VV, Lücking R, Boonmee S, Bhat JD, Liu NG, Tennakoon DS, Pem D, Karunarathna A, Jiang SH, Jones GEB, Phillips AJL, Manawasinghe IS, Tibpromma S, Jayasiri SC, Sandamali D, Jayawardena RS, Wijayawardene NN, Ekanayaka AH, Jeewon R, Lu YZ, Phukhamsakda C, Dissanayake AJ, Zeng XY, Luo ZL, Tian Q, Thambugala KM, Dai D, Samarakoon MC, Chethana KWT, Ertz D, Doilom M, Liu JK(J, Pérez-Ortega S, Suija A, Senwanna C, Wijesinghe SN, Niranjan M, Zhang SN, Ariyawansa HA, Jiang HB, Zhang JF, Norphanphoun C, de Silva NI, Thiyagaraja V, Zhang H, Bezerra JDP, Miranda-González R, Aptroot A, Kashiwadani H, Harishchandra D, Sérusiaux E, Abeywickrama PD, Bao DF, Devadatha B, Wu HX, Moon KH, Gueidan C, Schumm F, Bundhun D, Mapook A, Monkai J, Bhunjun CS, Chomnunti P, Suetrong S, Chaiwan N, Dayarathne MC, Yang J, Rathnayaka AR, Xu JC, Zheng J, Liu G, Feng Y, Xie N. Refined families of Dothideomycetes: orders and families incertae sedis in Dothideomycetes. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00462-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AbstractNumerous new taxa and classifications of Dothideomycetes have been published following the last monograph of families of Dothideomycetes in 2013. A recent publication by Honsanan et al. in 2020 expanded information of families in Dothideomycetidae and Pleosporomycetidae with modern classifications. In this paper, we provide a refined updated document on orders and families incertae sedis of Dothideomycetes. Each family is provided with an updated description, notes, including figures to represent the morphology, a list of accepted genera, and economic and ecological significances. We also provide phylogenetic trees for each order. In this study, 31 orders which consist 50 families are assigned as orders incertae sedis in Dothideomycetes, and 41 families are treated as families incertae sedis due to lack of molecular or morphological evidence. The new order, Catinellales, and four new families, Catinellaceae, Morenoinaceae Neobuelliellaceae and Thyrinulaceae are introduced. Seven genera (Neobuelliella, Pseudomicrothyrium, Flagellostrigula, Swinscowia, Macroconstrictolumina, Pseudobogoriella, and Schummia) are introduced. Seven new species (Acrospermum urticae, Bogoriella complexoluminata, Dothiorella ostryae, Dyfrolomyces distoseptatus, Macroconstrictolumina megalateralis, Patellaria microspora, and Pseudomicrothyrium thailandicum) are introduced base on morphology and phylogeny, together with two new records/reports and five new collections from different families. Ninety new combinations are also provided in this paper.
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Kõljalg U, Nilsson HR, Schigel D, Tedersoo L, Larsson KH, May TW, Taylor AFS, Jeppesen TS, Frøslev TG, Lindahl BD, Põldmaa K, Saar I, Suija A, Savchenko A, Yatsiuk I, Adojaan K, Ivanov F, Piirmann T, Pöhönen R, Zirk A, Abarenkov K. The Taxon Hypothesis Paradigm-On the Unambiguous Detection and Communication of Taxa. Microorganisms 2020; 8:E1910. [PMID: 33266327 PMCID: PMC7760934 DOI: 10.3390/microorganisms8121910] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/24/2020] [Indexed: 12/27/2022] Open
Abstract
Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.
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Affiliation(s)
- Urmas Kõljalg
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Henrik R. Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; (H.R.N.); (K.-H.L.)
| | - Dmitry Schigel
- Global Biodiversity Information Facility, 2100 Copenhagen, Denmark; (D.S.); (T.S.J.)
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Karl-Henrik Larsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; (H.R.N.); (K.-H.L.)
| | - Tom W. May
- Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, Victoria 3004, Australia;
| | - Andy F. S. Taylor
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK;
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
| | | | | | - Björn D. Lindahl
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden;
| | - Kadri Põldmaa
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Irja Saar
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Ave Suija
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Anton Savchenko
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Iryna Yatsiuk
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Kristjan Adojaan
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Filipp Ivanov
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Timo Piirmann
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Raivo Pöhönen
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Allan Zirk
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
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Suija A, Haldeman M, Zimmermann E, Braun U, Diederich P. Phylogenetic placement and lectotypification of Pseudotryblidium neesii ( Helotiales, Leotiomycetes). Fungal Syst Evol 2020; 5:139-149. [PMID: 32467920 PMCID: PMC7250013 DOI: 10.3114/fuse.2020.05.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A phylogenetic analysis of combined rDNA LSU and ITS sequence data was carried out to determine the phylogenetic placement of specimens identified as Pseudotryblidium neesii. The species forms a distinct clade within Dermateaceae (Helotiales, Leotiomycetes) with Rhizodermea veluwiensis and two Dermea species. The geographical distribution of this species, previously known only from Europe on Abies alba, is extended to north-western North America where it grows exclusively on A. grandis. The name P. neesii is lectotypified in order to disentangle the complicated nomenclature of the species. A new, detailed description of P. neesii with illustrations is provided after comparison of sequenced specimens with the type material. Furthermore, the new combination Pseudographis rufonigra (basionym Peziza rufonigra) is made for a fungus previously known as Pseudographis pinicola.
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Affiliation(s)
- A Suija
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - M Haldeman
- 1402 23 Street, Bellingham, Washington, USA
| | | | - U Braun
- Martin-Luther-Universität, Institut für Biologie, Bereich Geobotanik, Herbarium, Neuwerk 21, 06099 Halle (Saale), Germany
| | - P Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
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Zamora JC, Svensson M, Kirschner R, Olariaga I, Ryman S, Parra LA, Geml J, Rosling A, Adamčík S, Ahti T, Aime MC, Ainsworth AM, Albert L, Albertó E, García AA, Ageev D, Agerer R, Aguirre-Hudson B, Ammirati J, Andersson H, Angelini C, Antonín V, Aoki T, Aptroot A, Argaud D, Sosa BIA, Aronsen A, Arup U, Asgari B, Assyov B, Atienza V, Bandini D, Baptista-Ferreira JL, Baral HO, Baroni T, Barreto RW, Beker H, Bell A, Bellanger JM, Bellù F, Bemmann M, Bendiksby M, Bendiksen E, Bendiksen K, Benedek L, Bérešová-Guttová A, Berger F, Berndt R, Bernicchia A, Biketova AY, Bizio E, Bjork C, Boekhout T, Boertmann D, Böhning T, Boittin F, Boluda CG, Boomsluiter MW, Borovička J, Brandrud TE, Braun U, Brodo I, Bulyonkova T, Burdsall HH, Buyck B, Burgaz AR, Calatayud V, Callac P, Campo E, Candusso M, Capoen B, Carbó J, Carbone M, Castañeda-Ruiz RF, Castellano MA, Chen J, Clerc P, Consiglio G, Corriol G, Courtecuisse R, Crespo A, Cripps C, Crous PW, da Silva GA, da Silva M, Dam M, Dam N, Dämmrich F, Das K, Davies L, De Crop E, De Kesel A, De Lange R, De Madrignac Bonzi B, dela Cruz TEE, Delgat L, Demoulin V, Desjardin DE, Diederich P, Dima B, Dios MM, Divakar PK, Douanla-Meli C, Douglas B, Drechsler-Santos ER, Dyer PS, Eberhardt U, Ertz D, Esteve-Raventós F, Salazar JAE, Evenson V, Eyssartier G, Farkas E, Favre A, Fedosova AG, Filippa M, Finy P, Flakus A, Fos S, Fournier J, Fraiture A, Franchi P, Molano AEF, Friebes G, Frisch A, Fryday A, Furci G, Márquez RG, Garbelotto M, García-Martín JM, Otálora MAG, Sánchez DG, Gardiennet A, Garnica S, Benavent IG, Gates G, da Cruz Lima Gerlach A, Ghobad-Nejhad M, Gibertoni TB, Grebenc T, Greilhuber I, Grishkan B, Groenewald JZ, Grube M, Gruhn G, Gueidan C, Gulden G, Gusmão LFP, Hafellner J, Hairaud M, Halama M, Hallenberg N, Halling RE, Hansen K, Harder CB, Heilmann-Clausen J, Helleman S, Henriot A, Hernandez-Restrepo M, Herve R, Hobart C, Hoffmeister M, Høiland K, Holec J, Holien H, Hughes K, Hubka V, Huhtinen S, Ivančević B, Jagers M, Jaklitsch W, Jansen A, Jayawardena RS, Jeppesen TS, Jeppson M, Johnston P, Jørgensen PM, Kärnefelt I, Kalinina LB, Kantvilas G, Karadelev M, Kasuya T, Kautmanová I, Kerrigan RW, Kirchmair M, Kiyashko A, Knapp DG, Knudsen H, Knudsen K, Knutsson T, Kolařík M, Kõljalg U, Košuthová A, Koszka A, Kotiranta H, Kotkova V, Koukol O, Kout J, Kovács GM, Kříž M, Kruys Å, Kučera V, Kudzma L, Kuhar F, Kukwa M, Arun Kumar TK, Kunca V, Kušan I, Kuyper TW, Lado C, Læssøe T, Lainé P, Langer E, Larsson E, Larsson KH, Laursen G, Lechat C, Lee S, Lendemer JC, Levin L, Lindemann U, Lindström H, Liu X, Hernandez RCL, Llop E, Locsmándi C, Lodge DJ, Loizides M, Lőkös L, Luangsa-ard J, Lüderitz M, Lumbsch T, Lutz M, Mahoney D, Malysheva E, Malysheva V, Manimohan P, Marin-Felix Y, Marques G, Martínez-Gil R, Marson G, Mata G, Matheny PB, Mathiassen GH, Matočec N, Mayrhofer H, Mehrabi M, Melo I, Mešić A, Methven AS, Miettinen O, Romero AMM, Miller AN, Mitchell JK, Moberg R, Moreau PA, Moreno G, Morozova O, Morte A, Muggia L, González GM, Myllys L, Nagy I, Nagy LG, Neves MA, Niemelä T, Nimis PL, Niveiro N, Noordeloos ME, Nordin A, Noumeur SR, Novozhilov Y, Nuytinck J, Ohenoja E, Fiuza PO, Orange A, Ordynets A, Ortiz-Santana B, Pacheco L, Pál-Fám F, Palacio M, Palice Z, Papp V, Pärtel K, Pawlowska J, Paz A, Peintner U, Pennycook S, Pereira OL, Daniëls PP, Pérez-De-Gregorio Capella MÀ, del Amo CMP, Gorjón SP, Pérez-Ortega S, Pérez-Vargas I, Perry BA, Petersen JH, Petersen RH, Pfister DH, Phukhamsakda C, Piątek M, Piepenbring M, Pino-Bodas R, Esquivel JPP, Pirot P, Popov ES, Popoff O, Álvaro MP, Printzen C, Psurtseva N, Purahong W, Quijada L, Rambold G, Ramírez NA, Raja H, Raspé O, Raymundo T, Réblová M, Rebriev YA, de Dios Reyes García J, Ripoll MÁR, Richard F, Richardson MJ, Rico VJ, Robledo GL, Barbosa FR, Rodriguez-Caycedo C, Rodriguez-Flakus P, Ronikier A, Casas LR, Rusevska K, Saar G, Saar I, Salcedo I, Martínez SMS, Montoya CAS, Sánchez-Ramírez S, Sandoval-Sierra JV, Santamaria S, Monteiro JS, Schroers HJ, Schulz B, Schmidt-Stohn G, Schumacher T, Senn-Irlet B, Ševčíková H, Shchepin O, Shirouzu T, Shiryaev A, Siepe K, Sir EB, Sohrabi M, Soop K, Spirin V, Spribille T, Stadler M, Stalpers J, Stenroos S, Suija A, Sunhede S, Svantesson S, Svensson S, Svetasheva TY, Świerkosz K, Tamm H, Taskin H, Taudière A, Tedebrand JO, Lahoz RT, Temina M, Thell A, Thines M, Thor G, Thüs H, Tibell L, Tibell S, Timdal E, Tkalčec Z, Tønsberg T, Trichies G, Triebel D, Tsurykau A, Tulloss RE, Tuovinen V, Sosa MU, Urcelay C, Valade F, Garza RV, van den Boom P, Van Vooren N, Vasco-Palacios AM, Vauras J, Velasco Santos JM, Vellinga E, Verbeken A, Vetlesen P, Vizzini A, Voglmayr H, Volobuev S, von Brackel W, Voronina E, Walther G, Watling R, Weber E, Wedin M, Weholt Ø, Westberg M, Yurchenko E, Zehnálek P, Zhang H, Zhurbenko MP, Ekman S. Considerations and consequences of allowing DNA sequence data as types of fungal taxa. IMA Fungus 2018; 9:167-175. [PMID: 30018877 PMCID: PMC6048565 DOI: 10.5598/imafungus.2018.09.01.10] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 05/21/2018] [Indexed: 11/11/2022] Open
Abstract
Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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Affiliation(s)
- Juan Carlos Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden
| | - Måns Svensson
- Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden
| | | | - Ibai Olariaga
- Universidad Rey Juan Carlos, 28933 Móstoles, Madrid, Spain
| | - Svengunnar Ryman
- Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden
| | | | - József Geml
- Naturalis Biodiversity Center, Vondellaan 55, 2332AA Leiden, The Netherlands
| | - Anna Rosling
- Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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- Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden
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Suija A, van den Boom P, Zimmermann E, Zhurbenko MP, Diederich P. Lichenicolous species of Hainesia belong to Phacidiales (Leotiomycetes) and are included in an extended concept of Epithamnolia. Mycologia 2018. [PMID: 29517949 DOI: 10.1080/00275514.2017.1413891] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The lichenicolous taxa currently included in the genus Hainesia were studied based on the nuclear rDNA (18S, 28S, and internal transcribed spacer [ITS]) genes. The authors found that lichenicolous taxa form a distinct lineage sister to Epiglia gloeocapsae (Phacidiales, Leotiomycetes), only distantly related to the type species of Hainesia (Chaetomellaceae, Helotiales). Owing to morphological similarities, the authors include the lichenicolous species into the previously monotypic genus Epithamnolia. A new species, Epithamnolia rangiferinae, is described, several names are reduced into synonymy, and a key to the species of Epithamnolia is provided. The incorporation of public environmental ITS sequences showed that the closest relatives of these lichenicolous taxa are various endophytic, endolichenic, and soil-inhabiting fungi.
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Affiliation(s)
- Ave Suija
- a Institute of Ecology and Earth Sciences, University of Tartu , 40 Lai Street, 51005 Tartu , Estonia
| | | | | | - Mikhail P Zhurbenko
- d Komarov Botanical Institute , Professor Popov 2, St. Petersburg , 197376 , Russia
| | - Paul Diederich
- e Musée national d'histoire naturelle , 25 rue Munster, L-2160 Luxembourg, Luxembourg
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Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou NS, Wijesundera R, Villarreal Ruiz L, Vasco-Palacios AM, Thu PQ, Suija A, Smith ME, Sharp C, Saluveer E, Saitta A, Rosas M, Riit T, Ratkowsky D, Pritsch K, Põldmaa K, Piepenbring M, Phosri C, Peterson M, Parts K, Pärtel K, Otsing E, Nouhra E, Njouonkou AL, Nilsson RH, Morgado LN, Mayor J, May TW, Majuakim L, Lodge DJ, Lee SS, Larsson KH, Kohout P, Hosaka K, Hiiesalu I, Henkel TW, Harend H, Guo LD, Greslebin A, Grelet G, Geml J, Gates G, Dunstan W, Dunk C, Drenkhan R, Dearnaley J, De Kesel A, Dang T, Chen X, Buegger F, Brearley FQ, Bonito G, Anslan S, Abell S, Abarenkov K. Fungal biogeography. Global diversity and geography of soil fungi. Science 2014; 346:1256688. [PMID: 25430773 DOI: 10.1126/science.1256688] [Citation(s) in RCA: 1501] [Impact Index Per Article: 150.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.
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Affiliation(s)
- Leho Tedersoo
- Natural History Museum, University of Tartu, Tartu, Estonia.
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sergei Põlme
- Natural History Museum, University of Tartu, Tartu, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Nourou S Yorou
- Faculté d'Agronomie, Université de Parakou, Parakou, Benin
| | - Ravi Wijesundera
- Department of Plant Sciences, University of Colombo, Colombo 3, Sri Lanka
| | - Luis Villarreal Ruiz
- Postgrado en Recursos Genéticos y Productividad-Genética, LARGEMBIO, Colegio de Postgraduados-Líneas Prioritarias de Investigación 6, México City, Mexico
| | - Aída M Vasco-Palacios
- The Fungal Biodiversity Centre, Centraalbureau voor Schimmelcultures-Royal Netherlands Academy of Arts and Sciences, Utrecht, Netherlands
| | | | - Ave Suija
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | | | - Erki Saluveer
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Alessandro Saitta
- Department of Agricultural and Forest Sciences, Università di Palermo, Palermo, Italy
| | - Miguel Rosas
- Department of Mycology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Taavi Riit
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - David Ratkowsky
- Tasmanian Institute of Agriculture, Hobart, Tasmania, Australia
| | - Karin Pritsch
- Institute of Soil Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Meike Piepenbring
- Department of Mycology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Marko Peterson
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kaarin Parts
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kadri Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Eveli Otsing
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Eduardo Nouhra
- Instituto Multidisciplinario de Biología Vegetal, Córdoba, Argentina
| | - André L Njouonkou
- Department of Biological Sciences, University of Bamenda, Bambili, Cameroon
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | | | - Jordan Mayor
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Tom W May
- Royal Botanic Gardens Melbourne, Melbourne, Victoria, Australia
| | - Luiza Majuakim
- Institute for Tropical Biology and Conservation, University Malaysia Sabah, Sabah, Malaysia
| | - D Jean Lodge
- Center for Forest Mycology Research, U.S. Department of Agriculture--Forest Service, Luquillo, Puerto Rico
| | - Su See Lee
- Forest Research Institute Malaysia, Kepong, Selangor, Malaysia
| | | | - Petr Kohout
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, Tsukuba, Japan
| | - Indrek Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | - Helery Harend
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Liang-dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Alina Greslebin
- Consejo Nacional de Investigaciones Científicas y Técnicas-Facultad de Cs. Naturales, Universidad Nacional de la Patagonia SJB, Esquel, Chubut, Argentina
| | - Gwen Grelet
- Ecosystems and Global Change team, Landcare Research, Lincoln, New Zealand
| | - Jozsef Geml
- Naturalis Biodiversity Center, Leiden, Netherlands
| | - Genevieve Gates
- Tasmanian Institute of Agriculture, Hobart, Tasmania, Australia
| | - William Dunstan
- School of Veterinary & Life Sciences, Murdoch University, Western Australia, Australia
| | - Chris Dunk
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Rein Drenkhan
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - John Dearnaley
- Faculty of Health, Engineering and Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia
| | | | - Tan Dang
- Vietnamese Academy of Forest Sciences, Hanoi, Vietnam
| | - Xin Chen
- College of Life Sciences, Zhejiag University, Hangzhou 310058, China
| | - Franz Buegger
- Institute of Soil Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Francis Q Brearley
- School of Science and the Environment, Manchester Metropolitan University, Manchester, UK
| | - Gregory Bonito
- Royal Botanic Gardens Melbourne, Melbourne, Victoria, Australia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sandra Abell
- School of Marine and Tropical Biology, James Cook University, Cairns, Queensland, Australia
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Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiss M, Larsson KH. Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 2013; 22:5271-5277. [PMID: 24112409 DOI: 10.1111/j.1365-2745.2011.01940.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/08/2013] [Accepted: 07/17/2013] [Indexed: 05/20/2023]
Abstract
The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
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Affiliation(s)
- Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia; Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
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Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiss M, Larsson KH. Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 2013; 22:5271-7. [DOI: 10.1111/mec.12481] [Citation(s) in RCA: 2233] [Impact Index Per Article: 203.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/08/2013] [Accepted: 07/17/2013] [Indexed: 02/06/2023]
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