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  • 1.
    Abarenkov, Kessy
    et al.
    Univ Tartu, Nat Hist Museum, Tartu, Estonia..
    Adams, Rachel I.
    Univ Calif Berkeley, Plant & Microbial Biol, Berkeley, CA 94720 USA..
    Irinyi, Laszlo
    Westmead Hosp, Ctr Infect Dis & Microbiol, Mol Mycol Res Lab, Sydney Med Sch, Sydney, NSW, Australia.;Univ Sydney, Marie Bashir Inst Infect Dis & Biosecur, Sydney, NSW, Australia.;Westmead Inst Med Res, Westmead, NSW, Australia..
    Agan, Ahto
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Ambrosio, Elia
    Univ Tartu, Nat Hist Museum, Tartu, Estonia.;Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.;Via Calamandrei 2, I-53035 Siena, Italy..
    Antonelli, Alexandre
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden.;Gothenburg Bot Garden, Carl Skottsbergs Gata 22A, S-41319 Gothenburg, Sweden..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Bengtsson-Palme, Johan
    Univ Gothenburg, Sahlgrenska Acad, Dept Infect Dis, Guldhedsgatan 10, S-41346 Gothenburg, Sweden..
    Bok, Gunilla
    SP Tech Res Inst Sweden, Box 857, S-50115 Boras, Sweden..
    Cangren, Patrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Coimbra, Victor
    Univ Fed Pernambuco UFPE, Dept Micol, CCB, Av Prof Nelson Chaves S-N, BR-50670901 Recife, PE, Brazil..
    Coleine, Claudia
    Univ Tuscia, Dept Ecol & Biol Sci, I-01100 Viterbo, Italy..
    Gustafsson, Claes
    Univ Gothenburg, Herbarium GB, Box 461, S-40530 Gothenburg, Sweden..
    He, Jinhong
    Chinese Acad Sci, South China Bot Garden, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China..
    Hofmann, Tobias
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Kristiansson, Erik
    Chalmers, Dept Math Sci, S-41296 Gothenburg, Sweden..
    Larsson, Ellen
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Larsson, Tomas
    Univ Gothenburg, Dept Marine Sci, Box 460, S-40530 Gothenburg, Sweden..
    Liu, Yingkui
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Martinsson, Svante
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Meyer, Wieland
    Westmead Hosp, Ctr Infect Dis & Microbiol, Mol Mycol Res Lab, Sydney Med Sch, Sydney, NSW, Australia.;Westmead Inst Med Res, Westmead, NSW, Australia..
    Panova, Marina
    Univ Gothenburg, Dept Marine Sci Tjarno, S-45296 Stromstad, Sweden..
    Pombubpa, Nuttapon
    Univ Calif Riverside, Dept Plant Pathol & Microbiol, Riverside, CA 92521 USA.;Univ Calif Riverside, Inst Integrat Genome Biol, Riverside, CA 92521 USA..
    Ritter, Camila
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Svantesson, Sten
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Scharn, Ruud
    Univ Gothenburg, Dept Earth Sci, Box 460, S-40530 Gothenburg, Sweden..
    Svensson, Ola
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Töpel, Mats
    Univ Gothenburg, Dept Marine Sci, Box 460, S-40530 Gothenburg, Sweden..
    Unterseher, Martin
    Ernst Moritz Arndt Univ Greifswald, Inst Bot & Landscape Ecol, Soldmannstr 15, D-17487 Greifswald, Germany..
    Visagie, Cobus
    Agr & Agri Food Canada, Biodivers Mycol, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.;Univ Ottawa, Dept Biol, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada..
    Wurzbacher, Christian
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Taylor, Andy F. S.
    James Hutton Inst, Aberdeen AB15 8QH, Scotland.;Univ Aberdeen, Inst Biol & Environm Sci, Cruickshank Bldg, Aberdeen AB24 3UU, Scotland..
    Köljalg, Urmas
    Univ Tartu, Nat Hist Museum, Tartu, Estonia.;Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Schriml, Lynn
    Univ Maryland, Sch Med, Dept Epidemiol & Publ Hlth, Baltimore, MD 21201 USA.;Univ Maryland, Sch Med, Inst Genome Sci, Baltimore, MD 21201 USA..
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard - a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)2016In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 16, p. 1-15Article in journal (Refereed)
    Abstract [en]

    Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data - for example, "retrieve all fungal sequences recovered from bathrooms" - a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http:// gensc.org/ mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http:// its. mycologylab.org).

  • 2.
    Anslan, Sten
    et al.
    Braunschweig Univ Technol, Zool Inst, Mendelssohnstr 4, D-38106 Braunschweig, Germany.
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg Global Biodivers Ctr, Box 461, S-40530 Gothenburg, Sweden.
    Wurzbacher, Christian
    Tech Univ Munich, Coulombwall 3, D-85748 Garching, Germany.
    Baldrian, Petr
    Czech Acad Sci, Inst Microbiol, Videnska 1083, Prague 14220 4, Czech Republic.
    Tedersoo, Leho
    Tartu Univ, Nat Hist Museum, 14a Ravila, Tartu 50411, Estonia.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Tartu Univ, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Ulls Vag 16, S-75651 Uppsala, Sweden.
    Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding2018In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 39, p. 29-40Article in journal (Refereed)
    Abstract [en]

    Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.

  • 3.
    Badou, Sylvestre A.
    et al.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Soil Plant Fungi Interact, Lab Ecol Bot & Plant Biol, 03 BOX 125, Parakou, Benin.
    De Kesel, Andre
    Meise Bot Garden, Nieuwelaan 38, B-1860 Meise, Belgium.
    Raspe, Olivier
    Meise Bot Garden, Nieuwelaan 38, B-1860 Meise, Belgium;Federat Wallonie Bruxelles, Rue A Lavallee 1, B-1080 Brussels, Belgium.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Guelly, Atsu K.
    Univ Lome, Fac Sci, Dept Bot & Ecol Vegetale, BP1515, Lome, Togo.
    Yorou, Nourou S.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Soil Plant Fungi Interact, Lab Ecol Bot & Plant Biol, 03 BOX 125, Parakou, Benin.
    Two new African siblings of Pulveroboletus ravenelii (Boletaceae)2018In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 43, p. 115-130Article in journal (Refereed)
    Abstract [en]

    This paper sorts out the taxonomy of species affiliated with Pulveroboletus ravenelii in the Guineo-soudanian and Zambezian woodlands of Africa. Morphological and genetic characters of African Pulveroboletus collections were studied and compared to those of North American and Asian species. A phylogenetic analysis showed that the African specimens form a subclade, sister to the Asian and American taxa. Although clamp connections have previously never been reported from Pulveroboletus, all specimens of the African subclade show very small clamp connections. Two new African species, Pulveroboletus africanus sp. nov. and P. sokponianus sp. nov., are described and illustrated. Comments concerning morphology and identification, as well as distribution and ecology, are given for both species.

  • 4.
    Ekman, Stefan
    et al.
    Uppsala University, Music and Museums, Museum of Evolution.
    Tönsberg, Tor
    Univ Bergen, Dept Nat Hist, Univ Museum, Allegaten 41,POB 7800, NO-5020 Bergen, Norway.
    Biatora alnetorum (Ramalinaceae, Lecanorales), a new lichen species from western North America2019In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 48, p. 55-65Article in journal (Refereed)
    Abstract [en]

    Biatora alnetorum S. Ekman & Tonsberg, a lichenised ascomycete in the family Ramalinaceae (Lecanorales, Lecanoromycetes), is described as new to science. It is distinct from other species of Biatora in the combination of mainly three-septate ascospores, a crustose thallus forming distinctly delimited soral is that develop by disintegration of convex pustules and the production of atranorin in the thallus and apothecia. The species is known from the Pacific Northwest of North America, where it inhabits the smooth bark of Alnua alnobetula subsp. sinuata and A. rubra. Biatora alnetorum is also a new host for the lichenicolous ascomycete Sclerococcum toensbagii Diederich.

  • 5.
    Košuthová, Alica
    et al.
    Swedish Museum Nat Hist, Dept Bot, Stockholm, Sweden.
    Westberg, Martin
    Uppsala University, Music and Museums, Museum of Evolution.
    Otálora, Mónica A.G.
    Swiss Fed Inst Technol, Inst Integrat Biol, Plant Ecol Genet, Zurich, Switzerland.
    Wedin, Mats
    Swedish Museum Nat Hist, Dept Bot, Stockholm, Sweden.
    Rostania revised: testing generic delimitations in Collemataceae (Peltigerales, Lecanoromycetes )2019In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 47, p. 17-33Article in journal (Refereed)
    Abstract [en]

    Here, we test the current generic delimitation of Rostania (Collemataceae, Peltigerales, Ascomycota) utilizing molecular phylogeny and morphological investigations. Using DNA sequence data from the mitochondrial SSU rDNA and two nuclear protein-coding genes (MCM7 and β-tubulin) and utilizing parsimony, maximum likelihood and Bayesian phylogenetic methods, Rostania is shown to be non-monophyletic in the current sense. A new generic delimitation of Rostania is thus proposed, in which the genus is monophyletic, and three species (Rostania coccophylla, R. paramensis, R. quadrifida) are excluded and transferred to other genera. Rostania occultata is further non-monophyletic, and a more detailed investigation of species delimitations in Rostania s. str. is needed. The new combinations Leptogium paramense and Scytinium quadrifidum are proposed.

  • 6.
    Nilsson, R. Henrik
    et al.
    University of Gothenburg, Department of Biological and Environmental Sciences; Gothenburg Global Biodiversity Centre.
    Sánchez-García, Marisol
    Clark University, Department of Biology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. University of Tennessee.
    Abarenkov, Kessy
    University of Tartu, Natural History Museum.
    Wurzbacher, Christian
    University of Gothenburg, Department of Biological and Environmental Sciences; Gothenburg Global Biodiversity Centre.
    Kristiansson, Erik
    Chalmers University of Technology, Department of Mathematical Statistics.
    Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory2017In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, Vol. 26, p. 13-24Article in journal (Refereed)
    Abstract [en]

    DNA sequences are increasingly used for taxonomic and functional assessment of environmental communities. In mycology, the nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen marker for such pursuits. Molecular identification is associated with many challenges, one of which is low read quality of the reference sequences used for inference of taxonomic and functional properties of the newly sequenced community (or single taxon). This study investigates whether public fungal ITS sequences are subjected to sufficient trimming in their distal (5’ and 3’) ends prior to deposition in the public repositories. We examined 86 species (and 10,584 sequences) across the fungal tree of life, and we found that on average 13.1% of the sequences were poorly trimmed in one or both of their 5’ and 3’ ends. Deposition of poorly trimmed entries was found to continue through 2016. Poorly trimmed reference sequences add noise and mask biological signal in sequence similarity searches and phylogenetic analyses, and we provide a set of recommendations on how to manage the sequence trimming problem.

  • 7.
    Nilsson, R. Henrik
    et al.
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Wurzbacher, Christian
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Ulikooli 18, EE-50090 Tartu, Estonia..
    Coimbra, Victor R. M.
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden.;Univ Fed Pernambuco UFPE, Ctr Ciencias Biol CCB, Dept Micol, Av Prof Nelson Chaves S-N, BR-50760901 Recife, PE, Brazil..
    Larsson, Ellen
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Tedersoo, Leho
    Univ Tartu, Inst Ecol & Earth Sci, Ulikooli 18, EE-50090 Tartu, Estonia..
    Eriksson, Jonna
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Ritter, Camila Duarte
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Svantesson, Sten
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Sanchez-Garcia, Marisol
    Univ Tennessee, Dept Ecol & Evolutionary Biol, Knoxville, TN 37996 USA..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kristiansson, Erik
    Univ Gothenburg, Chalmers Univ Technol, Dept Math Sci, S-41296 Gothenburg, Sweden..
    Abarenkov, Kessy
    Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51014 Tartu, Estonia..
    Top 50 most wanted fungi2016In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 12, p. 29-40Article in journal (Refereed)
    Abstract [en]

    Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond "Fungi". There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more.

  • 8.
    Rosenblad, Magnus Alm
    et al.
    Univ Gothenburg, Dept Marine Sci, Bioinformat Infrastruct Life Sci, Box 460, SE-40530 Gothenburg, Sweden..
    Martin, Maria P.
    CSIC, RJB, Dept Micol, Plaza Murillo 1, Madrid 28014, Spain..
    Tedersoo, Leho
    Univ Tartu, Inst Ecol & Earth Sci, Ulikooli 18, EE-50090 Tartu, Estonia..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Larsson, Ellen
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Wurzbacher, Christian
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Abarenkov, Kessy
    Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51014 Tartu, Estonia..
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)2016In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 13, p. 21-33Article in journal (Refereed)
    Abstract [en]

    During a routine scan for Signal Recognition Particle (SRP) RNAs in eukaryotic sequences, we surprisingly found in silico evidence in GenBank for a 265-base long SRP RNA sequence in the ITS1 region of a total of 11 fully identified species in three ectomycorrhizal genera of the Basidiomycota (Fungi): Astraeus, Russula, and Lactarius. To rule out sequence artifacts, one specimen from a species indicated to have the SRP RNA-containing ITS region in each of these genera was ordered and re-sequenced. Sequences identical to the corresponding GenBank entries were recovered, or in the case of a non-original but conspecific specimen differed by three bases, showing that these species indeed have an SRP RNA sequence incorporated into their ITS1 region. Other than the ribosomal genes, this is the first known case of non-coding RNAs in the eukaryotic ITS region, and it may assist in the examination of other types of insertions in fungal genomes.

  • 9.
    Ryberg, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden.;Gothenburg Global Biodivers Ctr, Box 461, S-40530 Gothenburg, Sweden..
    New light on names and naming of dark taxa2018In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 30, p. 31-39Article in journal (Refereed)
    Abstract [en]

    A growing proportion of fungal species and lineages are known only from sequence data and cannot be linked to any physical specimen or resolved taxonomic name. Such fungi are often referred to as "dark taxa" or "dark matter fungi". As they lack a taxonomic identity in the form of a name, they are regularly ignored in many important contexts, for example in legalisation and species counts. It is therefore very urgent to find a system to also deal with these fungi. Here, issues relating to the taxonomy and nomenclature of dark taxa are discussed and a number of questions that the mycological community needs to consider before deciding on what system/s to implement are highlighted.

  • 10.
    Svensson, Måns
    et al.
    Uppsala University, Music and Museums, Museum of Evolution.
    Ekman, Stefan
    Uppsala University, Music and Museums, Museum of Evolution.
    Klepsland, Jon T.
    BioFokus, Gaustadalleen 21, NO-0349 Oslo, Norway.
    Nordin, Anders
    Uppsala University, Music and Museums, Museum of Evolution.
    Thor, Goran
    Swedish Univ Agr Sci, Dept Ecol, POB 7044, SE-75007 Uppsala, Sweden.
    von Hirschheydt, Gesa
    Uppsala University, Music and Museums, Museum of Evolution.
    Jonsson, Fredrik
    Alsens Ede 227, SE-83047 Trangsviken, Sweden.
    Knutsson, Tommy
    Nedre Vasterstad 111, SE-38661 Morbylanga, Sweden.
    Lif, Mattias
    St Olofsgatan 37, SE-75030 Uppsala, Sweden.
    Spribille, Toby
    Univ Montana, Div Biol Sci, Missoula, MT 59812 USA.
    Westberg, Martin
    Uppsala University, Music and Museums, Museum of Evolution.
    Taxonomic novelties and new records of Fennoscandian crustose lichens2017In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 25, p. 51-86Article in journal (Refereed)
    Abstract [en]

    We present taxonomic, distributional and ecological notes on Fennoscandian crustose lichens and lichenicolous fungi, based on new collections as well as revision of herbarium material. Two new combinations are proposed: Frutidella furfuracea comb. nov. for F. pullata and Puttea duplex comb. nov. for Fellhanera duplex. Lecidea byssoboliza, L. carneoglauca and Variolaria torta are all reduced to synonymy with Bacidia antricola, Bacidia invertens is synonymized with B. igniarii, B. atrolivida with Mycobilimbia tetramera, and Gyalidea fruticola with Thelenella pertusariella. A new description is provided for Micarea hylocomii. 25 species of lichens and lichenicolous fungi are reported as new to Finland, Norway and/or Sweden: Absconditella lignicola (Norway), Bacidia antricola (Norway), B. polychroa (Norway), B. pycnidata (Sweden), Bacidina adastra (Sweden), Biatora veteranorum (Norway), Briancoppinsia cytospora (Finland), Catillaria scotinodes (Norway), Cliostomum subtenerum (Norway), Dirina fallax (Sweden), Fellhaneropsis almquistiorum (Norway), Gyalidea subscutellaris (Sweden), Lecania inundata (Norway), L. suavis (Norway), Micarea capitata (Norway), M. deminuta (Norway), M. hylocomii (Sweden), M. lynceola (Sweden), M. soralifera (Sweden), M. subconfusa (Sweden), Mycoblastus sanguinarioides (Finland, Sweden), Paralecia pratorum (Sweden), Puttea duplex (Sweden), Sarcogyne algoviae (Finland) and Toninia subnitida (Norway). Lectotypes are designated for Bacidia antricola, Lecidea byssoboliza, Lecidea carneoglauca, Lecidea subconfusa and Lecidea submoestula.

  • 11. Tedersoo, Leho
    Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi2015In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049Article in journal (Refereed)
  • 12. Tedersoo, Leho
    et al.
    Anslan, Sten
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Polme, Sergei
    Riit, Taavi
    Liiv, Ingrid
    Koljalg, Urmas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kisand, Veljo
    Nilsson, R. Henrik
    Hildebrand, Falk
    Bork, Peer
    Abarenkov, Kessy
    Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi2015In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 10, p. 1-43Article in journal (Refereed)
    Abstract [en]

    Rapid development of high-throughput (HTS) molecular identification methods has revolutionized our knowledge about taxonomic diversity and ecology of fungi. However, PCR-based methods exhibit multiple technical shortcomings that may bias our understanding of the fungal kingdom. This study was initiated to quantify potential biases in fungal community ecology by comparing the relative performance of amplicon-free shotgun metagenomics and amplicons of nine primer pairs over seven nuclear ribosomal DNA (rDNA) regions often used in metabarcoding analyses. The internal transcribed spacer (ITS) barcodes ITS1 and ITS2 provided greater taxonomic and functional resolution and richness of operational taxonomic units (OTUs) at the 97% similarity threshold compared to barcodes located within the ribosomal small subunit (SSU) and large subunit (LSU) genes. All barcode-primer pair combinations provided consistent results in ranking taxonomic richness and recovering the importance of floristic variables in driving fungal community composition in soils of Papua New Guinea. The choice of forward primer explained up to 2.0% of the variation in OTU-level analysis of the ITS1 and ITS2 barcode data sets. Across the whole data set, barcode-primer pair combination explained 37.6-38.1% of the variation, which surpassed any environmental signal. Overall, the metagenomics data set recovered a similar taxonomic overview, but resulted in much lower fungal rDNA sequencing depth, inability to infer OTUs, and high uncertainty in identification. We recommend the use of ITS2 or the whole ITS region for metabarcoding and we advocate careful choice of primer pairs in consideration of the relative proportion of fungal DNA and expected dominant groups.

  • 13.
    Tedersoo, Leho
    et al.
    Univ Tartu, Nat Hist Museum, 14A Ravila, EE-51005 Tartu, Estonia.
    Liiv, Ingrid
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-51005 Tartu, Estonia.
    Kivistik, Paula
    Univ Tartu, Estonian Genome Ctr, Riia 23b, EE-51010 Tartu, Estonia.
    Anslan, Sten
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-51005 Tartu, Estonia.
    Kõljalg, Urmas
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-51005 Tartu, Estonia.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens2016In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 13, p. 1-20Article in journal (Refereed)
    Abstract [en]

    High-throughput sequencing (HTS) has become a standard technique for genomics, metagenomics and taxonomy, but these analyses typically require large amounts of high-quality DNA that is difficult to obtain from uncultivable organisms including fungi with no living culture or fruit-body representatives. By using 1 ng DNA and low coverage Illumina HiSeqHTS, we evaluated the usefulness of genomics and metagenomics tools to recover fungal barcoding genes from old and problematic specimens of fruit-bodies and ectomycorrhizal (EcM) root tips. Ribosomal DNA and single-copy genes were successfully recovered from both fruit-body and EcM specimens typically <10 years old (maximum, 17 years). Samples with maximum obtained DNA concentration <0.2 ng µl-1 were sequenced poorly. Fungal rDNA molecules assembled from complex mock community and soil revealed a large proportion of chimeras and artefactual consensus sequences of closely related taxa. Genomics and metagenomics tools enable recovery of fungal genomes from very low initial amounts of DNA from fruit-bodies and ectomycorrhizas, but these genomes include a large proportion of prokaryote and other eukaryote DNA. Nonetheless, the recovered scaffolds provide an important source for phylogenetic and phylogenomic analyses and mining of functional genes.

  • 14.
    Wurzbacher, Christian
    et al.
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Ecosyst Res, Berlin, Germany.;Berlin Ctr Genom Biodivers Res, Berlin, Germany.;Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Stechlin, Germany.;Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden..
    Warthmann, Norman
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Ecosyst Res, Berlin, Germany.;Berlin Ctr Genom Biodivers Res, Berlin, Germany.;Australian Natl Univ, Res Sch Biol, Div Plant Sci, Canberra, ACT, Australia..
    Bourne, Elizabeth C.
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Ecosyst Res, Berlin, Germany.;Berlin Ctr Genom Biodivers Res, Berlin, Germany..
    Attermeyer, Katrin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Stechlin, Germany.
    Allgaier, Martin
    Berlin Ctr Genom Biodivers Res, Berlin, Germany.;Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Stechlin, Germany..
    Powell, Jeff R.
    Univ Western Sydney, Hawkesbury Inst Environm, Penrith, NSW, Australia..
    Detering, Harald
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Ecosyst Res, Berlin, Germany.;Berlin Ctr Genom Biodivers Res, Berlin, Germany.;Univ Vigo, Dept Biochem Genet & Immunol, Vigo, Spain..
    Mbedi, Susan
    Berlin Ctr Genom Biodivers Res, Berlin, Germany.;Leibniz Inst Evolut & Biodivers Sci, Museum Nat Kunde, Berlin, Germany..
    Grossart, Hans-Peter
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Stechlin, Germany.;Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany..
    Monaghan, Michael T.
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Ecosyst Res, Berlin, Germany.;Berlin Ctr Genom Biodivers Res, Berlin, Germany..
    High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany)2016In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 16, p. 17-44Article in journal (Refereed)
    Abstract [en]

    Freshwater fungi are a poorly studied ecological group that includes a high taxonomic diversity. Most studies on aquatic fungal diversity have focused on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in the meso-oligotrophic, temperate Lake Stechlin in North-East Germany. These included the pelagic and littoral water column, sediments, and biotic substrates. We performed high throughput sequencing using the Roche 454 platform, employing a universal eukaryotic marker region within the large ribosomal subunit (LSU) to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1027 fungal OTUs (97% sequence similarity). Richness estimates were highest in the sediment, biofilms, and benthic samples (189-231 OTUs), intermediate in water samples (42-85 OTUs), and lowest in plankton samples (8 OTUs). NMDS grouped the eight studied habitats into six clusters, indicating that community composition was strongly influenced by turnover among habitats. Fungal communities exhibited changes at the phylum and order levels along three different substrate categories from littoral to pelagic habitats. The large majority of OTUs (> 75%) could not be classified below the order level due to the lack of aquatic fungal entries in public sequence databases. Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat heterogeneity to overall diversity and community composition. Habitat diversity should be considered in any sampling strategy aiming to assess the fungal diversity of a water body.

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