Publications by authors named "Johannes Z Groenewald"

64 Publications

Mating-type locus rearrangements and shifts in thallism states in Citrus-associated Phyllosticta species.

Fungal Genet Biol 2020 Nov 18;144:103444. Epub 2020 Aug 18.

Laboratório de Bioprospecção e Genética Molecular de Microrganismos, Postgraduate Program in Genetics. Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990 Curitiba, Paraná State, Brazil. Electronic address:

Currently, eight Phyllosticta species are known to be associated with several Citrus hosts, incorporating diverse lifestyles: while some of them are endophytic (P. capitalensis and P. citribraziliensis), others are pathogenic (P. citriasiana, P. citricarpa, P. citrichinaensis and P. paracitricarpa). Sexual reproduction plays a key role in the interaction between these Phyllosticta species and their Citrus hosts, especially for the spread and persistence of the pathogenic species in the environment. Given this, differences in sexual reproduction strategies could be related to the differences in lifestyles. To evaluate this hypothesis, we characterized the mating-type loci of six Citrus-associated Phyllosticta species from whole genome assemblies. Mating-type genes in the Citrus-associated Phyllosticta species are highly variable in their sequence content, but the genomic locations and organization of the mating-type loci are conserved. Phyllosticta citriasiana, P. citribraziliensis, P. citricarpa and P. paracitricarpa are heterothallic, while P. capitalensis and P. citrichinaensis are homothallic. In addition, the P. citrichinaensis MAT1-2 idiomorph occurs in a separate location from the mating-type locus. Ancestral state reconstruction suggests that homothallism is the ancestral thallism state in Phyllosticta, with a shift to heterothallism in Phyllosticta species that are pathogenic to Citrus. Moreover, the homothallic strategies of P. capitalensis and P. citrichinaensis result from independent evolutionary events, as P. capitalensis locus likely represents the ancestral state, and P. citrichinaensis homothallism has risen through a reversion in a heterothallic ancestor and underwent remodelling events. As the pathogenic species P. citriasiana, P. citricarpa and P. paracitricarpa are heterothallic and incapable of selfing, disease management practices focused in preventing the occurrence of sexual reproduction could assist in the control of Citrus Black Spot and Citrus Tan Spot diseases. This study emphasizes the importance of studying Citrus-Phyllosticta interactions under evolutionary and genomic perspectives, as these approaches can provide valuable information about the association between Phyllosticta species and their hosts, and also serve as guidance for the improvement of disease management practices.
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http://dx.doi.org/10.1016/j.fgb.2020.103444DOI Listing
November 2020

Identification, prevalence and pathogenicity of species causing anthracnose of in Asia.

IMA Fungus 2019 28;10. Epub 2019 Jun 28.

1Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia.

Anthracnose of chili ( spp.) causes major production losses throughout Asia where chili plants are grown. A total of 260 isolates, associated with necrotic lesions of chili leaves and fruit were collected from chili producing areas of Indonesia, Malaysia, Sri Lanka, Thailand and Taiwan. was the most commonly isolated species from infected chili fruit and was readily identified by its falcate spores and abundant setae in the necrotic lesions. The other isolates consisted of straight conidia (cylindrical and fusiform) which were difficult to differentiate to species based on morphological characters. Taxonomic analysis of these straight conidia isolates based on multi-gene phylogenetic analyses (ITS) revealed a further seven known species, , and . In addition, three novel species are also described as and , associated with anthracnose of chili fruit in West Java (Indonesia); Makassar, South Sulawesi (Indonesia); and Tainan (Taiwan), respectively. is reported for the first time causing anthracnose of in Indonesia and Sri Lanka. This is also the first report of causing anthracnose of chili in Taiwan and Thailand and in Malaysia and Thailand. Of the species with straight conidia, (acutatum complex), was the most prevalent throughout the surveyed countries, except for Sri Lanka from where this species was not isolated. (gloeosporioides complex) was also common in Indonesia, Sri Lanka and Thailand. Pathogenicity tests on chili fruit showed that and were highly aggressive, especially when inoculated on non-wounded fruit, compared to all other species. The existence of new, highly aggressive exotic species, such as , poses a biosecurity risk to production in countries which do not have adequate quarantine regulations to restrict the entry of exotic pathogens.
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http://dx.doi.org/10.1186/s43008-019-0001-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7184891PMC
June 2019

Anthracnose Disease of Carpetgrass () Caused by sp. nov.

Plant Dis 2020 Jun 14;104(6):1744-1750. Epub 2020 Apr 14.

School of Life Science and Technology, Lingnan Normal University, Zhanjiang 524048, China.

Carpetgrass () is a creeping, stoloniferous, perennial warm-season grass that is adapted to humid tropical and subtropical climates. Recently, outbreaks of anthracnose disease of caused by an unidentified sp. were observed in the Hainan and Guangdong provinces in southern China. In late winter and early spring, the disease incidence reached 100% in some badly infected lawns. Under high-moisture conditions, the crowns and oldest leaf sheaths of the majority of the plants became necrotic, which led to whole lawns turning reddish brown. Pathogenicity was confirmed by inoculating uninfected plants with a conidial suspension of the sp. isolated from diseased plants. Phylogenetic analyses of the combined internal transcribed spacer, , , and sequences revealed the pathogen to be a novel species of the species complex. Microscopic examination showed that the species was also morphologically distinct from related species. As a result of the phylogenetic, morphological, and pathogenicity analyses, we propose the name for this pathogen of in southern China.
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http://dx.doi.org/10.1094/PDIS-10-19-2183-REDOI Listing
June 2020

New species of associated with leaf spot diseases in Iran.

Mycologia 2019 Nov-Dec;111(6):1056-1071. Epub 2019 Nov 8.

Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.

Species of are commonly associated with leaf spot diseases of a broad range of plant hosts worldwide. During our investigation of fungi associated with leaf spot diseases in northern and northwestern Iran, several isolates were recovered from symptomatic leaves on different herbaceous and woody plants in the Asteraceae, Betulaceae, and Salicaceae families. These isolates were studied by applying a polyphasic approach including morphological and cultural data and a multigene phylogeny using a combined data set of partial sequences of the 28S nuc rRNA gene (large subunit [28S]), internal transcribed spacer regions and intervening 5.8S nuc rRNA gene (ITS) of the nuc rDNA operon, actin (), translation elongation factor 1-α (), calmodulin (), β-tubulin (), and DNA-directed RNA polymerase II second largest subunit (). Four novel species are proposed, namely, on on on , and on . All species are illustrated, and their morphology and phylogenetic relationships with other species are discussed.
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http://dx.doi.org/10.1080/00275514.2019.1669376DOI Listing
June 2020

Phyllosticta citricarpa and sister species of global importance to Citrus.

Mol Plant Pathol 2019 12 11;20(12):1619-1635. Epub 2019 Sep 11.

Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.

Several Phyllosticta species are known as pathogens of Citrus spp., and are responsible for various disease symptoms including leaf and fruit spots. One of the most important species is P. citricarpa, which causes a foliar and fruit disease called citrus black spot. The Phyllosticta species occurring on citrus can most effectively be distinguished from P. citricarpa by means of multilocus DNA sequence data. Recent studies also demonstrated P. citricarpa to be heterothallic, and reported successful mating in the laboratory. Since the domestication of citrus, different clones of P. citricarpa have escaped Asia to other continents via trade routes, with obvious disease management consequences. This pathogen profile represents a comprehensive literature review of this pathogen and allied taxa associated with citrus, focusing on identification, distribution, genomics, epidemiology and disease management. This review also considers the knowledge emerging from seven genomes of Phyllosticta spp., demonstrating unknown aspects of these species, including their mating behaviour.

Taxonomy: Phyllosticta citricarpa (McAlpine) Aa, 1973. Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Botryosphaeriales, Family Phyllostictaceae, Genus Phyllosticta, Species citricarpa.

Host Range: Confirmed on more than 12 Citrus species, Phyllosticta citricarpa has only been found on plant species in the Rutaceae.

Disease Symptoms: P. citricarpa causes diverse symptoms such as hard spot, virulent spot, false melanose and freckle spot on fruit, and necrotic lesions on leaves and twigs.

Useful Websites: DOE Joint Genome Institute MycoCosm portals for the Phyllosticta capitalensis (https://genome.jgi.doe.gov/Phycap1), P. citriasiana (https://genome.jgi.doe.gov/Phycit1), P. citribraziliensis (https://genome.jgi.doe.gov/Phcit1), P. citrichinaensis (https://genome.jgi.doe.gov/Phcitr1), P. citricarpa (https://genome.jgi.doe.gov/Phycitr1, https://genome.jgi.doe.gov/Phycpc1), P. paracitricarpa (https://genome.jgi.doe.gov/Phy27169) genomes. All available Phyllosticta genomes on MycoCosm can be viewed at https://genome.jgi.doe.gov/Phyllosticta.
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http://dx.doi.org/10.1111/mpp.12861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859488PMC
December 2019

Novel primers improve species delimitation in .

IMA Fungus 2018 Jul 26;9:299-332. Epub 2018 Sep 26.

Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.

The genus includes many important plant pathogens that are commonly associated with leaf spot diseases on a wide range of cultivated and wild plant species. Due to the lack of useful morphological features and high levels of intraspecific variation, host plant association has long been a decisive criterion for species delimitation in . Because several taxa have broader host ranges, reliance on host data in taxonomy has proven problematic. Recent studies have revealed multi-gene DNA sequence data to be highly informative for species identification in Cercospora, especially when used in a concatenated alignment. In spite of this approach, however, several species complexes remained unresolved as no single gene proved informative enough to act as DNA barcoding locus for the genus. Therefore, the aims of the present study were firstly to improve species delimitation in the genus by testing additional genes and primers on a broad set of species, and secondly to find the best DNA barcoding gene(s) for species delimitation. Novel primers were developed for and to supplement previously published primers for these loci. To this end, 145 isolates from the Iranian mycobiota together with 25 additional reference isolates preserved in the Westerdijk Fungal Biodiversity Institute were subjected to an eight-gene (ITS, , , , , , and ) analysis. Results from this study provided new insights into DNA barcoding in , and revealed to be a promising gene for species delimitation when supplemented with , and . The robust eight-gene phylogeny revealed several novel clades within the existing species complexes, such as , , , cf. and sp. G. The isolates are distributed over three clades, namely , and sp. nov. The isolates are distributed over two clades, and . The isolates are distributed over two clades, namely and , which is newly described.
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http://dx.doi.org/10.5598/imafungus.2018.09.02.06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317581PMC
July 2018

Considerations and consequences of allowing DNA sequence data as types of fungal taxa.

Authors:
Juan Carlos Zamora Måns Svensson Roland Kirschner Ibai Olariaga Svengunnar Ryman Luis Alberto Parra József Geml Anna Rosling Slavomír Adamčík Teuvo Ahti M Catherine Aime A Martyn Ainsworth László Albert Edgardo Albertó Alberto Altés García Dmitry Ageev Reinhard Agerer Begoña Aguirre-Hudson Joe Ammirati Harry Andersson Claudio Angelini Vladimír Antonín Takayuki Aoki André Aptroot Didier Argaud Blanca Imelda Arguello Sosa Arne Aronsen Ulf Arup Bita Asgari Boris Assyov Violeta Atienza Ditte Bandini João Luís Baptista-Ferreira Hans-Otto Baral Tim Baroni Robert Weingart Barreto Henry Beker Ann Bell Jean-Michel Bellanger Francesco Bellù Martin Bemmann Mika Bendiksby Egil Bendiksen Katriina Bendiksen Lajos Benedek Anna Bérešová-Guttová Franz Berger Reinhard Berndt Annarosa Bernicchia Alona Yu Biketova Enrico Bizio Curtis Bjork Teun Boekhout David Boertmann Tanja Böhning Florent Boittin Carlos G Boluda Menno W Boomsluiter Jan Borovička Tor Erik Brandrud Uwe Braun Irwin Brodo Tatiana Bulyonkova Harold H Burdsall Bart Buyck Ana Rosa Burgaz Vicent Calatayud Philippe Callac Emanuele Campo Massimo Candusso Brigitte Capoen Joaquim Carbó Matteo Carbone Rafael F Castañeda-Ruiz Michael A Castellano Jie Chen Philippe Clerc Giovanni Consiglio Gilles Corriol Régis Courtecuisse Ana Crespo Cathy Cripps Pedro W Crous Gladstone Alves da Silva Meiriele da Silva Marjo Dam Nico Dam Frank Dämmrich Kanad Das Linda Davies Eske De Crop Andre De Kesel Ruben De Lange Bárbara De Madrignac Bonzi Thomas Edison E Dela Cruz Lynn Delgat Vincent Demoulin Dennis E Desjardin Paul Diederich Bálint Dima Maria Martha Dios Pradeep Kumar Divakar Clovis Douanla-Meli Brian Douglas Elisandro Ricardo Drechsler-Santos Paul S Dyer Ursula Eberhardt Damien Ertz Fernando Esteve-Raventós Javier Angel Etayo Salazar Vera Evenson Guillaume Eyssartier Edit Farkas Alain Favre Anna G Fedosova Mario Filippa Péter Finy Adam Flakus Simón Fos Jacques Fournier André Fraiture Paolo Franchi Ana Esperanza Franco Molano Gernot Friebes Andreas Frisch Alan Fryday Giuliana Furci Ricardo Galán Márquez Matteo Garbelotto Joaquina María García-Martín Mónica A García Otálora Dania García Sánchez Alain Gardiennet Sigisfredo Garnica Isaac Garrido Benavent Genevieve Gates Alice da Cruz Lima Gerlach Masoomeh Ghobad-Nejhad Tatiana B Gibertoni Tine Grebenc Irmgard Greilhuber Bella Grishkan Johannes Z Groenewald Martin Grube Gérald Gruhn Cécile Gueidan Gro Gulden Luis Fp Gusmão Josef Hafellner Michel Hairaud Marek Halama Nils Hallenberg Roy E Halling Karen Hansen Christoffer Bugge Harder Jacob Heilmann-Clausen Stip Helleman Alain Henriot Margarita Hernandez-Restrepo Raphaël Herve Caroline Hobart Mascha Hoffmeister Klaus Høiland Jan Holec Håkon Holien Karen Hughes Vit Hubka Seppo Huhtinen Boris Ivančević Marian Jagers Walter Jaklitsch AnnaElise Jansen Ruvishika S Jayawardena Thomas Stjernegaard Jeppesen Mikael Jeppson Peter Johnston Per Magnus Jørgensen Ingvar Kärnefelt Liudmila B Kalinina Gintaras Kantvilas Mitko Karadelev Taiga Kasuya Ivona Kautmanová Richard W Kerrigan Martin Kirchmair Anna Kiyashko Dániel G Knapp Henning Knudsen Kerry Knudsen Tommy Knutsson Miroslav Kolařík Urmas Kõljalg Alica Košuthová Attila Koszka Heikki Kotiranta Vera Kotkova Ondřej Koukol Jiří Kout Gábor M Kovács Martin Kříž Åsa Kruys Viktor Kučera Linas Kudzma Francisco Kuhar Martin Kukwa T K Arun Kumar Vladimír Kunca Ivana Kušan Thomas W Kuyper Carlos Lado Thomas Læssøe Patrice Lainé Ewald Langer Ellen Larsson Karl-Henrik Larsson Gary Laursen Christian Lechat Serena Lee James C Lendemer Laura Levin Uwe Lindemann Håkan Lindström Xingzhong Liu Regulo Carlos Llarena Hernandez Esteve Llop Csaba Locsmándi Deborah Jean Lodge Michael Loizides László Lőkös Jennifer Luangsa-Ard Matthias Lüderitz Thorsten Lumbsch Matthias Lutz Dan Mahoney Ekaterina Malysheva Vera Malysheva Patinjareveettil Manimohan Yasmina Marin-Felix Guilhermina Marques Rubén Martínez-Gil Guy Marson Gerardo Mata P Brandon Matheny Geir Harald Mathiassen Neven Matočec Helmut Mayrhofer Mehdi Mehrabi Ireneia Melo Armin Mešić Andrew S Methven Otto Miettinen Ana M Millanes Romero Andrew N Miller James K Mitchell Roland Moberg Pierre-Arthur Moreau Gabriel Moreno Olga Morozova Asunción Morte Lucia Muggia Guillermo Muñoz González Leena Myllys István Nagy László G Nagy Maria Alice Neves Tuomo Niemelä Pier Luigi Nimis Nicolas Niveiro Machiel E Noordeloos Anders Nordin Sara Raouia Noumeur Yuri Novozhilov Jorinde Nuytinck Esteri Ohenoja Patricia Oliveira Fiuza Alan Orange Alexander Ordynets Beatriz Ortiz-Santana Leticia Pacheco Ferenc Pál-Fám Melissa Palacio Zdeněk Palice Viktor Papp Kadri Pärtel Julia Pawlowska Aurelia Paz Ursula Peintner Shaun Pennycook Olinto Liparini Pereira Pablo Pérez Daniëls Miquel À Pérez-De-Gregorio Capella Carlos Manuel Pérez Del Amo Sergio Pérez Gorjón Sergio Pérez-Ortega Israel Pérez-Vargas Brian A Perry Jens H Petersen Ronald H Petersen Donald H Pfister Chayanard Phukhamsakda Marcin Piątek Meike Piepenbring Raquel Pino-Bodas Juan Pablo 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Svantesson Sigvard Svensson Tatyana Yu Svetasheva Krzysztof Świerkosz Heidi Tamm Hatira Taskin Adrien Taudière Jan-Olof Tedebrand Raúl Tena Lahoz Marina Temina Arne Thell Marco Thines Göran Thor Holger Thüs Leif Tibell Sanja Tibell Einar Timdal Zdenko Tkalčec Tor Tønsberg Gérard Trichies Dagmar Triebel Andrei Tsurykau Rodham E Tulloss Veera Tuovinen Miguel Ulloa Sosa Carlos Urcelay François Valade Ricardo Valenzuela Garza Pieter van den Boom Nicolas Van Vooren Aida M Vasco-Palacios Jukka Vauras Juan Manuel Velasco Santos Else Vellinga Annemieke Verbeken Per Vetlesen Alfredo Vizzini Hermann Voglmayr Sergey Volobuev Wolfgang von Brackel Elena Voronina Grit Walther Roy Watling Evi Weber Mats Wedin Øyvind Weholt Martin Westberg Eugene Yurchenko Petr Zehnálek Huang Zhang Mikhail P Zhurbenko Stefan Ekman

IMA Fungus 2018 Jun 24;9(1):167-175. Epub 2018 May 24.

Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden.

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 11 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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http://dx.doi.org/10.5598/imafungus.2018.09.01.10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048565PMC
June 2018

The Genera of Fungi - G 4: and .

IMA Fungus 2017 Jun 23;8(1):131-152. Epub 2017 May 23.

Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.

The current paper represents the fourth contribution in the Genera of Fungi series, linking type species of fungal genera to their morphology and DNA sequence data. The present paper focuses on two genera of microfungi, and , which are respectively epi- and neotypified. The genus is typified by , which has a karstenula-like sexual morph, and phoma-like synasexual morph. Furthermore, and are introduced as new camarosporium-like genera, while is introduced as a new phoma-like genus. is introduced as a new family to accommodate and . , which is typified by , is shown to produce dothichiza- and hormonema-like synasexual morphs in culture, and is introduced as a new species. In addition to their typification, ex-type cultures have been deposited in the Westerdijk Fungal Biodiversity Institute (CBS Culture Collection), and species-specific DNA barcodes in GenBank. Authors interested in contributing accounts of individual genera to larger multi-authored papers in this series should contact the associate editors listed on the List of Protected Generic Names for Fungi.
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http://dx.doi.org/10.5598/imafungus.2017.08.01.10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493531PMC
June 2017

New endophytic species from cacti in Brazil, and description of gen. nov.

IMA Fungus 2017 Jun 1;8(1):77-97. Epub 2017 May 1.

Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.

Brazil harbours a unique ecosystem, the Caatinga, which belongs to the tropical dry forest biome. This region has an important diversity of organisms, and recently several new fungal species have been described from different hosts and substrates within it. During a survey of fungal endophyte diversity from cacti in this forest, we isolated cladosporium-like fungi that were subjected to morphological and multigene phylogenetic analyses including , ITS, LSU, and gene sequences. Based on these analyses we identified two new species belonging to the genus , described here as and spp. nov., isolated from subsp. and , respectively. To improve the species recognition and assess species diversity in we studied all ex-type strains of the genus, for which , and barcodes were also generated. After phylogenetic reconstruction using five loci, we differentiated 13 species in the genus. and are synonymized based on their phylogenetic position and limited number of unique nucleotide differences. Six strains previously assigned to , including the ex-type strain (CBS 131317) of that species, were found to belong to an undescribed genus here named as gen. nov., with comb. nov. as type species. Furthermore, this study proposes the , ITS, and as main phylogenetic loci to recognise species.
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http://dx.doi.org/10.5598/imafungus.2017.08.01.06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493539PMC
June 2017

Families, genera, and species of Botryosphaeriales.

Fungal Biol 2017 04 21;121(4):322-346. Epub 2016 Nov 21.

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. Electronic address:

Members of Botryosphaeriales are ecologically diverse, but most commonly associated with leaf spots, fruit and root rots, die-back or cankers of diverse woody hosts. Based on morphology and DNA sequence data, the Botryosphaeriales have to date been shown to contain eight families, with an additional two, Endomelanconiopsisaceae (Endomelanconiopsis) and Pseudofusicoccumaceae (Pseudofusicoccum) being newly described in this study. Furthermore, Oblongocollomyces is introduced as new genus, while Spencermartinsia is reduced to synonymy under Dothiorella. Novel species include Diplodia pyri (Pyrus sp., the Netherlands), Diplodia citricarpa (Citrus sp., Iran), Lasiodiplodia vitis (Vitis vinifera, Italy), L. sterculiae (Sterculia oblonga, Germany), Neofusicoccum pistaciarum (Pistacia vera, USA), N. buxi (Buxus sempervirens, France), N. stellenboschiana (Vitis vinifera, South Africa), and Saccharata hawaiiensis (Protea laurifolia, Hawaii). New combinations are also proposed for Camarosporium pistaciae (associated with fruit rot of Pistacia vera) in Neofusicoccum, and Sphaeria gallae (associated with galls of Quercus) in Diplodia. The combination of large subunit of the nuclear ribosomal RNA gene (LSU)-rpb2 proved effective at delineating taxa at family and generic level. Furthermore, rpb2 also added additional resolution for species delimitation, in combination with ITS, tef1 and tub2. In this study we analysed 499 isolates, and produce an expanded phylogenetic backbone for Botryosphaeriales, which will help to delimit novelties at species, genus and family level in future.
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http://dx.doi.org/10.1016/j.funbio.2016.11.001DOI Listing
April 2017

Botryosphaeriaceae: Systematics, pathology, and genetics.

Fungal Biol 2017 04 5;121(4):305-306. Epub 2017 Feb 5.

Department of Genetics, Forestry & Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa. Electronic address:

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http://dx.doi.org/10.1016/j.funbio.2017.01.003DOI Listing
April 2017

Global food and fibre security threatened by current inefficiencies in fungal identification.

Philos Trans R Soc Lond B Biol Sci 2016 12;371(1709)

Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa.

Fungal pathogens severely impact global food and fibre crop security. Fungal species that cause plant diseases have mostly been recognized based on their morphology. In general, morphological descriptions remain disconnected from crucially important knowledge such as mating types, host specificity, life cycle stages and population structures. The majority of current fungal species descriptions lack even the most basic genetic data that could address at least some of these issues. Such information is essential for accurate fungal identifications, to link critical metadata and to understand the real and potential impact of fungal pathogens on production and natural ecosystems. Because international trade in plant products and introduction of pathogens to new areas is likely to continue, the manner in which fungal pathogens are identified should urgently be reconsidered. The technologies that would provide appropriate information for biosecurity and quarantine already exist, yet the scientific community and the regulatory authorities are slow to embrace them. International agreements are urgently needed to enforce new guidelines for describing plant pathogenic fungi (including key DNA information), to ensure availability of relevant data and to modernize the phytosanitary systems that must deal with the risks relating to trade-associated plant pathogens.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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http://dx.doi.org/10.1098/rstb.2016.0024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5095547PMC
December 2016

They seldom occur alone.

Fungal Biol 2016 11 30;120(11):1392-1415. Epub 2016 May 30.

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.

Species of Coleophoma have been reported as plant pathogenic, saprobic or endophytic on a wide host range. The genus is characterised by having pycnidial conidiomata, phialidic conidiogenous cells intermingled among paraphyses, and cylindrical conidia. Coleophoma has had a confusing taxonomic history with numerous synonyms, and its phylogeny has remained unresolved. The aim of the present study was to use a polyphasic approach incorporating morphology, ecology, and molecular data of the partial large subunit of nrDNA (LSU), the internal transcribed spacer region with intervening 5.8S nrDNA (ITS), partial β-tubulin (tub2), and translation elongation factor 1-alpha (tef1) gene sequences to resolve its taxonomy and phylogeny. Based on these results the genus was found to be polyphyletic, with taxa tentatively identified as Coleophoma clustering in Dothideomycetes and Leotiomycetes. Species corresponding to the concept of Coleophoma s.str. (Dermateaceae, Helotiales, Leotiomycetes) were found to form a distinct clade, with five new species. Furthermore, Coleophoma was found to be linked to the newly established sexual genus, Parafabraea, which is reduced to synonymy. Isolates occurring on Ilex aquifolium in the Netherlands also clustered in Dermateaceae, representing a novel genus, Davidhawksworthia. In the Dothideomycetes, several taxa clustered in Dothiora (Dothideaceae, Dothideales), which is shown to have Dothichiza and Hormonema-like asexual morphs, with four new species. Furthermore, Pseudocamaropycnis is introduced as a new genus (Mytilinidiaceae, Mytilinidiales), along with Briansuttonomyces (Didymellaceae, Pleosporales) and Dimorphosporicola (Pleosporaceae, Pleosporales).
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http://dx.doi.org/10.1016/j.funbio.2016.05.009DOI Listing
November 2016

Redefining common endophytes and plant pathogens in Neofabraea, Pezicula, and related genera.

Fungal Biol 2016 11 23;120(11):1291-1322. Epub 2015 Oct 23.

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands; Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. Electronic address:

Species in Neofabraea, Pezicula, and related genera have been reported as saprobes, plant pathogens or endophytes from a wide range of hosts. The asexual morphs of Neofabraea and Pezicula had been placed in Cryptosporiopsis, now a synonym of Pezicula, while Neofabraea was also linked to Phlyctema. Based on morphology and molecular data of the partial large subunit nrDNA (LSU), the internal transcribed spacer region with intervening 5.8S nrDNA (ITS), partial β-tubulin region (tub2), and the partial RNA polymerase II second largest subunit region (rpb2), the taxonomy and phylogenetic relationships of these fungi were investigated. Five new species were described in Pezicula based on morphology, while a further eight unnamed phylogenetic lineages revealed further diversity in the genus. Based on these results, the generic concept of Neofabraea was also emended. Phlyctema, which was previously associated with Neofabraea, formed a distinct clade, separate from Neofabraea s. str. Two new neofabraea-like genera, Parafabraea and Pseudofabraea were proposed, along with one new combination in Neofabraea s. str. To stabilise the application of these names, an epitype was designated for Pe. carpinea, the type species of Pezicula, and for N. malicorticis, the type species of Neofabraea.
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http://dx.doi.org/10.1016/j.funbio.2015.09.013DOI Listing
November 2016

Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China.

Antonie Van Leeuwenhoek 2017 Jan 12;110(1):87-103. Epub 2016 Oct 12.

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.

The phylum Neocallimastigomycota contains eight genera (about 20 species) of strictly anaerobic fungi. The evolutionary relationships of these genera are uncertain due to insufficient sequence data to infer their phylogenies. Based on morphology and molecular phylogeny, thirteen isolates obtained from yak faeces and rumen digesta in China were assigned to Neocallimastix frontalis (nine isolates), Orpinomyces joyonii (two isolates) and Caecomyces sp. (two isolates), respectively. The phylogenetic relationships of the eight genera were evaluated using complete ITS and partial LSU sequences, compared to the ITS1 region which has been widely used in this phylum in the past. Five monophyletic lineages corresponding to six of the eight genera were statistically supported. Isolates of Caecomyces and Cyllamyces were present in a single lineage and could not be separated properly. Members of Neocallimastigomycota with uniflagellate zoospores represented by Piromyces were polyphyletic. The Piromyces-like genus Oontomyces was consistently closely related to the traditional Anaeromyces, and separated the latter genus into two clades. The phylogenetic position of the Piromyces-like genus Buwchfawromyces remained unresolved. Orpinomyces and Neocallimastix, sharing polyflagellate zoospores, were supported as sister genera in the LSU phylogeny. Apparently ITS, specifically ITS1 alone, is not a good marker to resolve the generic affinities of the studied fungi. The LSU sequences are easier to align and appear to work well to resolve generic relationships. This study provides a comparative phylogenetic revision of Neocallimastigomycota isolates known from culture and sequence data.
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http://dx.doi.org/10.1007/s10482-016-0779-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5222902PMC
January 2017

Recommended names for pleomorphic genera in Dothideomycetes.

IMA Fungus 2015 Dec 2;6(2):507-23. Epub 2015 Dec 2.

Institute of Microbiology, Beijing Forestry University, P.O. Box 61, Beijing 100083, PR China.

This paper provides recommendations of one name for use among pleomorphic genera in Dothideomycetes by the Working Group on Dothideomycetes established under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). A number of these generic names are proposed for protection because they do not have priority and/or the generic name selected for use is asexually typified. These include: Acrogenospora over Farlowiella; Alternaria over Allewia, Lewia, and Crivellia; Botryosphaeria over Fusicoccum; Camarosporula over Anthracostroma; Capnodium over Polychaeton; Cladosporium over Davidiella; Corynespora over Corynesporasca; Curvularia over Pseudocochliobolus; Elsinoë over Sphaceloma; Excipulariopsis over Kentingia; Exosporiella over Anomalemma; Exserohilum over Setosphaeria; Gemmamyces over Megaloseptoria; Kellermania over Planistromella; Kirschsteiniothelia over Dendryphiopsis; Lecanosticta over Eruptio; Paranectriella over Araneomyces; Phaeosphaeria over Phaeoseptoria; Phyllosticta over Guignardia; Podonectria over Tetracrium; Polythrincium over Cymadothea; Prosthemium over Pleomassaria; Ramularia over Mycosphaerella; Sphaerellopsis over Eudarluca; Sphaeropsis over Phaeobotryosphaeria; Stemphylium over Pleospora; Teratosphaeria over Kirramyces and Colletogloeopsis; Tetraploa over Tetraplosphaeria; Venturia over Fusicladium and Pollaccia; and Zeloasperisporium over Neomicrothyrium. Twenty new combinations are made: Acrogenospora carmichaeliana (Berk.) Rossman & Crous, Alternaria scrophulariae (Desm.) Rossman & Crous, Pyrenophora catenaria (Drechsler) Rossman & K.D. Hyde, P. dematioidea (Bubák & Wróbl.) Rossman & K.D. Hyde, P. fugax (Wallr.) Rossman & K.D. Hyde, P. nobleae (McKenzie & D. Matthews) Rossman & K.D. Hyde, P. triseptata (Drechsler) Rossman & K.D. Hyde, Schizothyrium cryptogamum (Batzer & Crous) Crous & Batzer, S. cylindricum (G.Y. Sun et al.) Crous & Batzer, S. emperorae (G.Y. Sun & L. Gao) Crous & Batzer, S. inaequale (G.Y. Sun & L. Gao) Crous & Batzer, S. musae (G.Y. Sun & L. Gao) Crous & Batzer, S. qianense (G.Y. Sun & Y.Q. Ma) Crous & Batzer, S. tardecrescens (Batzer & Crous) Crous & Batzer, S. wisconsinense (Batzer & Crous) Crous & Batzer, Teratosphaeria epicoccoides (Cooke & Massee) Rossman & W.C. Allen, Venturia catenospora (Butin) Rossman & Crous, V. convolvularum (Ondrej) Rossman & Crous, V. oleaginea (Castagne) Rossman & Crous, and V. phillyreae (Nicolas & Aggéry) Rossman & Crous, combs. nov. Three replacement names are also proposed: Pyrenophora grahamii Rossman & K.D. Hyde, Schizothyrium sunii Crous & Batzer, and Venturia barriae Rossman & Crous noms. nov.
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http://dx.doi.org/10.5598/imafungus.2015.06.02.14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681266PMC
December 2015

Phaeoacremonium: from esca disease to phaeohyphomycosis.

Fungal Biol 2015 Sep 23;119(9):759-83. Epub 2015 Jun 23.

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. Electronic address:

Phaeoacremonium spp. are commonly isolated from stems and branches of diseased woody hosts, and humans with phaeohyphomycosis. The genus Phaeoacremonium (Togniniaceae, Togniniales) has recently been monographed, and presently contains 46 species, while its sexual morph, Togninia, contains 26 epithets, of which 13 are insufficiently known. In this review we summarise information pertaining to the global distribution, pathology, ecology, and detection of these species, and present a case for retaining the genus Phaeoacremonium over that of Togninia. Furthermore, to obtain a single nomenclature, the following new combinations are also proposed: Phaeoacremonium africanum, P. aquaticum, P. fraxinopennsylvanicum, P. griseo-olivaceum, P. inconspicuum, P. leptorrhynchum, P. minimum, and P. vibratile.
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http://dx.doi.org/10.1016/j.funbio.2015.06.004DOI Listing
September 2015

The Genera of Fungi - fixing the application of the type species of generic names - G 2: Allantophomopsis, Latorua, Macrodiplodiopsis, Macrohilum, Milospium, Protostegia, Pyricularia, Robillarda, Rotula, Septoriella, Torula, and Wojnowicia.

IMA Fungus 2015 Jun 11;6(1):163-98. Epub 2015 Jun 11.

ARC - Plant Protection Research Institute, P. Bag X5017, Stellenbosch 7599, South Africa.

The present paper represents the second contribution in the Genera of Fungi series, linking type species of fungal genera to their morphology and DNA sequence data, and where possible, ecology. This paper focuses on 12 genera of microfungi, 11 of which the type species are neo- or epitypified here: Allantophomopsis (A. cytisporea, Phacidiaceae, Phacidiales, Leotiomycetes), Latorua gen. nov. (Latorua caligans, Latoruaceae, Pleosporales, Dothideomycetes), Macrodiplodiopsis (M. desmazieri, Macrodiplodiopsidaceae, Pleosporales, Dothideomycetes), Macrohilum (M. eucalypti, Macrohilaceae, Diaporthales, Sordariomycetes), Milospium (M. graphideorum, incertae sedis, Pezizomycotina), Protostegia (P. eucleae, Mycosphaerellaceae, Capnodiales, Dothideomycetes), Pyricularia (P. grisea, Pyriculariaceae, Magnaporthales, Sordariomycetes), Robillarda (R. sessilis, Robillardaceae, Xylariales, Sordariomycetes), Rutola (R. graminis, incertae sedis, Pleosporales, Dothideomycetes), Septoriella (S. phragmitis, Phaeosphaeriaceae, Pleosporales, Dothideomycetes), Torula (T. herbarum, Torulaceae, Pleosporales, Dothideomycetes) and Wojnowicia (syn. of Septoriella, S. hirta, Phaeosphaeriaceae, Pleosporales, Dothideomycetes). Novel species include Latorua grootfonteinensis, Robillarda africana, R. roystoneae, R. terrae, Torula ficus, T. hollandica, and T. masonii spp. nov., and three new families: Macrodiplodiopsisceae, Macrohilaceae, and Robillardaceae. Authors interested in contributing accounts of individual genera to larger multi-authored papers to be published in IMA Fungus, should contact the associate editors listed for the major groups of fungi on the List of Protected Generic Names for Fungi (www.generaoffungi.org).
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http://dx.doi.org/10.5598/imafungus.2015.06.01.11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500082PMC
June 2015

Mycoparasitic species of Sphaerellopsis, and allied lichenicolous and other genera.

IMA Fungus 2014 Dec 27;5(2):391-414. Epub 2014 Nov 27.

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands ; Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa ; Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.

Species of Sphaerellopsis (sexual morph Eudarluca) are well-known cosmopolitan mycoparasites occurring on a wide range of rusts. Although their potential role as biocontrol agents has received some attention, the molecular phylogeny of the genus has never been resolved. Based on morphology and DNA sequence data of the large subunit nuclear ribosomal RNA gene (LSU, 28S) and the internal transcribed spacers (ITS) and 5.8S rRNA gene of the nrDNA operon, the genus Sphaerellopsis is shown to belong to Leptosphaeriaceae in Dothideomycetes. Sphaerellopsis is circumscribed, and the sexually typified generic name Eudarluca treated as a synonym on the basis that Sphaerellopsis is more commonly used in literature, is the older generic name, and is the morph commonly encountered by plant pathologists in the field. A neotype is designated for Sphaerellopsis filum, and two new species are introduced, S. macroconidialis and S. paraphysata spp. nov. Species previously incorrectly placed in Sphaerellopsis are allocated to Neosphaerellopsis gen. nov. as N. thailandica, and to the genus Acrocalymma, as A. fici. The genus Rhizopycnis is nestled among species of Acrocalymma, and reduced to synonymy based on its morphology and DNA phylogeny, while Acrocalymmaceae is introduced as novel family to accommodate members of this genus in the Dothideomycetes. Furthermore, Sphaerellopsis proved to be phylogenetically closely allied to a lichenicolous complex of phoma-like taxa, for which the new genera Diederichomyces and Xenophoma are established. Several new combinations are introduced, namely D. xanthomendozae, D. ficuzzae, D. caloplacae, D. cladoniicola, D. foliaceiphila, and X. puncteliae combs. nov, while Paraphaeosphaeria parmeliae sp. nov. is newly described.
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http://dx.doi.org/10.5598/imafungus.2014.05.02.05DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329322PMC
December 2014

Phacidium and Ceuthospora (Phacidiaceae) are congeneric: taxonomic and nomenclatural implications.

IMA Fungus 2014 Dec 9;5(2):173-93. Epub 2014 Oct 9.

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands;

The morphologically diverse genus Ceuthospora has traditionally been linked to Phacidium sexual morphs via association, though molecular or cultural data to confirm this relationship have been lacking. The aim of this study was thus to resolve the relationship of these two genera by generating nucleotide sequence data for three loci, ITS, LSU and RPB2. Based on these results, Ceuthospora is reduced to synonymy under the older generic name Phacidium. Phacidiaceae (currently Helotiales) is suggested to constitute a separate order, Phacidiales (Leotiomycetes), as sister to Helotiales, which is clearly paraphyletic. Phacidiaceae includes Bulgaria, and consequently the family Bulgariaceae becomes a synonym of Phacidiaceae. Several new combinations are introduced in Phacidium, along with two new species, P. pseudophacidioides, which occurs on Ilex and Chamaespartium in Europe, and Phacidium trichophori, which occurs on Trichophorum cespitosum subsp. germanicum in The Netherlands. The generic name Allantophomopsiella is introduced to accommodate A. pseudotsugae, a pathogen of conifers, while Gremmenia is resurrected to accommodate the snow-blight pathogens of conifers, G. abietis, G. infestans, and G. pini-cembrae.
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http://dx.doi.org/10.5598/imafungus.2014.05.02.02DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329319PMC
December 2014

Naming and outline of -2014 including proposals for the protection or suppression of generic names.

Fungal Divers 2014 Nov 4;69(1):1-55. Epub 2014 Nov 4.

Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, People's Republic of China; World Agroforestry Centre, East and Central Asia, Kunming 650201, Yunnan, People's Republic of China; Institute of Excellence in Fungal Research, Chiang Rai 57100, Thailand.

Article 59.1, of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN; Melbourne Code), which addresses the nomenclature of pleomorphic fungi, became effective from 30 July 2011. Since that date, each fungal species can have one nomenclaturally correct name in a particular classification. All other previously used names for this species will be considered as synonyms. The older generic epithet takes priority over the younger name. Any widely used younger names proposed for use, must comply with Art. 57.2 and their usage should be approved by the Nomenclature Committee for Fungi (NCF). In this paper, we list all genera currently accepted by us in (belonging to 23 orders and 110 families), including pleomorphic and nonpleomorphic genera. In the case of pleomorphic genera, we follow the rulings of the current ICN and propose single generic names for future usage. The taxonomic placements of 1261 genera are listed as an outline. Protected names and suppressed names for 34 pleomorphic genera are listed separately. Notes and justifications are provided for possible proposed names after the list of genera. Notes are also provided on recent advances in our understanding of asexual and sexual morph linkages in . A phylogenetic tree based on four gene analyses supported 23 orders and 75 families, while 35 families still lack molecular data.
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http://dx.doi.org/10.1007/s13225-014-0309-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896388PMC
November 2014

The Genera of Fungi: fixing the application of type species of generic names.

IMA Fungus 2014 Jun 19;5(1):141-60. Epub 2014 Jun 19.

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands;

To ensure a stable platform for fungal taxonomy, it is of paramount importance that the genetic application of generic names be based on their DNA sequence data, and wherever possible, not morphology or ecology alone. To facilitate this process, a new database, accessible at www.GeneraofFungi.org (GoF) was established, which will allow deposition of metadata linked to holo-, lecto-, neo- or epitype specimens, cultures and DNA sequence data of the type species of genera. Although there are presently more than 18 000 fungal genera described, we aim to initially focus on the subset of names that have been placed on the "Without-prejudice List of Protected Generic Names of Fungi" (see IMA Fungus 4(2): 381-443, 2013). To enable the global mycological community to keep track of typification events and avoid duplication, special MycoBank Typification identfiers (MBT) will be issued upon deposit of metadata in MycoBank. MycoBank is linked to GoF, thus deposited metadata of generic type species will be displayed in GoF (and vice versa), but will also be linked to Index Fungorum (IF) and the curated RefSeq Targeted Loci (RTL) database in GenBank at the National Center for Biotechnology Information (NCBI). This initial paper focuses on eight genera of appendaged coelomycetes, the type species of which are neo- or epitypified here: Bartalinia (Bartalinia robillardoides; Amphisphaeriaceae, Xylariales), Chaetospermum (Chaetospermum chaetosporum, incertae sedis, Sebacinales), Coniella (Coniella fragariae, Schizoparmaceae, Diaporthales), Crinitospora (Crinitospora pulchra, Melanconidaceae, Diaporthales), Eleutheromyces (Eleutheromyces subulatus, Helotiales), Kellermania (Kellermania yuccigena, Planistromataceae, Botryosphaeriales), Mastigosporium (Mastigosporium album, Helotiales), and Mycotribulus (Mycotribulus mirabilis, Agaricales). Authors interested in contributing accounts of individual genera to larger multi-authored papers to be published in IMA Fungus, should contact the associate editors listed below for the major groups of fungi on the List of Protected Generic Names for Fungi.
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http://dx.doi.org/10.5598/imafungus.2014.05.01.14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4107892PMC
June 2014

Foliicolous fungi from Arctostaphylos pungens in Mexico.

IMA Fungus 2014 Jun 4;5(1):7-15. Epub 2014 Mar 4.

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; ; Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ; Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.

Arctostaphylos pungens "Manzanita" is an important shrub in the southwestern USA, and northern and central Mexico. Manzanita bears apple-like fruit that is utilised for a range of edible products. Over the past two years, several foliar disease problems were noted on this host in the San José de Gracia region of Mexico. The aim of the present study was to elucidate their identity through the analysis of morphological characters and DNA phylogeny (based on the large subunit nuclear ribosomal RNA gene and the ITS spacers and the intervening 5.8S rRNA gene of the nrDNA operon) of the fungi associated with these disease symptoms. Three species are newly described: Phaeococcomyces mexicanus sp. nov., a presumed epiphyte, and two species associated with leaf spots and defoliation, namely Coccomyces arctostaphyloides sp. nov. and Passalora arctostaphyli sp. nov. A fourth species is also associated with leaf spots and tip dieback is Harknessia arctostaphyli, for which an epitype is designated. All species can co-occur on the same shrub, which adds to the stress experienced by the plant, leading to further defoliation and dieback.
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http://dx.doi.org/10.5598/imafungus.2014.05.01.02DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4107899PMC
June 2014

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Authors:
Conrad L Schoch Barbara Robbertse Vincent Robert Duong Vu Gianluigi Cardinali Laszlo Irinyi Wieland Meyer R Henrik Nilsson Karen Hughes Andrew N Miller Paul M Kirk Kessy Abarenkov M Catherine Aime Hiran A Ariyawansa Martin Bidartondo Teun Boekhout Bart Buyck Qing Cai Jie Chen Ana Crespo Pedro W Crous Ulrike Damm Z Wilhelm De Beer Bryn T M Dentinger Pradeep K Divakar Margarita Dueñas Nicolas Feau Katerina Fliegerova Miguel A García Zai-Wei Ge Gareth W Griffith Johannes Z Groenewald Marizeth Groenewald Martin Grube Marieka Gryzenhout Cécile Gueidan Liangdong Guo Sarah Hambleton Richard Hamelin Karen Hansen Valérie Hofstetter Seung-Beom Hong Jos Houbraken Kevin D Hyde Patrik Inderbitzin Peter R Johnston Samantha C Karunarathna Urmas Kõljalg Gábor M Kovács Ekaphan Kraichak Krisztina Krizsan Cletus P Kurtzman Karl-Henrik Larsson Steven Leavitt Peter M Letcher Kare Liimatainen Jian-Kui Liu D Jean Lodge Janet Jennifer Luangsa-ard H Thorsten Lumbsch Sajeewa S N Maharachchikumbura Dimuthu Manamgoda María P Martín Andrew M Minnis Jean-Marc Moncalvo Giuseppina Mulè Karen K Nakasone Tuula Niskanen Ibai Olariaga Tamás Papp Tamás Petkovits Raquel Pino-Bodas Martha J Powell Huzefa A Raja Dirk Redecker J M Sarmiento-Ramirez Keith A Seifert Bhushan Shrestha Soili Stenroos Benjamin Stielow Sung-Oui Suh Kazuaki Tanaka Leho Tedersoo M Teresa Telleria Dhanushka Udayanga Wendy A Untereiner Javier Diéguez Uribeondo Krishna V Subbarao Csaba Vágvölgyi Cobus Visagie Kerstin Voigt Donald M Walker Bevan S Weir Michael Weiß Nalin N Wijayawardene Michael J Wingfield J P Xu Zhu L Yang Ning Zhang Wen-Ying Zhuang Scott Federhen

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
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http://dx.doi.org/10.1093/database/bau061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075928PMC
February 2015

Porocercospora seminalis gen. et comb. nov., the causal organism of buffalograss false smut.

Mycologia 2014 Jan-Feb;106(1):77-85

Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583.

False smut caused by Cercospora seminalis is an important disease of buffalograss (Buchloë dactyloides) affecting seed production. The pathogen prevents normal caryopsis development and causes considerable yield loss and reduced seed germination. The current taxonomic placement of the false-smut causal pathogen in the genus Cercospora is incorrect based on its morphological characteristics and DNA phylogeny. In the present study the phylogenetic position of C. seminalis is clarified based on DNA sequence analysis of three loci namely the internal transcribed spacer (ITS) region, partial nuclear ribosomal large subunit (LSU) and partial sequences of the RNA polymerase II second largest subunit (RPB2). A collection of C. seminalis isolates was made from buffalograss sites near Lincoln, Nebraska. DNA sequence data indicated that Cercospora seminalis is phylogenetically close to but distinct from species of Bipolaris and Curvularia (Pleosporaceae, Pleosporales). Cercospora seminalis morphologically had unique characteristics, namely densely aggregated and repeatedly branched conidiophores arising from a brown stroma, monotretic conidiogenous cells with inconspicuous loci, and scolecosporous conidia with distosepta, and thickened, darkened hila. Porocercospora is introduced as a new genus to accommodate the buffalograss false-smut pathogen.
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http://dx.doi.org/10.3852/13-147DOI Listing
April 2014

Yet more "weeds" in the garden: fungal novelties from nests of leaf-cutting ants.

PLoS One 2013 20;8(12):e82265. Epub 2013 Dec 20.

Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil ; Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil ; Centre for Agriculture and Biosciences International, Egham, Surrey, United Kingdom.

Background: Symbiotic relationships modulate the evolution of living organisms in all levels of biological organization. A notable example of symbiosis is that of attine ants (Attini; Formicidae: Hymenoptera) and their fungal cultivars (Lepiotaceae and Pterulaceae; Agaricales: Basidiomycota). In recent years, this mutualism has emerged as a model system for studying coevolution, speciation, and multitrophic interactions. Ubiquitous in this ant-fungal symbiosis is the "weedy" fungus Escovopsis (Hypocreales: Ascomycota), known only as a mycoparasite of attine fungal gardens. Despite interest in its biology, ecology and molecular phylogeny--noting, especially, the high genetic diversity encountered--which has led to a steady flow of publications over the past decade, only two species of Escovopsis have formally been described.

Methods And Results: We sampled from fungal gardens and garden waste (middens) of nests of the leaf-cutting ant genus Acromyrmex in a remnant of subtropical Atlantic rainforest in Minas Gerais, Brazil. In culture, distinct morphotypes of Escovopsis sensu lato were recognized. Using both morphological and molecular analyses, three new species of Escovopsis were identified. These are described and illustrated herein--E. lentecrescens, E. microspora, and E. moelleri--together with a re-description of the genus and the type species, E. weberi. The new genus Escovopsioides is erected for a fourth morphotype. We identify, for the first time, a mechanism for horizontal transmission via middens.

Conclusions: The present study makes a start at assigning names and formal descriptions to these specific fungal parasites of attine nests. Based on the results of this exploratory and geographically-restricted survey, we expect there to be many more species of the genus Escovopsis and its relatives associated with nests of both the lower and higher Attini throughout their neotropical range, as suggested in previous studies.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082265PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869688PMC
March 2015

A phylogenetic re-evaluation of Arthrinium.

IMA Fungus 2013 Jul 24;4(1):133-54. Epub 2013 Jun 24.

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands ; Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ; Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.

Although the genus Arthrinium (sexual morph Apiospora) is commonly isolated as an endophyte from a range of substrates, and is extremely interesting for the pharmaceutical industry, its molecular phylogeny has never been resolved. Based on morphology and DNA sequence data of the large subunit nuclear ribosomal RNA gene (LSU, 28S) and the internal transcribed spacers (ITS) and 5.8S rRNA gene of the nrDNA operon, the genus Arthrinium is shown to belong to Apiosporaceae in Xylariales. Arthrinium is morphologically and phylogenetically circumscribed, and the sexual genus Apiospora treated as synonym on the basis that Arthinium is older, more commonly encountered, and more frequently used in literature. An epitype is designated for Arthrinium pterospermum, and several well-known species are redefined based on their morphology and sequence data of the translation elongation factor 1-alpha (TEF), beta-tubulin (TUB) and internal transcribed spacer (ITS1, 5.8S, ITS2) gene regions. Newly described are A. hydei on Bambusa tuldoides from Hong Kong, A. kogelbergense on dead culms of Restionaceae from South Africa, A. malaysianum on Macaranga hullettii from Malaysia, A. ovatum on Arundinaria hindsii from Hong Kong, A. phragmites on Phragmites australis from Italy, A. pseudospegazzinii on Macaranga hullettii from Malaysia, A. pseudosinense on bamboo from The Netherlands, and A. xenocordella from soil in Zimbabwe. Furthermore, the genera Pteroconium and Cordella are also reduced to synonymy, rejecting spore shape and the presence of setae as characters of generic significance separating them from Arthrinium.
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http://dx.doi.org/10.5598/imafungus.2013.04.01.13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719201PMC
July 2013

Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria.

Fungal Genet Biol 2013 Mar 26;52:20-31. Epub 2013 Jan 26.

Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, US Department of Agriculture, Agricultural Research Service, 1815 North University Street, Peoria, IL 61604, USA.

Fusarium (Hypocreales, Nectriaceae) is one of the most economically important and systematically challenging groups of mycotoxigenic phytopathogens and emergent human pathogens. We conducted maximum likelihood (ML), maximum parsimony (MP) and Bayesian (B) analyses on partial DNA-directed RNA polymerase II largest (RPB1) and second largest subunit (RPB2) nucleotide sequences of 93 fusaria to infer the first comprehensive and well-supported phylogenetic hypothesis of evolutionary relationships within the genus and 20 of its near relatives. Our analyses revealed that Cylindrocarpon formed a basal monophyletic sister to a 'terminal Fusarium clade' (TFC) comprising 20 strongly supported species complexes and nine monotypic lineages, which we provisionally recognize as Fusarium (hypothesis F1). The basal-most divergences within the TFC were only significantly supported by Bayesian posterior probabilities (B-PP 0.99-1). An internode of the remaining TFC, however, was strongly supported by MP and ML bootstrapping and B-PP (hypothesis F2). Analysis of seven Fusarium genome sequences and Southern analysis of fusaria elucidated the distribution of genes required for synthesis of 26 families of secondary metabolites within the phylogenetic framework. Diversification time estimates date the origin of the TFC to the middle Cretaceous 91.3 million years ago. We also dated the origin of several agriculturally important secondary metabolites as well as the lineage responsible for Fusarium head blight of cereals. Dating of several plant-associated species complexes suggests their evolution may have been driven by angiosperm diversification during the Miocene. Our results support two competing hypotheses for the circumscription of Fusarium and provide a framework for future comparative phylogenetic and genomic analyses of this agronomically and medically important genus.
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http://dx.doi.org/10.1016/j.fgb.2012.12.004DOI Listing
March 2013

Homortomyces gen. nov., a new dothidealean pycnidial fungus from the Cradle of Humankind.

IMA Fungus 2012 Dec 5;3(2):109-15. Epub 2012 Nov 5.

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands;

Homortomyces is introduced as a new coelomycetous genus associated with leaf spots onCombretum erythrophyllum trees growing near and around the Sterkfontein caves, Maropeng, South Africa. Based on its transversely septate, brown conidia, the presence of paraphyses, and percurrent proliferation of the conidiogenous cells, the genus resembles Stilbospora (Melanoconidaceae, Diaporthales). It is distinct in having pycnidial condiomata, conidia lacking mucoid sheaths, and becoming muriform when mature. Its morphology and phylogenetic placement based on analyses of sequence data for the large subunit nuclear ribosomal RNA gene (LSU, 28S) as well as the ITS and 5.8S rRNA gene of the nrDNA operon, show that Homortomyces represents a novel genus in Dothideomycetes, although its familial relationships remain unresolved.
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http://dx.doi.org/10.5598/imafungus.2012.03.02.02DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539313PMC
December 2012

Pilidiella tibouchinae sp. nov. associated with foliage blight of Tibouchina granulosa (quaresmeira) in Brazil.

IMA Fungus 2012 Jun 5;3(1):1-7. Epub 2012 Apr 5.

Universidade Federal de Viçosa, Departamento de Fitopatologia, 36570-000, Viçosa, MG, Brazil.

Tibouchina granulosa (Melastomataceae), Brazilian glorytree (Brazilian common name - quaresmeira), a common tree of the Atlantic Forest of Brazil, is widely used as an ornamental for its violet or pink blossoms. Little is known about fungal diseases affecting this species, although these represent a known limitation for its cultivation in nurseries. Among these there is a foliage blight that occurs in combination with distortion of branch apices and die-back. A consistent association of a species of Pilidiella with the diseased tissues was observed. The fungus was isolated in pure culture and based on its morphology and DNA phylogeny, we conclude that it represents a new species, for which the name Pilidiella tibouchinae is introduced.
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http://dx.doi.org/10.5598/imafungus.2012.03.01.01DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399098PMC
June 2012