Author
E. B. Gareth Jones
Other affiliations: Mae Fah Luang University, Thailand National Science and Technology Development Agency, Chiang Mai University
Bio: E. B. Gareth Jones is an academic researcher from King Saud University. The author has contributed to research in topics: Dothideomycetes & Marine fungi. The author has an hindex of 25, co-authored 84 publications receiving 6752 citations. Previous affiliations of E. B. Gareth Jones include Mae Fah Luang University & Thailand National Science and Technology Development Agency.
Topics: Dothideomycetes, Marine fungi, Sordariomycetes, Genus, Phylogenetic tree
Papers
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Conrad L. Schoch1, Keith A. Seifert, Sabine M. Huhndorf2, Vincent Robert3 +157 more•Institutions (59)
TL;DR: Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation.
Abstract: Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
4,116 citations
TL;DR: This paper is a compilation of notes on 142 fungal taxa, including five new families, 20 new genera, and 100 new species, representing a wide taxonomic and geographic range.
Abstract: Notes on 113 fungal taxa are compiled in this paper, including 11 new genera, 89 new species, one new subspecies, three new combinations and seven reference specimens. A wide geographic and taxonomic range of fungal taxa are detailed. In the Ascomycota the new genera Angustospora (Testudinaceae), Camporesia (Xylariaceae), Clematidis, Crassiparies (Pleosporales genera incertae sedis), Farasanispora, Longiostiolum (Pleosporales genera incertae sedis), Multilocularia (Parabambusicolaceae), Neophaeocryptopus (Dothideaceae), Parameliola (Pleosporales genera incertae sedis), and Towyspora (Lentitheciaceae) are introduced. Newly introduced species are Angustospora nilensis, Aniptodera aquibella, Annulohypoxylon albidiscum, Astrocystis thailandica, Camporesia sambuci, Clematidis italica, Colletotrichum menispermi, C. quinquefoliae, Comoclathris pimpinellae, Crassiparies quadrisporus, Cytospora salicicola, Diatrype thailandica, Dothiorella rhamni, Durotheca macrostroma, Farasanispora avicenniae, Halorosellinia rhizophorae, Humicola koreana, Hypoxylon lilloi, Kirschsteiniothelia tectonae, Lindgomyces okinawaensis, Longiostiolum tectonae, Lophiostoma pseudoarmatisporum, Moelleriella phukhiaoensis, M. pongdueatensis, Mucoharknessia anthoxanthi, Multilocularia bambusae, Multiseptospora thysanolaenae, Neophaeocryptopus cytisi, Ocellularia arachchigei, O. ratnapurensis, Ochronectria thailandica, Ophiocordyceps karstii, Parameliola acaciae, P. dimocarpi, Parastagonospora cumpignensis, Pseudodidymosphaeria phlei, Polyplosphaeria thailandica, Pseudolachnella brevifusiformis, Psiloglonium macrosporum, Rhabdodiscus albodenticulatus, Rosellinia chiangmaiensis, Saccothecium rubi, Seimatosporium pseudocornii, S. pseudorosae, Sigarispora ononidis and Towyspora aestuari. New combinations are provided for Eutiarosporella dactylidis (sexual morph described and illustrated) and Pseudocamarosporium pini. Descriptions, illustrations and / or reference specimens are designated for Aposphaeria corallinolutea, Cryptovalsa ampelina, Dothiorella vidmadera, Ophiocordyceps formosana, Petrakia echinata, Phragmoporthe conformis and Pseudocamarosporium pini. The new species of Basidiomycota are Agaricus coccyginus, A. luteofibrillosus, Amanita atrobrunnea, A. digitosa, A. gleocystidiosa, A. pyriformis, A. strobilipes, Bondarzewia tibetica, Cortinarius albosericeus, C. badioflavidus, C. dentigratus, C. duboisensis, C. fragrantissimus, C. roseobasilis, C. vinaceobrunneus, C. vinaceogrisescens, C. wahkiacus, Cyanoboletus hymenoglutinosus, Fomitiporia atlantica, F. subtilissima, Ganoderma wuzhishanensis, Inonotus shoreicola, Lactifluus armeniacus, L. ramipilosus, Leccinum indoaurantiacum, Musumecia alpina, M. sardoa, Russula amethystina subp. tengii and R. wangii are introduced. Descriptions, illustrations, notes and / or reference specimens are designated for Clarkeinda trachodes, Dentocorticium ussuricum, Galzinia longibasidia, Lentinus stuppeus and Leptocorticium tenellum. The other new genera, species new combinations are Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis from Neocallimastigomycota, Phytophthora estuarina, P. rhizophorae, Salispina, S. intermedia, S. lobata and S. spinosa from Oomycota, and Absidia stercoraria, Gongronella orasabula, Mortierella calciphila, Mucor caatinguensis, M. koreanus, M. merdicola and Rhizopus koreanus in Zygomycota.
488 citations
Mae Fah Luang University1, World Agroforestry Centre2, King Saud University3, Guizhou University4, Goa University5, Centre national de la recherche scientifique6, Chinese Academy of Sciences7, Beijing Forestry University8, Botanic Garden Meise9, Indonesian Institute of Sciences10, University of Mauritius11, Thailand National Science and Technology Development Agency12, Landcare Research13, University of Toronto14, Iranian Research Organization for Science and Technology15, University of Gothenburg16, National Taiwan Ocean University17, Universidade Federal de Viçosa18, Universidade Nova de Lisboa19, Lincoln Memorial University20, Facultad de Ciencias Exactas y Naturales21, Ahi Evran University22, University of Arkansas23, Royal Botanic Garden Edinburgh24, University of British Columbia25, University of Turin26, Sohag University27, Flinders University28, Chiang Mai University29
TL;DR: The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups.
Abstract: Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org
(FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.
458 citations
Mae Fah Luang University1, Chinese Academy of Sciences2, King Saud University3, Goa University4, Landcare Research5, National Institute of Oceanography, India6, Sohag University7, Beijing Forestry University8, National Taiwan Ocean University9, Ruhr University Bochum10, Thailand National Science and Technology Development Agency11, Hirosaki University12, Guizhou University13, Slovak Academy of Sciences14, Southern Federal University15, Institut national de la recherche agronomique16, University of Bayreuth17, Iwate University18, Ghent University19
TL;DR: This paper is a compilation of notes on 110 fungal taxa, including one new family, 10 new genera, and 76 new species, representing a wide taxonomic and geographic range.
Abstract: This paper is a compilation of notes on 110 fungal taxa, including one new family, 10 new genera, and 76 new species, representing a wide taxonomic and geographic range. The new family, Paradictyoarthriniaceae is introduced based on its distinct lineage in Dothideomycetes and its unique morphology. The family is sister to Biatriosporaceae and Roussoellaceae. The new genera are Allophaeosphaeria (Phaeosphaeriaceae), Amphibambusa (Amphisphaeriaceae), Brunneomycosphaerella (Capnodiales genera incertae cedis), Chaetocapnodium (Capnodiaceae), Flammeascoma (Anteagloniaceae), Multiseptospora (Pleosporales genera incertae cedis), Neogaeumannomyces (Magnaporthaceae), Palmiascoma (Bambusicolaceae), Paralecia (Squamarinaceae) and Sarimanas (Melanommataceae). The newly described species are the Ascomycota Aliquandostipite manochii, Allophaeosphaeria dactylidis, A. muriformia, Alternaria cesenica, Amphibambusa bambusicola, Amphisphaeria sorbi, Annulohypoxylon thailandicum, Atrotorquata spartii, Brunneomycosphaerella laburni, Byssosphaeria musae, Camarosporium aborescentis, C. aureum, C. frutexensis, Chaetocapnodium siamensis, Chaetothyrium agathis, Colletotrichum sedi, Conicomyces pseudotransvaalensis, Cytospora berberidis, C. sibiraeae, Diaporthe thunbergiicola, Diatrype palmicola, Dictyosporium aquaticum, D. meiosporum, D. thailandicum, Didymella cirsii, Dinemasporium nelloi, Flammeascoma bambusae, Kalmusia italica, K. spartii, Keissleriella sparticola, Lauriomyces synnematicus, Leptosphaeria ebuli, Lophiostoma pseudodictyosporium, L. ravennicum, Lophiotrema eburnoides, Montagnula graminicola, Multiseptospora thailandica, Myrothecium macrosporum, Natantispora unipolaris, Neogaeumannomyces bambusicola, Neosetophoma clematidis, N. italica, Oxydothis atypica, Palmiascoma gregariascomum, Paraconiothyrium nelloi, P. thysanolaenae, Paradictyoarthrinium tectonicola, Paralecia pratorum, Paraphaeosphaeria spartii, Pestalotiopsis digitalis, P. dracontomelon, P. italiana, Phaeoisaria pseudoclematidis, Phragmocapnias philippinensis, Pseudocamarosporium cotinae, Pseudocercospora tamarindi, Pseudotrichia rubriostiolata, P. thailandica, Psiloglonium multiseptatum, Saagaromyces mangrovei, Sarimanas pseudofluviatile, S. shirakamiense, Tothia spartii, Trichomerium siamensis, Wojnowicia dactylidicola, W. dactylidis and W. lonicerae. The Basidiomycota Agaricus flavicentrus, A. hanthanaensis, A. parvibicolor, A. sodalis, Cantharellus luteostipitatus, Lactarius atrobrunneus, L. politus, Phylloporia dependens and Russula cortinarioides are also introduced. Epitypifications or reference specimens are designated for Hapalocystis berkeleyi, Meliola tamarindi, Pallidocercospora acaciigena, Phaeosphaeria musae, Plenodomus agnitus, Psiloglonium colihuae, P. sasicola and Zasmidium musae while notes and/or new sequence data are provided for Annulohypoxylon leptascum, A. nitens, A. stygium, Biscogniauxia marginata, Fasciatispora nypae, Hypoxylon fendleri, H. monticulosum, Leptosphaeria doliolum, Microsphaeropsis olivacea, Neomicrothyrium, Paraleptosphaeria nitschkei, Phoma medicaginis and Saccotheciaceae. A full description of each species is provided with light micrographs (or drawings). Molecular data is provided for 90 taxa and used to generate phylogenetic trees to establish a natural classification for species.
304 citations
TL;DR: An updated outline of the Sordariomycetes and a backbone tree incorporating asexual and sexual genera in the class are provided and new links between sexual and asexual genera and thus synonymies are provided.
Abstract: Sordariomycetes is one of the largest classes of Ascomycota and is characterised by perithecial ascomata and inoperculate unitunicate asci. The class includes many important plant pathogens, as well as endophytes, saprobes, epiphytes, and fungicolous, lichenized or lichenicolous taxa. The class includes freshwater, marine and terrestrial taxa and has a worldwide distribution. This paper provides an updated outline of the Sordariomycetes and a backbone tree incorporating asexual and sexual genera in the class. Based on phylogeny and morphology we introduced three subclasses; Diaporthomycetidae, Lulworthiomycetidae and Meliolomycetidae and five orders; Amplistromatales, Annulatascales, Falcocladiales, Jobellisiales and Togniniales. The outline is based on literature to the end of 2014 and the backbone tree published in this paper. Notes for 397 taxa with information, such as new family and genera novelties, novel molecular data published since the Outline of Ascomycota 2009, and new links between sexual and asexual genera and thus synonymies, are provided. The Sordariomycetes now comprises six subclasses, 28 orders, 90 families and 1344 genera. In addition a list of 829 genera with uncertain placement in Sordariomycetes is also provided.
266 citations
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TL;DR: Increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease.
Abstract: Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.
7,032 citations
TL;DR: The approach to utilizing available RNA-Seq and other data types in the authors' manual curation process for vertebrate, plant, and other species is summarized, and a new direction for prokaryotic genomes and protein name management is described.
Abstract: The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
4,104 citations
University of Tartu1, American Museum of Natural History2, University of Gothenburg3, University of Aberdeen4, James Hutton Institute5, Cooperative Institute for Research in Environmental Sciences6, University of California, Berkeley7, Aberystwyth University8, Estonian University of Life Sciences9, Spanish National Research Council10, Royal Botanic Gardens11, Academy of Sciences of the Czech Republic12, Swedish University of Agricultural Sciences13, University of Tennessee14, University of Helsinki15, Stanford University16, Ludwig Maximilian University of Munich17, University of Toronto18, University of Florida19, University of New Mexico20, University of Tübingen21
TL;DR: All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type, and the term ‘species hypothesis’ (SH) is introduced for the taxa discovered in clustering on different similarity thresholds.
Abstract: The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
2,605 citations
American Museum of Natural History1, University of Tartu2, University of Colombo3, Royal Netherlands Academy of Arts and Sciences4, University of Florida5, University of Palermo6, Goethe University Frankfurt7, Hobart Corporation8, Nakhon Phanom University9, University of Bamenda10, University of Gothenburg11, Naturalis12, Swedish University of Agricultural Sciences13, Royal Botanic Gardens14, Universiti Malaysia Sabah15, United States Department of Agriculture16, Forest Research Institute Malaysia17, Humboldt State University18, Chinese Academy of Sciences19, Landcare Research20, University of Western Australia21, Estonian University of Life Sciences22, University of Southern Queensland23, Botanic Garden Meise24, Manchester Metropolitan University25, James Cook University26
TL;DR: Diversity of most fungal groups peaked in tropical ecosystems, but ectomycorrhizal fungi and several fungal classes were most diverse in temperate or boreal ecosystems, and manyfungal groups exhibited distinct preferences for specific edaphic conditions (such as pH, calcium, or phosphorus).
Abstract: Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.
2,346 citations
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01 Jan 1944
TL;DR: The only previously known species of Myrsidea from bulbuls, M. warwicki ex Ixos philippinus, is redescribed and sixteen new species are described; they and their type hosts are described.
Abstract: We redescribe the only previously known species of Myrsidea from bulbuls, M. pycnonoti Eichler. Sixteen new species are described; they and their type hosts are: M. phillipsi ex Pycnonotus goiavier goiavier (Scopoli), M. gieferi ex P. goiavier suluensis Mearns, M. kulpai ex P. flavescens Blyth, M. finlaysoni ex P. finlaysoni Strickland, M. kathleenae ex P. cafer (L.), M. warwicki ex Ixos philippinus (J. R. Forster), M. mcclurei ex Microscelis amaurotis (Temminck), M. zeylanici ex P. zeylanicus (Gmelin), M. plumosi ex P. plumosus Blyth, M. eutiloti ex P. eutilotus (Jardine and Selby), M. adamsae ex P. urostictus (Salvadori), M. ochracei ex Criniger ochraceus F. Moore, M. borbonici ex Hypsipetes borbonicus (J. R. Forster), M. johnsoni ex P. atriceps (Temminck), M. palmai ex C. ochraceus, and M. claytoni ex P. eutilotus. A key is provided for the identification of these 17 species.
1,756 citations