Publications by authors named "Bryn T M Dentinger"

27 Publications

  • Page 1 of 1

What's for dinner this time?: DNA authentication of "wild mushrooms" in food products sold in the USA.

PeerJ 2021 2;9:e11747. Epub 2021 Aug 2.

Natural History Museum of Utah & School of Biological Sciences, University of Utah, Salt Lake City, UT, United States.

Mushrooms have been consumed by humans for thousands of years, and while some have gastronomic and nutritional value, it has long been recognized that only select species of mushrooms are suitable for consumption. Adverse health effects of consuming poisonous mushrooms range from mild illness to death. Many valuable edible mushrooms are either impractical or unable to be grown commercially, requiring them to be harvested from the wild. In the U.S., products containing these wild-collected mushrooms are often sold with the nonspecific and undefined label "wild mushrooms," although in some cases particular species are listed in the ingredients. However, the ambiguity of the definition of "wild mushrooms" in foods makes it impossible to know which species are involved or whether they are truly wild-collected or cultivated varieties. As a consequence, any individual adverse reactions to consuming the mushrooms in these products cannot be traced to the source due to the minimal regulations around the harvest and sale of wild mushrooms. For this study, we set out to shed light on what species of fungi are being sold as "wild mushrooms" using DNA metabarcoding to identify fungal contents of various food products acquired from locally sourced grocers and a large online retail site. Twenty-eight species of mushroom were identified across 16 food products, ranging from commonly cultivated species to wild species not represented in global DNA databases. Our results demonstrate that "wild mushroom" ingredients often consist entirely or in part of cultivated species such as the ubiquitous white and brown "button" mushrooms and portabella (), oyster spp.) and shiitake (). In other cases truly wild mushrooms were detected but they were not always consistent with the species on the label. More alarmingly, a few products with large distribution potential contained species whose edibility is at best dubious, and at worst potentially toxic.
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http://dx.doi.org/10.7717/peerj.11747DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8340906PMC
August 2021

Emerimicins V-X, 15-Residue Peptaibols Discovered from an sp. through Integrated Genomic and Chemical Approaches.

J Nat Prod 2021 04 22;84(4):1113-1126. Epub 2021 Feb 22.

Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States.

Fermentation of W. Gams isolated from a soil sample collected from the University of Utah led to the isolation and characterization of six new linear pentadecapeptides, emerimicins V-X (-). Peptaibols containing 15-residues are quite rare, with only 22 reported. Genome mining and bioinformatic analysis were used to identify the emerimicin 60 kbp biosynthetic cluster harboring a single 16-module hybrid polyketide-nonribosomal peptide synthetase. A detailed bioinformatic investigation of the corresponding 15 adenylation domains, combined with 1D and 2D NMR experiments, LC-MS/MS data, and advanced Marfey's method, allowed for the elucidation and absolute configuration of all proteinogenic and nonproteinogenic amino acid residues in -. As some peptaibols possess cytotoxic activity, a zebrafish embryotoxicity assay was used to evaluate the toxicity of the six emerimicins and showed that emerimicin V () and VI () exhibit the most potent activity. Additionally, out of the six emerimicins, displayed modest activity against , methicillin-resistant , and vancomycin-resistant with MIC values of 64, 32, and 64 μg/mL, respectively.
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http://dx.doi.org/10.1021/acs.jnatprod.0c01186DOI Listing
April 2021

Reclassification of Corner (Basidiomycota: Agaricales) introducing the ant-associated genus gen. nov., Henn. and the corticioid fam. nov.

IMA Fungus 2020 30;11. Epub 2020 Jan 30.

Natural History Museum of Utah & Biology Department, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108 USA.

was formally proposed to group six coralloid and dimitic genera: (=, , , , and . Recent molecular studies have shown that some of the characters currently used in do not distinguish the genera. and have been removed, and a few other resupinate genera were added to the family. However, none of these studies intended to investigate the relationship between genera. In this study, we generated 278 sequences from both newly collected and fungarium samples. Phylogenetic analyses supported with morphological data allowed a reclassification of where we propose the introduction of gen. nov. and fam. nov., the reintroduction of , the synonymisation of in and 53 new combinations. is rendered polyphyletic requiring a reclassification; thus, it is split into , gen. nov., and . is recovered as paraphyletic alongside several species and and is sunk into the latter genus. is reintroduced to accommodate species with darker basidiomes. The neotropical gen. nov. forms a distinct clade adjacent to , and most members of this clade are associated with active or inactive attine ant nests. The resupinate genera and are recovered in a strongly supported clade close to . The other resupinate genera previously included in , and which form basidiomes lacking cystidia and with monomitic hyphal structure (, and ), are reclassified into Radulomycetaceae fam. nov. is still an enigmatic piece in this puzzle known only from the type specimen that requires molecular investigation. A key for the genera of and fam. nov. is also provided here.
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http://dx.doi.org/10.1186/s43008-019-0022-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325140PMC
January 2020

Lost in translation: Population genomics and long-read sequencing reveals relaxation of concerted evolution of the ribosomal DNA cistron.

Mol Phylogenet Evol 2020 07 2;148:106804. Epub 2020 Apr 2.

School of Biological Sciences, University of Utah, 257 1400 E, Salt Lake City, UT 84112, USA; Natural History Museum of Utah, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108, USA. Electronic address:

Concerted evolution of the ribosomal DNA array has been studied in numerous eukaryotic taxa, yet is still poorly understood. rDNA genes are repeated dozens to hundreds of times in the eukaryotic genome (Eickbush and Eickbush, 2007) and it is believed that these arrays are homogenized through concerted evolution (Zimmer et al., 1980; Dover, 1993) preventing the accumulation of intragenomic, and intraspecific, variation. However, numerous studies have reported rampant intragenomic and intraspecific variation in the rDNA array (Ganley and Kobayashi, 2011; Naidoo et al., 2013; Hughes and Petersen, 2001; Lindner and Banik, 2011; Li et al., 2013; Lindner et al., 2013; Hughes et al., 2018), contradicting our current understanding of concerted evolution. The internal transcribed spacers (ITS) of the rDNA cistron are the most commonly used DNA barcoding region in Fungi (Schoch et al., 2012), and rely on concerted evolution to homogenize the rDNA array leading to a "barcode gap" (Puillandre et al., 2012). Here we show that in Boletus edulis Bull., ITS intragenomic variation persists at low allele frequencies throughout the rDNA array, this variation does not correlate with genomic relatedness between populations, and rDNA genes may not evolve in a strictly concerted fashion despite the presence of unequal recombination and gene conversion. Under normal assumptions, heterozygous positions found in ITS sequences represent hybridization between populations, yet through allelic mapping of the rDNA array we found numerous heterozygous alleles to be stochastically introgressed throughout, presenting a dishonest signal of gene flow. Moreover, despite the signal of gene flow in ITS, our organisms were highly inbred, indicating a disconnect between true gene flow and barcoding signals. In addition, we show that while the mechanisms of concerted evolution are ongoing in pseudo-heterozygous individuals, they are not fully homogenizing the ITS array. Concerted evolution of the rDNA array may insufficiently homogenize the ITS gene, allowing for misleading signals of gene flow to persist, vastly complicating the use of the ITS locus for DNA barcoding in Fungi.
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http://dx.doi.org/10.1016/j.ympev.2020.106804DOI Listing
July 2020

Reclassification of Corner (Pterulaceae, Agaricales), contributions to Lachnocladiaceae and Peniophoraceae (Russulales) and introduction of gen. nov.

MycoKeys 2018 31(37):39-56. Epub 2018 Jul 31.

Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, UT, 84108 USA CAPES Foundation, Ministry of Education of Brazil Brasília Brazil.

The genus was first introduced to accommodate two Brazilian species of coralloid fungi with affinities to Pterulaceae (Agaricales). Despite the coralloid habit and the presence of skeletal hyphae, other features, notably the presence of gloeocystidia, dichophyses and papillate hyphal ends, differentiate this genus from Pterulaceae Fieldwork in Brazil resulted in the rediscovery of two coralloid fungi identifiable as , the first verified collections of this genus since Corner's original work in the 1950s. Molecular phylogenetic analyses of nrITS and nrLSU sequences from these modern specimens revealed affinities with the /peniophorales clade in the Russulales, rather than Pterulaceae. The presence of distinctive hyphal elements, homologous to the defining features of /peniophorales, is consistent with the phylogenetic evidence and thus clearly distinguished and its type species from Pterulaceae, placing this genus within /peniophorales. was also found to be polyphyletic so gen. nov. is proposed to accommodate , , and also within /peniophorales.
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http://dx.doi.org/10.3897/mycokeys.37.26303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6081468PMC
July 2018

New species of () from Cameroon, with a worldwide key to the known species.

IMA Fungus 2017 Dec 18;8(2):287-298. Epub 2017 Oct 18.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.

Two new species in the genus () are described as new from tropical rainforest in Cameroon. Descriptions, photographs, line drawings, and a worldwide taxonomic key to the described species of are presented. Phylogenetic analysis of 28S rDNA and nucleotide sequence data suggests at least five phylogenetic species that can be ascribed to occur in the region comprising Cameroon and Gabon and constitute a strongly supported monophyletic subgroup within the genus. Phylogenetic analysis of ITS data supports the conspecificity of numerous collections attributed to the two new species as well as the monophyly of Australian species of . This work raises the known number of described species of to thirteen worldwide, four of which occur in tropical Africa, one in tropical India, and eight in temperate and tropical regions of Australia. This is the first study to confirm an ectomycorrhizal status of using molecular data.
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http://dx.doi.org/10.5598/imafungus.2017.08.02.06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729713PMC
December 2017

gen. sp. nov. (), a new sequestrate fungus from Cameroon.

IMA Fungus 2016 Dec 11;7(2):239-245. Epub 2016 Oct 11.

Department of Biological Sciences, Humboldt State University, Arcata, CA 95521, USA.

gen. sp. nov. is described as new to science. This sequestrate, partially hypogeous fungus was collected around and within the stilt root system of an ectomycorrhizal (ECM) tree of the genus () in a Guineo-Congolian mixed tropical rainforest in Cameroon. Molecular data place this fungus in (, , ) with no clear relationship to previously described taxa within the family. Macro- and micromorphological characters, habitat, and DNA sequence data are provided. Unique morphological features and a molecular phylogenetic analysis of 304 sequences across the justify the recognition of the new taxa. is the fourth sequestrate described from the greater African tropics, and the first to be described from Cameroon.
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http://dx.doi.org/10.5598/imafungus.2016.07.02.03DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159594PMC
December 2016

Cortinarius subgenus Callistei in North America and Europe-type studies, diversity, and distribution of species.

Mycologia 2016 09 22;108(5):1018-1027. Epub 2016 Aug 22.

Department of Biology, Box 351800, University of Washington, Seattle, Washington 98195-1800.

Five species of Cortinarius subgenus Callistei, are recognized in Europe and North America. Cortinarius callisteus, C. infucatus, and C. neocallisteus sp. nov. have a broad distribution, extending from western North America to Europe. Cortinarius tofaceus is known from eastern North America and Europe, while C. callistei sp. is known only from one locality in Sweden. All five species are primarily associated with coniferous trees. Previously the species were included either in subgenus Leprocybe or subgenus Cortinarius, but recently they have been separated into subgenus Callistei based on molecular data. Type specimens of the names associated with this subgenus were studied and a neotype proposed for C. tofaceus and an epitype for C. infucatus Barcodes for the species are deposited in RefSeq and UNITE.
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http://dx.doi.org/10.3852/16-033DOI Listing
September 2016

Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches.

Philos Trans R Soc Lond B Biol Sci 2016 09;371(1702)

Royal Botanic Gardens Kew, Richmond, Surrey, UK Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Cledwyn Building, Penglais, Aberystwyth SY23 3DD, UK.

The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity in appearance to distantly related taxa. This multiplicity of hurdles resulted in the early adoption of DNA-based comparisons to study fungal diversity, including linking curated DNA sequence data to expertly identified voucher specimens. DNA-barcoding approaches in fungi were first applied in specimen-based studies for identification and discovery of taxonomic diversity, but are now widely deployed for community characterization based on sequencing of environmental samples. Collectively, fungal barcoding approaches have yielded important advances across biological scales and research applications, from taxonomic, ecological, industrial and health perspectives. A major outstanding issue is the growing problem of 'sequences without names' that are somewhat uncoupled from the traditional framework of fungal classification based on morphology and preserved specimens. This review summarizes some of the most significant impacts of fungal barcoding, its limitations, and progress towards the challenge of effective utilization of the exponentially growing volume of data gathered from high-throughput sequencing technologies.This article is part of the themed issue 'From DNA barcodes to biomes'.
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http://dx.doi.org/10.1098/rstb.2015.0336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971188PMC
September 2016

New species of Elaphomyces (Elaphomycetaceae, Eurotiales, Ascomycota) from tropical rainforests of Cameroon and Guyana.

IMA Fungus 2016 Jun 10;7(1):59-73. Epub 2016 Mar 10.

Department of Biological Sciences, Humboldt State University, Arcata, CA 95521, USA;

The sequestrate false truffles Elaphomyces favosus, E. iuppitercellus, and E. labyrinthinus spp. nov. are described as new to science from the Dja Biosphere Reserve, Cameroon. Elaphomyces adamizans sp. nov. is described as new from the Pakaraima Mountains of Guyana. The Cameroonian species are the first Elaphomyces taxa to be formally described from Africa, occurring in lowland Guineo-Congolian tropical rainforests dominated by the ectomycorrhizal (ECM) canopy tree Gilbertiodendron dewevrei (Fabaceae subfam. Caesalpinioideae). The Guyanese species is the third to be discovered in lowland tropical South America, occurring in forests dominated by the ECM trees Pakaraimaea dipterocarpacea (Dipterocarpaceae) and Dicymbe jenmanii (Fabaceae subfam. Caesalpinioideae). Macromorphological, micromorphological, habitat, and DNA sequence data are provided for each new species. Molecular and morphological data place these fungi in Elaphomycetaceae (Eurotiales, Ascomycota). Unique morphological features are congruent with molecular delimitation of each of the new species based on a phylogenetic analysis of the rDNA ITS and 28S loci across the Elaphomycetaceae. The phylogenetic analysis also suggests that a common ancestor is shared between some Elaphomyces species from Africa and South America, and that species of the stalked, volvate genus Pseudotulostoma may be nested in Elaphomyces.
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http://dx.doi.org/10.5598/imafungus.2016.07.01.05DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941688PMC
June 2016

New species of xerocomoid boletes (Boletaceae) from Himalayan India based on morphological and molecular evidence.

Mycologia 2016 Jul-Aug;108(4):753-64. Epub 2016 May 6.

Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey TW9 3DS, United Kingdom, and Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Penglais, Aberystwyth, Ceredigion SY23 3DD, United Kingdom

Xerocomus doodhcha and Hortiboletus indorubellus (Boletaceae) from broadleaf montane forest in Sikkim, India, are proposed as new. They are described in detail with supporting morphological illustrations and compared with related taxa using molecular phylogenetic analysis of ITS and 28S rDNA sequences. Xerocomus doodhcha is characterized by a pale brown pileus, basidiospores with a finely bacillate surface under SEM, and phylogenetic proximity to the type species of Xerocomus, X. subtomentosus Hortiboletus indorubellus is characterized by a dark brown to reddish brown pileus, context that turns brownish to brownish orange on bruising, and phylogenetic proximity to Hortiboletus rubellus.
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http://dx.doi.org/10.3852/15-206DOI Listing
January 2018

Decoupled genomic elements and the evolution of partner quality in nitrogen-fixing rhizobia.

Ecol Evol 2016 Mar 28;6(5):1317-27. Epub 2016 Jan 28.

Department of Plant Biology University of Illinois Urbana-Champaign 505 S. Goodwin Ave. Urbana Illinois 61801.

Understanding how mutualisms evolve in response to a changing environment will be critical for predicting the long-term impacts of global changes, such as increased N (nitrogen) deposition. Bacterial mutualists in particular might evolve quickly, thanks to short generation times and the potential for independent evolution of plasmids through recombination and/or HGT (horizontal gene transfer). In a previous work using the legume/rhizobia mutualism, we demonstrated that long-term nitrogen fertilization caused the evolution of less-mutualistic rhizobia. Here, we use our 63 previously isolated rhizobium strains in comparative phylogenetic and quantitative genetic analyses to determine the degree to which variation in partner quality is attributable to phylogenetic relationships among strains versus recent genetic changes in response to N fertilization. We find evidence of distinct evolutionary relationships between chromosomal and pSym genes, and broad similarity between pSym genes. We also find that nifD has a unique evolutionary history that explains much of the variation in partner quality, and suggest MoFe subunit interaction sites in the evolution of less-mutualistic rhizobia. These results provide insight into the mechanisms behind the evolutionary response of rhizobia to long-term N fertilization, and we discuss the implications of our results for the evolution of the mutualism.
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http://dx.doi.org/10.1002/ece3.1953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775534PMC
March 2016

Disentangling visual and olfactory signals in mushroom-mimicking Dracula orchids using realistic three-dimensional printed flowers.

New Phytol 2016 May 15;210(3):1058-71. Epub 2016 Feb 15.

Institute of Ecology & Evolution, 5289 University of Oregon, Eugene, OR, 97403, USA.

Flowers use olfactory and visual signals to communicate with pollinators. Disentangling the relative contributions and potential synergies between signals remains a challenge. Understanding the perceptual biases exploited by floral mimicry illuminates the evolution of these signals. Here, we disentangle the olfactory and visual components of Dracula lafleurii, which mimics mushrooms in size, shape, color and scent, and is pollinated by mushroom-associated flies. To decouple signals, we used three-dimensional printing to produce realistic artificial flower molds that were color matched and cast using scent-free surgical silicone, to which we could add scent. We used GC-MS to measure scents in co-occurring mushrooms, and related orchids, and used these scents in field experiments. By combining silicone flower parts with real floral organs, we created chimeras that identified the mushroom-like labellum as a source of volatile attraction. In addition, we showed remarkable overlap in the volatile chemistry between D. lafleurii and co-occurring mushrooms. The characters defining the genus Dracula - a mushroom-like, 'gilled' labellum and a showy, patterned calyx - enhance pollinator attraction by exploiting the visual and chemosensory perceptual biases of drosophilid flies. Our techniques for the manipulation of complex traits in a nonmodel system not conducive to gene silencing or selective breeding are useful for other systems.
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http://dx.doi.org/10.1111/nph.13855DOI Listing
May 2016

Long-term nitrogen addition causes the evolution of less-cooperative mutualists.

Evolution 2015 Mar 5;69(3):631-42. Epub 2015 Feb 5.

Department of Biology, St. Ambrose University, 518 West Locust St, Davenport, Iowa, 52803; Kellogg Biological Station and Department of Plant Biology, Michigan State University, 3700 E. Gull Lake Drive, Hickory Corners, Michigan, 49060.

Human activities have altered the global nitrogen (N) cycle, and as a result, elevated N inputs are causing profound ecological changes in diverse ecosystems. The evolutionary consequences of this global change have been largely ignored even though elevated N inputs are predicted to cause mutualism breakdown and the evolution of decreased cooperation between resource mutualists. Using a long-term (22 years) N-addition experiment, we find that elevated N inputs have altered the legume-rhizobium mutualism (where rhizobial bacteria trade N in exchange for photosynthates from legumes), causing the evolution of less-mutualistic rhizobia. Plants inoculated with rhizobium strains isolated from N-fertilized treatments produced 17-30% less biomass and had reduced chlorophyll content compared to plants inoculated with strains from unfertilized control plots. Because the legume-rhizobium mutualism is the major contributor of naturally fixed N to terrestrial ecosystems, the evolution of less-cooperative rhizobia may have important environmental consequences.
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http://dx.doi.org/10.1111/evo.12594DOI Listing
March 2015

What's for dinner? Undescribed species of porcini in a commercial packet.

PeerJ 2014 16;2:e570. Epub 2014 Sep 16.

Mycology Section, Jodrell Laboratory, Royal Botanic Gardens , Kew, Richmond, Surrey , UK.

Accurate diagnosis of the components of our food and a standard lexicon for clear communication is essential for regulating global food trade and identifying food frauds. Reliable identification of wild collected foods can be particularly difficult, especially when they originate in under-documented regions or belong to poorly known groups such as Fungi. Porcini, one of the most widely traded wild edible mushrooms in the world, are large and conspicuous and they are used as a food both on their own and in processed food products. China is a major exporter of porcini, most of it ending up in Europe. We used DNA-sequencing to identify three species of mushroom contained within a commercial packet of dried Chinese porcini purchased in London. Surprisingly, all three have never been formally described by science and required new scientific names. This demonstrates the ubiquity of unknown fungal diversity even in widely traded commercial food products from one of the most charismatic and least overlooked groups of mushrooms. Our rapid analysis and description makes it possible to reliably identify these species, allowing their harvest to be monitored and their presence tracked in the food chain.
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http://dx.doi.org/10.7717/peerj.570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4179395PMC
October 2014

Fungal ingestion in companion animals.

Vet Rec 2014 Aug;175(7):179-80

Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS.

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http://dx.doi.org/10.1136/vr.g5151DOI Listing
August 2014

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

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

New Porcini (Boletus sect. Boletus) from Australia and Thailand.

Mycologia 2014 Jul-Aug;106(4):830-4. Epub 2014 Jun 3.

Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.

Boletus albobrunnescens and B. austroedulis are described as new species in section Boletus from Thailand and Australia respectively. The former is easily characterized by the pure white basidiomata that stain brown. Boletus austroedulis has a gray-brown, slightly rugulose pileus with hymeniform pileipellis producing pileocystidia, and the stipe is only apically reticulate if at all. These new species represent ancient lineages inferred from prior molecular phylogenetic analyses.
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http://dx.doi.org/10.3852/13-340DOI Listing
October 2014

Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina).

PLoS One 2011 22;6(9):e25081. Epub 2011 Sep 22.

Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.

DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (~450 bp) representing ~100 morphospecies from ~650 collections of Agaricomycotina using several sets of new primers. Large introns (~1500 bp) at variable locations were detected in ~5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (~30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0025081PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178597PMC
June 2012

Rapid and reliable high-throughput methods of DNA extraction for use in barcoding and molecular systematics of mushrooms.

Mol Ecol Resour 2010 Jul 29;10(4):628-33. Epub 2009 Dec 29.

Department of Ecology and Evolutionary Biology, 25 Willcocks St., University of Toronto, Toronto, ON, Canada M5S 3B2 Department of Natural History, 100 Queen's Park, Royal Ontario Museum, Toronto, ON, Canada M5S 2C6.

We present two methods for DNA extraction from fresh and dried mushrooms that are adaptable to high-throughput sequencing initiatives, such as DNA barcoding. Our results show that these protocols yield ∼85% sequencing success from recently collected materials. Tests with both recent (<2 year) and older (>100 years) specimens reveal that older collections have low success rates and may be an inefficient resource for populating a barcode database. However, our method of extracting DNA from herbarium samples using small amount of tissue is reliable and could be used for important historical specimens. The application of these protocols greatly reduces time, and therefore cost, of generating DNA sequences from mushrooms and other fungi vs. traditional extraction methods. The efficiency of these methods illustrates that standardization and streamlining of sample processing should be shifted from the laboratory to the field.
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http://dx.doi.org/10.1111/j.1755-0998.2009.02825.xDOI Listing
July 2010

Molecular phylogenetics of porcini mushrooms (Boletus section Boletus).

Mol Phylogenet Evol 2010 Dec 21;57(3):1276-92. Epub 2010 Oct 21.

Department of Plant Biology, University of Minnesota, St. Paul, MN 55108, USA.

Porcini (Boletus section Boletus: Boletaceae: Boletineae: Boletales) are a conspicuous group of wild, edible mushrooms characterized by fleshy fruiting bodies with a poroid hymenophore that is "stuffed" with white hyphae when young. Their reported distribution is with ectomycorrhizal plants throughout the Northern Hemisphere. Little progress has been made on the systematics of this group using modern molecular phylogenetic tools because sampling has been limited primarily to European species and the genes employed were insufficient to resolve the phylogeny. We examined the evolutionary history of porcini by using a global geographic sampling of most known species, new discoveries from little explored areas, and multiple genes. We used 78 sequences from the fast-evolving nuclear internal transcribed spacers and are able to recognize 18 reciprocally monophyletic species. To address whether or not porcini form a monophyletic group, we compiled a broadly sampled dataset of 41 taxa, including other members of the Boletineae, and used separate and combined phylogenetic analysis of sequences from the nuclear large subunit ribosomal DNA, the largest subunit of RNA polymerase II, and the mitochondrial ATPase subunit six gene. Contrary to previous studies, our separate and combined phylogenetic analyses support the monophyly of porcini. We also report the discovery of two taxa that expand the known distribution of porcini to Australia and Thailand and have ancient phylogenetic connections to the rest of the group. A relaxed molecular clock analysis with these new taxa dates the origin of porcini to between 42 and 54 million years ago, coinciding with the initial diversification of angiosperms, during the Eocene epoch when the climate was warm and humid. These results reveal an unexpected diversity, distribution, and ancient origin of a group of commercially valuable mushrooms that may provide an economic incentive for conservation and support the hypothesis of a tropical origin of the ectomycorrhizal symbiosis.
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http://dx.doi.org/10.1016/j.ympev.2010.10.004DOI Listing
December 2010

Phylogenetic placement of an unusual coral mushroom challenges the classic hypothesis of strict coevolution in the apterostigma pilosum group ant-fungus mutualism.

Evolution 2009 Aug 27;63(8):2172-8. Epub 2009 Mar 27.

Plant Biology, 250 Biological Sciences Center, University of Minnesota, Saint Paul, Minnesota, USA.

The approximately 50 million-year-old fungus-farming ant mutualism is a classic example of coevolution, involving ants that subsist on asexual, fungal biomass, in turn propagating the fungus clonally through nest-to-nest transmission. Most mutualistic ants cultivate two closely related groups of gilled mushrooms, whereas one small group of ants in the genus Apterostigma cultivates a distantly related lineage comprised of the G2 and G4 groups. The G2 and G4 fungi were previously shown to form a monophyletic group sister to the thread-like coral mushroom family Pterulaceae. Here, we identify an enigmatic coral mushroom that produces both fertile and sterile fruiting structures as the closest free-living relative of the G4 fungi, challenging the monophyly of the Apterostigma-cultivated fungi for the first time. Both nonparametric bootstrap and Bayesian posterior probability support the node leading to the G4 cultivars and a free-living Pterula mushroom. These data suggest three scenarios that contradict the hypothesis of strict coevolution: (1) multiple domestications, (2) escape from domestication, (3) selection of single cultivar lineages from an ancestral mixed-fungus garden. These results illustrate how incomplete phylogenies for coevolved symbionts impede our understanding of the patterns and processes of coevolution.
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http://dx.doi.org/10.1111/j.1558-5646.2009.00697.xDOI Listing
August 2009

Conservation of cytoplasmic organization in the cystidia of Suillus species.

Mycologia 2008 Jul-Aug;100(4):539-47

Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA.

Cystidia of Suillus americanus and S. granulatus (Boletales) were examined cytochemically and ultrastructurally with cells prepared by freeze substitution. We present the first study showing ultrastructural details and cytological functions of the cystidium to be conserved in two closely related species. The results are presented for inclusion in the AFTOL Structural and Biochemical Database to aid in the application of morphological characters to phylogenetic studies. The cystidia of these Suillus species appear to be united by a series of conserved characters, including specialized secretion mechanisms, smooth tubular endoplasmic reticulum and abundant free ribosomes. The conservation of these subcellular traits among members of this genus suggests that ultrastructural details of cystidia may provide a suite of phylogenetically informative characters. Inclusion of such characters in phylogenetic analyses might resolve or provide support for monophyletic groups at the level of family or genus.
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http://dx.doi.org/10.3852/07-095rDOI Listing
October 2008

Septal pore apparatus and nuclear division of Auriscalpium vulgare.

Mycologia 2007 Sep-Oct;99(5):644-54

Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA.

Ultrastructure of the septal pore apparatus and nuclear division of Auriscalpium vulgare (Russulales) was examined with freeze substitution and is presented for inclusion in the AFTOL Structural and Biochemical Database (http://aftol.umn.edu). Previously unreported septal characters for the Russulales (Agaricomycotina) were observed: Septa of the hymenophore had bell-shaped perforated septal pore caps that may extend along the septum and a zone of organelle exclusion surrounded the septal pore apparatus. Metaphase I of meiosis and metaphase of mitosis were similar. Globular spindle pole bodies with electron-opaque inclusions were set within polar fenestrae of the nuclear envelope. The nuclear envelope was mostly intact with occasional gaps. Fragments of endoplasmic reticulum were present near the spindle pole bodies but did not form a polar cap. Structural characters may distinguish one or more clades of the Agaricomycotina and provide additional signal in phylogenetic analyses.
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http://dx.doi.org/10.3852/mycologia.99.5.644DOI Listing
April 2008

The mushroom family Psathyrellaceae: evidence for large-scale polyphyly of the genus Psathyrella.

Mol Phylogenet Evol 2008 Feb 21;46(2):415-29. Epub 2007 Nov 21.

Department of Plant Biology, University of Minnesota, 250 Biological Sciences Center, 1445 Gortner Avenue, Saint Paul, MN 55108, USA.

Psathyrella is the archetypal little brown mushroom genus with few easily discernable characters causing it to be considered a "clean-up" genus for other small brown-spored saprotrophic species found worldwide. While molecular studies have demonstrated that mushroom genera based on homoplastic morphological characters are artificial, the degree of phylogenetic heterogeneity contained within Psathyrella and Psathyrellaceae has never been appropriately addressed. For this study, 132 ribosomal sequences from approximately one-tenth of the known Psathyrella species worldwide, including representatives of most subgeneric subdivisions, and three closely related coprinoid genera (Parasola, Coprinopsis, Coprinellus) were evaluated using multiple phylogenetic methods, including likelihood, with Agaricaceae as the outgroup. Our results indicated that Psathyrella was polyphyletic. Conservatively, the genus can be separated into 11 clades of which five can be raised to generic status. Most species of Psathyrella, including its type species P. gracilis, formed a large clade with Coprinellus, which appeared to be derived from within Psathyrella. Generic limits of Parasola, Lacrymaria, and Coprinopsis should be reevaluated. Several taxa previously synonymized based on morphological features were phylogenetically distinct. Morphological features traditionally used to subdivide Psathyrella appeared to be mostly convergent (homoplasious) when traced upon the resulting phylogenies, although several had high RI values. These results were interpreted in light of the two major taxonomic treatments of Psathyrella and revealed substantial inconsistencies between the molecular- and morphology-derived inferences of relationships.
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http://dx.doi.org/10.1016/j.ympev.2007.11.004DOI Listing
February 2008

Reconstructing the Clavariaceae using nuclear large subunit rDNA sequences and a new genus segregated from Clavaria.

Mycologia 2006 Sep-Oct;98(5):746-62

Department of Plant Biology, 1445 Gortner Avenue, University of Minnesota, Saint Paul, Minnesota 55108, USA.

Fungi that produce clavarioid fruit bodies have evolved independently many times in the Basidiomycota. The evolutionary significance of this morphology is difficult to interpret because the phylogenetic positions of many clavarioid fungi are still unknown. In this study we examined the phylogenetic diversity of the Clavariaceae sensu lato among Homobasidiomycetidae by adding partial nuclear large subunit ribosomal DNA sequences from clavarioid and corticioid fungi to a large euagaric dataset and analyzing them both together and separately. Our results indicate that the clavarioid morphology has evolved at least five times in the euagarics while the inclusion of type species enabled us to evaluate the taxonomic consequences of this polyphyletic distribution. Although the sampling available at present is incomplete, a qualitative assessment of our phylogenetic hypotheses indicates that the clavarioid habit might not be as evolutionary labile as previously reported. We propose the new genus Alloclavaria to accommodate Clavaria purpurea, which is not related to Clavaria but is derived within the hymenochaetoid clade. The Physalacriaceae and Clavariaceae are redefined to reflect monophyletic groups, and the limits of Clavaria, Clavulinopsis and Ramariopsis should be reconsidered when additional data are available.
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http://dx.doi.org/10.3852/mycologia.98.5.746DOI Listing
March 2007
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