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  • 1.
    Attitalla, Idress Hamad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, Jamshid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Levenfors, Jens
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Brishammar, Sture
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    A rapid molecular method for differentiating two special forms (lycopersici and radicis-lycopersici) of Fusarium oxysporum2004In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 108, no 7, p. 787-794Article in journal (Refereed)
    Abstract [en]

    Two pathogenic special forms (f. sp.) of the Fusarium oxysporum species complex f. sp. lycopersici (Fol) and f. sp. radicis-lycopersici (Forl) are morphologically indistinguishable. Although they are pathogenic to the same host genus Lycopersicon (tomato), and infect the same tomato cultivar, they form distinct diseases; Fol causes wilt and Forl causes crown rot and root rot. These two special forms apparently exist as genetically isolated populations, based on vegetative compatibility and molecular variation at the DNA level. In seeking efficient diagnostic tools for differentiating Fol and Forl isolates, we examined three techniques: isozyme analysis, mitochondrial DNA (mtDNA) RFLP by HaeIII-digestion of total genomic DNA, and an osmotic method using high performance liquid chromatography (HPLC) to detect fungal pigments. The isolates were collected from geographically widespread locations. Distinct HPLC-profile differences were found between an endophytic non-pathogenic isolate and the other pathogenic isolates. However, the direct mtDNA RFLP technique proved to be an efficient diagnostic tool for routine differentiation of Fol and Forl isolates.

  • 2. Dieguez-Uribeondo, Javier
    et al.
    Cerenius, Lage
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Comparative Physiology.
    The inhibition of extracellular proteinases from Aphanomyces spp by three different proteinase inhibitors from crayfish blood1998In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 102, no 7, p. 820-824Article in journal (Refereed)
    Abstract [en]

    Three different proteinase inhibitors purified from crayfish blood, a 23 kDa inhibitor of subtilisin, a 155 kDa trypsin-inhibitor (pacifastin) and an alpha(2)-macroglobulin were tested for their inhibitory activities against extracellular proteinases from

  • 3.
    Diéguez-Uribeondo, Javier
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Comparative Physiology.
    Huang, TS
    Cerenius, Lage
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Comparative Physiology.
    Söderhäll, Kenneth
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Comparative Physiology.
    Physiological adaptation of an Aphanomyces astaci strain isolated from the freshwater crayfish Procambarus clarkii 1995In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 99, no 5, p. 574-578Article in journal (Refereed)
    Abstract [en]

    Physiological, epidemiological and genetical properties of an Aphanomyces astaci strain (Pc) isolated from the warm water crayfish, Procambarus clarkii, were compared to other A. astaci strains isolated from the cold water crayfish Astacus astacus,

  • 4. Hibbett, David S.
    et al.
    Binder, Manfred
    Bischoff, Joseph F.
    Blackwell, Meredith
    Cannon, Paul F.
    Eriksson, Ove E.
    Huhndorf, Sabine
    James, Timothy
    Kirk, Paul M.
    Lücking, Robert
    Thorsten Lumbsch, H.
    Lutzoni, François
    Matheny, P. Brandon
    McLaughlin, David J.
    Powell, Martha J.
    Redhead, Scott
    Schoch, Conrad L.
    Spatafora, Joseph W.
    Stalpers, Joost A.
    Vilgalys, Rytas
    Aime, M. Catherine
    Aptroot, André
    Bauer, Robert
    Begerow, Dominik
    Benny, Gerald L.
    Castlebury, Lisa A.
    Crous, Pedro W.
    Dai, Yu-Cheng
    Gams, Walter
    Geiser, David M.
    Griffith, Gareth W.
    Gueidan, Cécile
    Hawksworth, David L.
    Hestmark, Geir
    Hosaka, Kentaro
    Humber, Richard A.
    Hyde, Kevin D.
    Ironside, Joseph E.
    Kõljalg, Urmas
    Kurtzman, Cletus P.
    Larsson, Karl-Henrik
    Lichtwardt, Robert
    Longcore, Joyce
    Miadlikowska, Jolanta
    Miller, Andrew
    Moncalvo, Jean-Marc
    Mozley-Standridge, Sharon
    Oberwinkler, Franz
    Parmasto, Erast
    Reeb, Valérie
    Rogers, Jack D.
    Roux, Claude
    Ryvarden, Leif
    Sampaio, José Paulo
    Schüssler, Arthur
    Sugiyama, Junta
    Thorn, R. Greg
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Untereiner, Wendy A.
    Walker, Christopher
    Wang, Zheng
    Weir, Alex
    Weiss, Michael
    White, Merlin M.
    Winka, Katarina
    Yao, Yi-Jian
    Zhang, Ning
    A higher-level phylogenetic classification of the Fungi2007In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 111, no 5, p. 509-547Article, review/survey (Refereed)
    Abstract [en]

    A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella.

  • 5.
    James, Timothy Y.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Johansson, Stina B. K.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Trikaryon formation and nuclear selection in pairings between heterokaryons and homokaryons of the root rot pathogen Heterobasidion parviporum2009In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 113, no 5, p. 583-590Article in journal (Refereed)
    Abstract [en]

    Pairings between heterokaryons and homokaryons of Agaricomycete fungi (he-ho pairings) can lead to either heterokaryotization of the homokaryon or displacement of the homokaryotic nucleus through migration of nuclei from the heterokaryon into the homokaryon. in species of Agaricomycetes with multinucleate cells (> 2 nuclei per cell), he-ho pairings could result in the stable or transient formation of a hypha with three genetically different nuclei (trikaryons). in this study, he-ho pairings were conducted using the multinucleate Agaricomycete Heterobasidion parviporum to determine whether trikaryons can be formed in the laboratory and whether nuclear genotype affects migration and heterokaryon formation. Nuclei were tracked by genotyping the heterokaryotic mycelium using nucleus-specific microsatellite markers. The data indicated that certain nuclear combinations were favored, and that nuclei from some strains had a higher rate of migration. A high percentage of trikaryons (19 %) displaying three microsatellite alleles per locus were identified among subcultures of the he-ho pairings. Using hyphal tip and conidial isolation, we verified that nuclei of three different mating types can inhabit the same mycelium, and one of the trikaryotic strains was judged to be semi-stable over multiple sub-culturing steps, with some hyphal tips that retained three alleles and others that reduced to two alleles per locus. These results demonstrate that nuclear competition and selection are possible outcomes of heterokaryon-homokaryon interactions in H. parviporum and confirm that ratios of component nuclei in heterokaryons are not strictly 1:1. The high rate of trikaryon formation in this study suggests that fungi with multinucleate cells may have the potential for greater genetic diversity and recombination relative to dikaryotic fungi.

  • 6. Jennessen, Jennifer
    et al.
    Schnürer, Johan
    Olsson, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution.
    Samson, Robert A.
    Dijksterhuis, Jan
    Morphological characteristics of sporangiospores of the tempe fungus Rhizopus oligosporus differentiate it from other taxa of the R-microsporus group2008In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 112, p. 547-563Article in journal (Refereed)
    Abstract [en]

    The fungus Rhizopus oligosporus (R. microsporus var. oligosporus) is traditionally used to make tempe, a fermented food based on soybeans. Interest in the fungus has steadily increased, as it can also ferment other substrates, produce enzymes, and treat waste material. R. oligosporus belongs to the R. microsporus group consisting of morphologically similar taxa, which are associated with food fermentation, pathogenesis, or unwanted metabolite production (rhizonins and rhizoxins). The ornamentation pattern, shape, and size of sporangiospores of 26 R. microsporus group strains and two R. oryzae strains were studied using low-temperature SEM (LT-SEM) and LM. This study has shown that: (1) LT-SEM generates images from well-conserved sporangiophores, sporangia, and spores. (2) Robust spore ornamentation patterns can be linked to all different taxa of the R. microsporus group, some previously incorrectly characterized as smooth. Ornamentation included valleys and ridges running in parallel, granular plateaus, or smooth polar areas. Distribution of ornamentation patterns was related to spore shape, which either was regular, ranging from globose to ellipsoidal, or irregular. Specific differences in spore shape, size, and ornamentation were observed between Rhizopus taxa, and sometimes between strains. (3) R. oligosporus has a defect in the spore formation process, which may be related to the domesticated nature of this taxon. It had a high proportion, 10-31 %, of large and irregular spores, and was significantly differentiated from other, natural Rhizopus taxa as evaluated with partial least squares discriminant analysis. it is remarkable that the vehicle of distribution, the sporangiospore, is affected in the strains that are distributed by human activity. This provides information about the specificity and speed of changes that occur in fungal strains because of their use in (food) industry.

  • 7. Kruys, Åsa
    et al.
    Eriksson, Ove E
    Wedin, Mats
    Phylogenetic relationships of coprophilous Pleosporales (Dothideomycetes, Ascomycota), and the classification of some bitunicate taxa of unknown position.2006In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 110, p. 527-536Article in journal (Refereed)
  • 8. Nyberg, Åsa
    et al.
    Persson, Ingalill
    Habitat differences of coprophilous fungi on moose dung.2002In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 106, p. 1360-1366Article in journal (Refereed)
  • 9.
    Reese Næsborg, Rikke
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Ekman, Stefan
    Uppsala University, Music and Museums, Museum of Evolution.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Molecular phylogeny of the genus Lecania (Ramalinaceae, lichenized Ascomycota)2007In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 111, no 5, p. 581-591Article in journal (Refereed)
    Abstract [en]

    The molecular phylogeny of the lichen genus Lecaniawas investigated using nucleotide sequences from the mt-SSU rRNA, the ITS region of the nu-rDNA, and the RNA polymerase II second largest subunit. Forty-six species representing Lecania and other genera likely to influence the phylogeny were included in the study. Phylogenetic reconstructions were carried out using Bayesian inference, ML, and MP approaches. Lecania, as traditionally circumscribed, is not a monophyletic genus. However, a monophyletic group containing a large number of Lecania species, including the type species L. fuscella, was discovered in the analysis, and recognition of Lecania sensu stricto is suggested. L. baeomma, L. glauca, L. gerlachei, L. brialmontii, L. racovitzae, L. hyalina (alias Biatora globulosa), L. chlorotiza, L. naegelii, and L. furfuracea do not belong in Lecania s. str., although the latter two are closely related to Lecania s. str. Representatives of the genus Bilimbia form a well-supported group, as does the ‘Thamnolecania’ group containing the Antarctic ‘Lecania’ species, L. gerlachei, L. brialmontii, and L. racovitzae. An alternative to recognizing these two genera would be a wider circumscription of Bilimbia to include the ‘Thamnolecania’ group as well as affiliated taxa.

  • 10.
    Savić, Sanja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Gueidan, Cécile
    Lutzoni, François
    Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera2008In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 112, no Part 11, p. 1307-1318Article in journal (Refereed)
    Abstract [en]

    Phylogenetic relationships of the lichen genus Polyblastia and closely related taxa in the family Verrucariaceae (Verrucariales, Chaetothyriomycetidae) were studied. A total of 130 sets of sequences (nuLSU rDNA, nuITS rDNA and RPB1 region A-D), including 129 newly generated sequences, were analysed. Phylogenetic relationships were inferred using a Bayesian approach based on two datasets. A first analysis of a larger, two-locus dataset (nuLSU and RPB1) for 128 members of the Verrucariaceae, confirmed the polyphyly of Polyblastia, Thelidium, Staurothele, and Verrucaria, as currently construed. The second analysis focused on 56 Polyblastia and allied taxa, but using an additional locus (nuITS rDNA) and two closely related outgroup taxa. The latter analysis revealed strongly supported groups, such as Polyblastia s. str., the Thelidium group (a mixture of Polyblastia, Thelidium, Staurothele and Verrucaria species). The genus Sporodictyon, which is here accepted, also accommodates Sporodictyon terrestre comb. nov. Morphological features traditionally used for characterizing Polyblastia, Thelidium, Staurothele and Verrucaria, such as spore septation and colour, occurrence of hymenial photobiont, involucrellum structure, and substrate preference, were found to be only partially consistent within the strongly supported clades, and thus are not always reliable features for characterizing natural groups.

  • 11.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Botany.
    Tholurna dissimilis and generic delimitations in Caliciaceae inferred from nuclear ITS and LSU rDNA phylogenies (Lecanorales, lichenized ascomycetes)2003In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 107, no 12, p. 1403-1418Article in journal (Refereed)
    Abstract [en]

    The phylogenetic relationships of Tholurna dissimilis were investigated in relation to a phylogeny of twenty-three species in Caliciaceae and eighteen species from Physciaceae. ITS and LSU regions of the nuclear ribosomal DNA were used for the reconstruction of phylogenies by maximum parsimony methods. Calicium adaequatum was shown to be the closest relative of and possibly congeneric with Tholurna. Calicium is thus not monophyletic unless Tholurna is included. Calicium in the molecular phylogeny contains several distinct clades, which to some extent can be characterized morphologically. Cyphelium in a traditional sense is probably not monophyletic. Cyphelium s. str. has immersed apothecia, large smooth spores and a very thin excipulum throughout. C. inquinans and C. karelicum, which form a distinct and highly supported clade, may be accommodated in Acolium, possibly along with other Cyphelium and Calicium species. The phylogenies presented here do not support the recognition of neither Physciaceae nor Caliciaceae in a narrow sense, but they also do not exclude this. Numerous spliceosomal and unclassified insertions were found in the LSU sequences. They to some extent offered phylogenetic information both with respect to location and by their sequence similarities.

  • 12.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Botany.
    Tholurna dissimilis and generic delimitations in Caliciaceae inferred from nuclear ITS and LSU rDNA phylogenies (Lecanorales, lichenized ascomycetes)2003In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 107, no 12, p. 1403-1418Article in journal (Refereed)
    Abstract [en]

    The phylogenetic relationships of Tholurna dissimilis were investigated in relation to a phylogeny of twenty-three species in Caliciaceae and eighteen species fromPhysciaceae. ITS and LSU regions of the nuclear ribosomal DNA were used for the reconstruction of phylogenies by maximum parsimony methods. Calicium adaequatumwas shown to be the closest relative of and possibly congeneric with Tholurna. Caliciumis thus not monophyletic unless Tholurna is included. Calicium in the molecular phylogeny contains several distinct clades, which to some extent can be characterized morphologically. Cyphelium in a traditional sense is probably not monophyletic.Cyphelium s. str. has immersed apothecia, large smooth spores and a very thin excipulum throughout. C. inquinans and C. karelicum, which form a distinct and highly supported clade, may be accommodated in Acolium, possibly along with otherCyphelium and Calicium species. The phylogenies presented here do not support the recognition of neither Physciaceae nor Caliciaceae in a narrow sense, but they also do not exclude this. Numerous spliceosomal and unclassified insertions were found in the LSU sequences. They to some extent offered phylogenetic information both with respect to location and by their sequence similarities.

  • 13.
    Voglmayr, Hermann
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Constantinescu, Ovidiu
    Uppsala University, Museums etc., Museum of Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Revision and reclassification of three Plasmopara species based on morphological and molecular phylogenetic data2008In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 112, no 5, p. 487-501Article in journal (Refereed)
    Abstract [en]

    Based on the results of morphological and DNA sequence (partial D1–D3/D7–D8 nuLSU and partial nuSSU-ITS1-5.8S rDNA) data, three species of Plasmopara are revised and reclassified. A species of Plasmopara parasitic on Scorzonera, invalidly published several times, is assigned to a new genus and species under Novotelnova scorzonerae. Plasmopara euphrasiae sp. nov. is segregated from P. densa, and P. centaureae-mollis is revised and relegated to synonymy of Bremia centaureae. All taxa are described and illustrated.

  • 14. Voglmayr, Hermann
    et al.
    Fatehi, Jamshid
    Constantinescu, Ovidiu
    Uppsala University, Music and Museums, Museum of Evolution.
    Revision of Plasmopara (Chromista, Peronosporales) parasitic on Geraniaceae2006In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 110, no 6, p. 633-645Article in journal (Refereed)
    Abstract [en]

    Following a phenetic and phylogenetic analysis, five species of Plasmopara are recognized on Geraniaceae: P. pusilla and P. geranii-syluatici in Eurasia, P. geranii in North America, P. praetermissa sp. nov. in Eurasia and North America, and P. wilsonii sp. nov. in North America and Far East Asia. Both the D1/D2 domains of the nuLSU-rDNA and the complete ITS1-5.8S rDNA-ITS2 region were analysed with MP and Bayesian methods to reveal phylogenetic relationships of the species. All species formed highly supported monophyletic lineages, which is corroborated by their distinct morphology. A key for identification, detailed descriptions, illustrations, and data on distribution are provided.

  • 15. Wedin, M
    et al.
    Wiklund, E
    Crewe, A
    Döring, H
    Ekman, S
    Nyberg, Åsa
    Schmitt, I
    Lumbsch, T
    Phylogenetic relationships of Lecanoromycetes (Ascomycota) as revealed by analyses of mtSSU and nLSU rDNA sequence data.2005In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 109, p. 159-172Article in journal (Refereed)
1 - 15 of 15
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