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Demain JG, Choi YJ, Oh JW. The Impact of Climate Change on the Pollen Allergy and Sporulation of Allergic Fungi. CURRENT TREATMENT OPTIONS IN ALLERGY 2021. [DOI: 10.1007/s40521-020-00277-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Celakovská J, Josef B, Ettler K, Vaneckova J, Ettlerova K, Jan K. Sensitization to Fungi in Atopic Dermatitis Patients 14 Year and Older - Association with Other Atopic Diseases and Parameters. Indian J Dermatol 2018; 63:391-398. [PMID: 30210160 PMCID: PMC6124231 DOI: 10.4103/ijd.ijd_493_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background: Fungi as a source of allergen are still largely neglected in basic research as well as in clinical practice. This study aimed to highlight the impact of fungal allergens in a group of patients suffering from atopic dermatitis (AD). Aims and Objectives: The evaluation of the sensitization to fungi in AD patients aged 14 year and older and the evaluation of the relation of fungal sensitization to the occurrence of other atopic diseases and parameters. Materials and Methods: All patients satisfying inclusion criteria attending our hospital between 2008 and 2017 were included in the study. The complete dermatological and allergological examinations were performed in all included patients including examination of specific immunoglobulin E, skin prick test to mixture of fungi and inhalant allergens, evaluation of asthma bronchiale, rhinitis, onset of AD, family history about atopy, duration of eczematous lesions, severity of AD. Pairs of these categories were entered in the contingency tables and the Chi-square test for relationship of these variables was performed with the level of significance set below 5%. Results: Three hundred and thirty-one patients were included in the study; the average age was 26.8 years. The sensitization to fungi was recorded in 100 patients (30%). In these patients, the occurrence of asthma bronchiale, rhinitis, family history about atopy, sensitization to grass and trees was significantly higher than in patients without sensitization to fungi. We did not find any significant relation between the sensitization to fungi and the severity of AD, no relation was also found between the sensitization to fungi and sensitization to mites, animal dander, bird feather, and dust. Conclusion: The occurrence of asthma bronchiale, rhinitis, family history about atopy, sensitization to grass and trees was significantly higher in AD patients with sensitization to fungi. No relation was found between the severity of AD and the sensitization to fungi.
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Affiliation(s)
- Jarmila Celakovská
- Department of Dermatology and Venereology, Faculty Hospital and Medical Faculty of Charles University, Hradec Králové, Czech Republic
| | - Bukac Josef
- Department of Medical Biophysic, Medical Faculty of Charles University, Hradec Králové, Czech Republic
| | - Karel Ettler
- Department of Dermatology and Venereology, Faculty Hospital and Medical Faculty of Charles University, Hradec Králové, Czech Republic
| | - Jaroslava Vaneckova
- Department of Dermatology and Venereology, Faculty Hospital and Medical Faculty of Charles University, Hradec Králové, Czech Republic
| | - Kvetuse Ettlerova
- Department of Allergy and Clinical Immunology, Outpatient Clinic, Hradec Králové, Czech Republic
| | - Krejsek Jan
- Department of Clinical Immunology and Allergy, Faculty Hospital and Medical Faculty of Charles University, Hradec Králové, Czech Republic
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Taylor T, Hass H, Kerp H, Krings M, Hanlin R. Perithecial ascomycetes from the 400 million year old Rhynie chert: an example of ancestral polymorphism. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832862] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- T.N. Taylor
- Department of Ecology and Evolutionary Biology, and Natural History Museum and Biodiversity Research Center, University of Kansas, Lawrence, Kansas 66045
| | | | - H. Kerp
- Forschungsstelle für Paläobotanik, Westfalische Wilhelms-Universität Münster, Germany
| | - M. Krings
- Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße 10, 80333 München, Germany
| | - R.T. Hanlin
- Department of Plant Pathology, University of Georgia, Athens, Georgia 30602
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Aime MC, Matheny PB, Henk DA, Frieders EM, Nilsson RH, Piepenbring M, McLaughlin DJ, Szabo LJ, Begerow D, Sampaio JP, Bauer R, Weiß M, Oberwinkler F, Hibbett D. An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832619] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- M. Catherine Aime
- USDA-ARS, Systematic Botany and Mycology Lab, Beltsville, Maryland 20705
| | | | - Daniel A. Henk
- USDA-ARS, Systematic Botany and Mycology Lab, Beltsville, Maryland 20705
| | | | - R. Henrik Nilsson
- Göteborg University, Department of Plant and Environmental Sciences, Göteborg, Sweden
| | - Meike Piepenbring
- J.W. Goethe-Universität Frankfurt, Department of Mycology, Frankfurt, Germany
| | - David J. McLaughlin
- Department of Plant Biology, University of Minnesota, St Paul, Minnesota 55108
| | - Les J. Szabo
- USDA-ARS, Cereal Disease Lab, University of Minnesota, St Paul, Minnesota 55108
| | - Dominik Begerow
- Universität Tübingen, Spezielle Botanik und Mykologie, Tübingen, Germany
| | - José Paulo Sampaio
- CREM, SABT, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | | | | | - Franz Oberwinkler
- Universität Tübingen, Spezielle Botanik und Mykologie, Tübingen, Germany
| | - David Hibbett
- Biology Department, Clark University, Worcester, Massachusetts 01610
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Oberwinkler F. Dr. Robert Bauer (1950-2014) in memoriam: botanist, mycologist, and electron microscopist. Mycol Prog 2015. [DOI: 10.1007/s11557-015-1120-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Crameri R. Structural aspects of fungal allergens. Semin Immunopathol 2014; 37:117-21. [PMID: 25413498 DOI: 10.1007/s00281-014-0458-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 11/04/2014] [Indexed: 11/26/2022]
Abstract
Despite the increasing number of solved crystal structures of allergens, the key question why some proteins are allergenic and the vast majority is not remains unanswered. The situation is not different for fungal allergens which cover a wide variety of proteins with different chemical properties and biological functions. They cover enzymes, cell wall, secreted, and intracellular proteins which, except cross-reactive allergens, does not show any evidence for structural similarities at least at the three-dimensional level. However, from a diagnostic point of view, pure allergens biotechnologically produced by recombinant technology can provide us, in contrast to fungal extracts which are hardly producible as standardized reagents, with highly pure perfectly standardized diagnostic reagents.
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Affiliation(s)
- Reto Crameri
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland,
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Crameri R, Garbani M, Rhyner C, Huitema C. Fungi: the neglected allergenic sources. Allergy 2014; 69:176-85. [PMID: 24286281 DOI: 10.1111/all.12325] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2013] [Indexed: 12/15/2022]
Abstract
Allergic diseases are considered the epidemics of the twentieth century estimated to affect more than 30% of the population in industrialized countries with a still increasing incidence. During the past two decades, the application of molecular biology allowed cloning, production and characterization of hundreds of recombinant allergens. In turn, knowledge about molecular, chemical and biologically relevant allergens contributed to increase our understanding of the mechanisms underlying IgE-mediated type I hypersensitivity reactions. It has been largely demonstrated that fungi are potent sources of allergenic molecules covering a vast variety of molecular structures including enzymes, toxins, cell wall components and phylogenetically highly conserved cross-reactive proteins. Despite the large knowledge accumulated and the compelling evidence for an involvement of fungal allergens in the pathophysiology of allergic diseases, fungi as a prominent source of allergens are still largely neglected in basic research as well as in clinical practice. This review aims to highlight the impact of fungal allergens with focus on asthma and atopic dermatitis.
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Affiliation(s)
- R. Crameri
- Swiss Institute of Allergy and Asthma Research (SIAF); University of Zürich; Davos Switzerland
| | - M. Garbani
- Swiss Institute of Allergy and Asthma Research (SIAF); University of Zürich; Davos Switzerland
| | - C. Rhyner
- Swiss Institute of Allergy and Asthma Research (SIAF); University of Zürich; Davos Switzerland
| | - C. Huitema
- Swiss Institute of Allergy and Asthma Research (SIAF); University of Zürich; Davos Switzerland
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Glaser AG, Kirsch AI, Zeller S, Menz G, Rhyner C, Crameri R. Molecular and immunological characterization of Asp f 34, a novel major cell wall allergen of Aspergillus fumigatus. Allergy 2009; 64:1144-51. [PMID: 19416144 DOI: 10.1111/j.1398-9995.2009.02029.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Although fungal spores have been recognized as triggers of respiratory allergy and asthma, only two allergenic fungal cell wall components have so far been described. METHODS Eighty-one sequences derived from an Aspergillus fumigatus cDNA library encoding putative allergens were examined for the presence of cell wall components. A new allergen (Asp f 34) was evaluated by Western blots, enzyme-linked immunosorbent assay (ELISA), peripheral blood mononuclear cell (PBMC) proliferation assays, and skin prick test (SPT). RESULTS The cDNA encoding Asp f 34 contained an open reading frame predicting a protein of 185 amino acids with a molecular weight of 19.38 kDa, showing sequence homology to phiA, an essential protein for the formation of conidia in the genus Aspergillus. The recombinant Asp f 34 was binding IgE from sensitized individuals in Western blots. An ELISA survey showed that 94% of the ABPA and 46% of the A. fumigatus-sensitized individuals tested had Asp f 34-specific serum IgE. Asp f 34 induced allergen-specific proliferation exclusively of PBMCs from patients sensitized to the allergen. Eight patients with anti-Asp f 34 serum IgE tested reacted positively in SPT, whereas four A. fumigatus-sensitized individuals without Asp f 34-specific IgE and eight healthy controls scored negatively. CONCLUSIONS A cell wall protein of the phialides of A. fumigatus was identified as a major allergen. Asp f 34 belongs to the Aspergillus-specific proteins of the phiA family and has relevant potential for a specific diagnosis of Aspergillus sensitization.
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Affiliation(s)
- A G Glaser
- Department Molecular Allergology, Swiss Institute of Allergy and Asthma Research, University of Zürich, Zürich, Switzerland
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Tuller T, Kupiec M, Ruppin E. Co-evolutionary networks of genes and cellular processes across fungal species. Genome Biol 2009; 10:R48. [PMID: 19416514 PMCID: PMC2718514 DOI: 10.1186/gb-2009-10-5-r48] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 02/24/2009] [Accepted: 05/05/2009] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The introduction of measures such as evolutionary rate and propensity for gene loss have significantly advanced our knowledge of the evolutionary history and selection forces acting upon individual genes and cellular processes. RESULTS We present two new measures, the 'relative evolutionary rate pattern' (rERP), which records the relative evolutionary rates of conserved genes across the different branches of a species' phylogenetic tree, and the 'copy number pattern' (CNP), which quantifies the rate of gene loss of less conserved genes. Together, these measures yield a high-resolution study of the co-evolution of genes in 9 fungal species, spanning 3,540 sets of orthologs. We find that the evolutionary tempo of conserved genes varies in different evolutionary periods. The co-evolution of genes' Gene Ontology categories exhibits a significant correlation with their functional distance in the Gene Ontology hierarchy, but not with their location on chromosomes, showing that cellular functions are a more important driving force in gene co-evolution than their chromosomal proximity. Two fundamental patterns of co-evolution of conserved genes, cooperative and reciprocal, are identified; only genes co-evolving cooperatively functionally back each other up. The co-evolution of conserved and less conserved genes exhibits both commonalities and differences; DNA metabolism is positively correlated with nuclear traffic, transcription processes and vacuolar biology in both analyses. CONCLUSIONS Overall, this study charts the first global network view of gene co-evolution in fungi. The future application of the approach presented here to other phylogenetic trees holds much promise in characterizing the forces that shape cellular co-evolution.
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Affiliation(s)
- Tamir Tuller
- School of Computer Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
- School of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Martin Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Eytan Ruppin
- School of Computer Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
- School of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
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Schizonella caricis-atratae (Ustilaginomycetes): a new cryptic species on Carex atrata from Austria. Mycol Prog 2009. [DOI: 10.1007/s11557-009-0588-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Veerappan CS, Avramova Z, Moriyama EN. Evolution of SET-domain protein families in the unicellular and multicellular Ascomycota fungi. BMC Evol Biol 2008; 8:190. [PMID: 18593478 PMCID: PMC2474616 DOI: 10.1186/1471-2148-8-190] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2008] [Accepted: 07/01/2008] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The evolution of multicellularity is accompanied by the occurrence of differentiated tissues, of organismal developmental programs, and of mechanisms keeping the balance between proliferation and differentiation. Initially, the SET-domain proteins were associated exclusively with regulation of developmental genes in metazoa. However, finding of SET-domain genes in the unicellular yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that SET-domain proteins regulate a much broader variety of biological programs. Intuitively, it is expected that the numbers, types, and biochemical specificity of SET-domain proteins of multicellular versus unicellular forms would reflect the differences in their biology. However, comparisons across the unicellular and multicellular domains of life are complicated by the lack of knowledge of the ancestral SET-domain genes. Even within the crown group, different biological systems might use the epigenetic 'code' differently, adapting it to organism-specific needs. Simplifying the model, we undertook a systematic phylogenetic analysis of one monophyletic fungal group (Ascomycetes) containing unicellular yeasts, Saccharomycotina (hemiascomycetes), and a filamentous fungal group, Pezizomycotina (euascomycetes). RESULTS Systematic analysis of the SET-domain genes across an entire eukaryotic phylum has outlined clear distinctions in the SET-domain gene collections in the unicellular and in the multicellular (filamentous) relatives; diversification of SET-domain gene families has increased further with the expansion and elaboration of multicellularity in animal and plant systems. We found several ascomycota-specific SET-domain gene groups; each was unique to either Saccharomycotina or Pezizomycotina fungi. Our analysis revealed that the numbers and types of SET-domain genes in the Saccharomycotina did not reflect the habitats, pathogenicity, mechanisms of sexuality, or the ability to undergo morphogenic transformations. However, novel genes have appeared for functions associated with the transition to multicellularity. Descendents of most of the SET-domain gene families found in the filamentous fungi could be traced in the genomes of extant animals and plants, albeit as more complex structural forms. CONCLUSION SET-domain genes found in the filamentous species but absent from the unicellular sister group reflect two alternative evolutionary events: deletion from the yeast genomes or appearance of novel structures in filamentous fungal groups. There were no Ascomycota-specific SET-domain gene families (i.e., absent from animal and plant genomes); however, plants and animals share SET-domain gene subfamilies that do not exist in the fungi. Phylogenetic and gene-structure analyses defined several animal and plant SET-domain genes as sister groups while those of fungal origin were basal to them. Plants and animals also share SET-domain subfamilies that do not exist in fungi.
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Tsui CKM, Daniel HM, Robert V, Meyer W. Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses. FEMS Yeast Res 2008; 8:651-9. [PMID: 18248416 DOI: 10.1111/j.1567-1364.2007.00342.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Yeasts of the artificial genus Candida include plant endophytes, insect symbionts, and opportunistic human pathogens. Phylogenies based on rRNA gene and actin sequences confirmed that the genus is not monophyletic, and the relationships among Candida species and allied teleomorph genera are not clearly resolved. Protein-coding genes have been useful to resolve taxonomic positions among a broad range of fungi. Over 70 taxa of the genus Candida and its allied sexually reproducing genera were therefore selected, and their phylogenetic relationships were investigated using nuclear sequences of the largest subunit and second largest subunit of RNA polymerase II gene, actin, the second subunit of the mitochondrial cytochrome oxidase gene, and D1/D2 LSU rRNA gene. The DNA sequences were analysed by maximum parsimony and Bayesian inference, resulting in the recognition of six major phylogenetic groups (A-F). Group A contains six facultative pathogenic Candida species, which seem to have derived from nonpathogenic species, while Group B contains species of Clavispora, Metschnikowia, and Pichia guilliermondii. Species of Debaryomyces form an independent group C that is related to groups A and B. Pichia fermentans and other environmental species are concentrated in Group D. Group E, containing Pichia anomala, may be a sibling to group F, which is represented by the Saccharomyces species complex.
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Affiliation(s)
- Clement K M Tsui
- Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Hospital, Westmead Millennium Institute, Westmead, NSW, Australia
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Man O, Pilpel Y. Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species. Nat Genet 2007; 39:415-21. [PMID: 17277776 DOI: 10.1038/ng1967] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 01/03/2007] [Indexed: 11/08/2022]
Abstract
A major challenge in comparative genomics is to understand how phenotypic differences between species are encoded in their genomes. Phenotypic divergence may result from differential transcription of orthologous genes, yet less is known about the involvement of differential translation regulation in species phenotypic divergence. In order to assess translation effects on divergence, we analyzed approximately 2,800 orthologous genes in nine yeast genomes. For each gene in each species, we predicted translation efficiency, using a measure of the adaptation of its codons to the organism's tRNA pool. Mining this data set, we found hundreds of genes and gene modules with correlated patterns of translational efficiency across the species. One signal encompassed entire modules that are either needed for oxidative respiration or fermentation and are efficiently translated in aerobic or anaerobic species, respectively. In addition, the efficiency of translation of the mRNA splicing machinery strongly correlates with the number of introns in the various genomes. Altogether, we found extensive selection on synonymous codon usage that modulates translation according to gene function and organism phenotype. We conclude that, like factors such as transcription regulation, translation efficiency affects and is affected by the process of species divergence.
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Affiliation(s)
- Orna Man
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
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Dutilh BE, van Noort V, van der Heijden RTJM, Boekhout T, Snel B, Huynen MA. Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics 2007; 23:815-24. [PMID: 17237036 DOI: 10.1093/bioinformatics/btm015] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Phylogenomics integrates the vast amount of phylogenetic information contained in complete genome sequences, and is rapidly becoming the standard for reliably inferring species phylogenies. There are, however, fundamental differences between the ways in which phylogenomic approaches like gene content, superalignment, superdistance and supertree integrate the phylogenetic information from separate orthologous groups. Furthermore, they all depend on the method by which the orthologous groups are initially determined. Here, we systematically compare these four phylogenomic approaches, in parallel with three approaches for large-scale orthology determination: pairwise orthology, cluster orthology and tree-based orthology. RESULTS Including various phylogenetic methods, we apply a total of 54 fully automated phylogenomic procedures to the fungi, the eukaryotic clade with the largest number of sequenced genomes, for which we retrieved a golden standard phylogeny from the literature. Phylogenomic trees based on gene content show, relative to the other methods, a bias in the tree topology that parallels convergence in lifestyle among the species compared, indicating convergence in gene content. CONCLUSIONS Complete genomes are no guarantee for good or even consistent phylogenies. However, the large amounts of data in genomes enable us to carefully select the data most suitable for phylogenomic inference. In terms of performance, the superalignment approach, combined with restrictive orthology, is the most successful in recovering a fungal phylogeny that agrees with current taxonomic views, and allows us to obtain a high-resolution phylogeny. We provide solid support for what has grown to be a common practice in phylogenomics during its advance in recent years. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- B E Dutilh
- Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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Prillinger H, Lopandic K, Sugita T, Wuczkowski M. Asterotremella gen. nov. albida, an anamorphic tremelloid yeast isolated from the agarics Asterophora lycoperdoides and Asterophora parasitica. J GEN APPL MICROBIOL 2007; 53:167-75. [PMID: 17726297 DOI: 10.2323/jgam.53.167] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Using a genotypic approach (PCR-fingerprinting, DNA/DNA reassociation, partial sequences of the 26S rDNA gene, complete sequences of the 18S rDNA gene, and sequences of the internal transcribed spacers) five tremelloid yeast isolates from the agarics Asterophora lycoperdoides and A. parasitica were shown to be conspecific with Cryptococcus ramirezgomezianus. It was not possible to distinguish the yeast strains from A. lycoperdoides and A. parasitica using sequences from the intergenic spacer (IGS1). Phylogeny based on the 26S (D1/D2-domain), ITS1-5.8S-ITS2 and complete 18S rDNA demonstrated that C. ramirezgomezianus is closely related to several additional Cryptococcus species (C. humicola, C. longus, C. musci, C. pseudolongus) within the Trichosporonales. A new genus, Asterotremella, and a new family, Asterotremellaceae were introduced for Cryptococcus species clustering within the Trichosporonales having a ubiquinone Q-9. Cryptococcus ramirezgomezianus is a synonym of Asterotremella albida.
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Affiliation(s)
- Hansjörg Prillinger
- University of Natural Resources and Applied Life Sciences, Institute of Applied Microbiology (IAM), Austrian Center of Biological Resources and Applied Mycology (ACBR), Wien, Austria.
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Thrane U, Anderson B, Frisvad JC, Smedsgaard J. The exo-metabolome in filamentous fungi. TOPICS IN CURRENT GENETICS 2007. [DOI: 10.1007/4735_2007_0230] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Kuramae EE, Robert V, Snel B, Weiss M, Boekhout T. Phylogenomics reveal a robust fungal tree of life. FEMS Yeast Res 2006; 6:1213-20. [PMID: 17156018 DOI: 10.1111/j.1567-1364.2006.00119.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Our understanding of the tree of life (TOL) is still fragmentary. Until recently, molecular phylogeneticists have built trees based on ribosomal RNA sequences and selected protein sequences, which, however, usually suffered from lack of support for the deeper branches and inconsistencies probably due to limited subsampling of the entire genome. Now, phylogenetic hypotheses can be based on the analysis of full genomes. We used available complete genome data as well as the eukaryote orthologous group (KOG) proteins to reconstruct with confidence basal branches of the fungal TOL. Phylogenetic analysis of a core of 531 KOGs shared among 21 fungal genomes, three animal genomes and one plant genome showed a single tree with high support resulting from four different methods of phylogenetic reconstruction. The single tree that we inferred from our dataset showed excellent nodal support for each branch, suggesting that it reflects the true phylogenetic relationships of the species involved.
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Affiliation(s)
- Eiko E Kuramae
- Yeast Research, Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands.
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Kuramae EE, Robert V, Snel B, Boekhout T. Conflicting phylogenetic position of Schizosaccharomyces pombe. Genomics 2006; 88:387-93. [PMID: 16904286 DOI: 10.1016/j.ygeno.2006.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Revised: 07/04/2006] [Accepted: 07/06/2006] [Indexed: 11/26/2022]
Abstract
The phylogenetic position of the fission yeast Schizosaccharomyces pombe in the fungal Tree of Life is still controversial. Three alternative phylogenetic positions have been proposed in the literature, namely (1) a position basal to the Hemiascomycetes and Euascomycetes, (2) a position as a sister group to the Euascomycetes with the Hemiascomycetes as a basal branch, or (3) a sister group to the Hemiascomycetes with Euascomycetes as a basal branch. Here we compared 91 clusters of orthologous proteins containing a single orthologue that are shared by 19 eukaryote genomes. The major part of these 91 orthologues supports a phylogenetic position of S. pombe as a basal lineage among the Ascomycota, thus supporting the second proposition. Interestingly, part of the orthologous proteins supported a fourth, not yet described alternative, in which S. pombe is basal to both Basidiomycota and Ascomycota. Both topologies of phylogenetic trees are well supported. We believe that both reflect correctly the phylogenetic history of the species concerned. This apparent paradox may point to a heterogeneous nuclear genome of the fungi. Importantly, this needs to be taken in consideration for a correct understanding of the fungal Tree of Life.
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Affiliation(s)
- Eiko E Kuramae
- Centraalbureau voor Schimmelcultures, Comparative Genomics and Bioinformatics, Uppsalalaan 8, 3584 Utrecht, The Netherlands.
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Lopandic K, Molnár O, Suzuki M, Pinsker W, Prillinger H. Estimation of phylogenetic relationships within the Ascomycota on the basis of 18S rDNA sequences and chemotaxonomy. Mycol Prog 2005. [DOI: 10.1007/s11557-006-0124-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zámocký M, Hallberg M, Ludwig R, Divne C, Haltrich D. Ancestral gene fusion in cellobiose dehydrogenases reflects a specific evolution of GMC oxidoreductases in fungi. Gene 2004; 338:1-14. [PMID: 15302401 DOI: 10.1016/j.gene.2004.04.025] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2004] [Revised: 04/13/2004] [Accepted: 04/22/2004] [Indexed: 11/17/2022]
Abstract
Cellobiose dehydrogenases (CDHs) are extracellular hemoflavoenzymes that are thought to be involved in the degradation of two of the most abundant biopolymers in the biosphere, cellulose and lignin. To date, these enzymes, consisting of a cytochrome domain and a flavin domain, have been detected and sequenced exclusively in the kingdom of fungi. Independent phylogenetic analyses of two distinct domains of CDH genes reveal that they evolved in parallel as fused genes. Whereas the cytochrome domains are unique sequence motifs, the flavin domains clearly belong to the glucose-methanol-choline (GMC) oxidoreductase family--an evolution line of widespread flavoproteins extending from the Archae to higher eukaryotes. The most probable unrooted phylogenetic tree obtained from our analysis of 52 selected GMC members reveals five principal evolutionary branches: cellobiose dehydrogenase, cholesterol oxidase (COX), hydroxynitrile lyase, alcohol oxidase (AOX)/glucose oxidase (GOX)/choline dehydrogenase, and a branch of dehydrogenases with various specificities containing also an Archaeon open reading frame (ORF). Cellobiose dehydrogenases cluster with cholesterol oxidases and the clade of various specificities, whereas hydroxynitrile lyases are closely related to glucose oxidases, alcohol oxidases, and choline dehydrogenases. The results indicate that the evolutionary line from a primordial GMC flavoprotein to extant cellobiose dehydrogenases was augmented after an early acquisition of the cytochrome domain to form two distinct branches for basidiomycetes and ascomycetes. One ascomycetous evolutionary line of CDHs has acquired a carbohydrate-binding module (CBM) of type 1, the sequence of which is similar to that of corresponding domains in several glycosidases. This is the first attempt towards a comprehensive phylogenetic analysis of cellobiose dehydrogenases.
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Affiliation(s)
- Marcel Zámocký
- Division of Food Biotechnology, Department of Food Science and Technology, BOKU-University of Natural Resources and Applied Life Sciences Vienna, Muthgasse 18, A-1190 Wien, Austria.
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Phenotypic and genotypic identification and phylogenetic characterisation of Taphrina fungi on alder. Mycol Prog 2003. [DOI: 10.1007/s11557-006-0056-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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