ABSTRACT LEWIS, MARY HUNT. Genetic Structure of Soil
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Distribution of Methionine Sulfoxide Reductases in Fungi and Conservation of the Free- 2 Methionine-R-Sulfoxide Reductase in Multicellular Eukaryotes
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.26.433065; this version posted February 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Distribution of methionine sulfoxide reductases in fungi and conservation of the free- 2 methionine-R-sulfoxide reductase in multicellular eukaryotes 3 4 Hayat Hage1, Marie-Noëlle Rosso1, Lionel Tarrago1,* 5 6 From: 1Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, 7 Marseille, France. 8 *Correspondence: Lionel Tarrago ([email protected]) 9 10 Running title: Methionine sulfoxide reductases in fungi 11 12 Keywords: fungi, genome, horizontal gene transfer, methionine sulfoxide, methionine sulfoxide 13 reductase, protein oxidation, thiol oxidoreductase. 14 15 Highlights: 16 • Free and protein-bound methionine can be oxidized into methionine sulfoxide (MetO). 17 • Methionine sulfoxide reductases (Msr) reduce MetO in most organisms. 18 • Sequence characterization and phylogenomics revealed strong conservation of Msr in fungi. 19 • fRMsr is widely conserved in unicellular and multicellular fungi. 20 • Some msr genes were acquired from bacteria via horizontal gene transfers. 21 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.26.433065; this version posted February 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. -
Paula Cristina Azevedo Rodrigues S L T I F U N O N R T O I S P T
Universidade do Minho Escola de Engenharia m o f r o f e Paula Cristina Azevedo Rodrigues s l t i f u n o n r t o i s p t e a c i h s i c n l e a d i g n i c r x a e o s t m d a l n f m o a o c m d l Mycobiota and aflatoxigenic profile of n o a t a e n a s t o Portuguese almonds and chestnuts from e i o t u i c g b u u o production to commercialisation t d c r o y o r M P p s e u g i r d o R o d e v e z A a n i t s i r C a l u a P 0 1 0 2 | o h n i M U November 2010 Universidade do Minho Escola de Engenharia Paula Cristina Azevedo Rodrigues Mycobiota and aflatoxigenic profile of Portuguese almonds and chestnuts from production to commercialisation Dissertation for PhD degree in Chemical and Biological Engineering Supervisors Professor Doutor Nelson Lima Doutor Armando Venâncio November 2010 The integral reproduction of this thesis or parts thereof is authorized only for research purposes provided a written declaration for permission of use Universidade do Minho, November 2010 Assinatura: THIS THESIS WAS PARTIALLY SUPPORTED BY FUNDAÇÃO PARA A CIÊNCIA E A TECNOLOGIA AND THE EUROPEAN SOCIAL FUND THROUGH THE GRANT REF . SFRH/BD/28332/2006, AND BY FUNDAÇÃO PARA A CIÊNCIA E A TECNOLOGIA AND POLYTECHNIC INSTITUTE OF BRAGANÇA THROUGH THE GRANT REF . -
Sequencing Abstracts Msa Annual Meeting Berkeley, California 7-11 August 2016
M S A 2 0 1 6 SEQUENCING ABSTRACTS MSA ANNUAL MEETING BERKELEY, CALIFORNIA 7-11 AUGUST 2016 MSA Special Addresses Presidential Address Kerry O’Donnell MSA President 2015–2016 Who do you love? Karling Lecture Arturo Casadevall Johns Hopkins Bloomberg School of Public Health Thoughts on virulence, melanin and the rise of mammals Workshops Nomenclature UNITE Student Workshop on Professional Development Abstracts for Symposia, Contributed formats for downloading and using locally or in a Talks, and Poster Sessions arranged by range of applications (e.g. QIIME, Mothur, SCATA). 4. Analysis tools - UNITE provides variety of analysis last name of primary author. Presenting tools including, for example, massBLASTer for author in *bold. blasting hundreds of sequences in one batch, ITSx for detecting and extracting ITS1 and ITS2 regions of ITS 1. UNITE - Unified system for the DNA based sequences from environmental communities, or fungal species linked to the classification ATOSH for assigning your unknown sequences to *Abarenkov, Kessy (1), Kõljalg, Urmas (1,2), SHs. 5. Custom search functions and unique views to Nilsson, R. Henrik (3), Taylor, Andy F. S. (4), fungal barcode sequences - these include extended Larsson, Karl-Hnerik (5), UNITE Community (6) search filters (e.g. source, locality, habitat, traits) for 1.Natural History Museum, University of Tartu, sequences and SHs, interactive maps and graphs, and Vanemuise 46, Tartu 51014; 2.Institute of Ecology views to the largest unidentified sequence clusters and Earth Sciences, University of Tartu, Lai 40, Tartu formed by sequences from multiple independent 51005, Estonia; 3.Department of Biological and ecological studies, and for which no metadata Environmental Sciences, University of Gothenburg, currently exists. -
Lists of Names in Aspergillus and Teleomorphs As Proposed by Pitt and Taylor, Mycologia, 106: 1051-1062, 2014 (Doi: 10.3852/14-0
Lists of names in Aspergillus and teleomorphs as proposed by Pitt and Taylor, Mycologia, 106: 1051-1062, 2014 (doi: 10.3852/14-060), based on retypification of Aspergillus with A. niger as type species John I. Pitt and John W. Taylor, CSIRO Food and Nutrition, North Ryde, NSW 2113, Australia and Dept of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA Preamble The lists below set out the nomenclature of Aspergillus and its teleomorphs as they would become on acceptance of a proposal published by Pitt and Taylor (2014) to change the type species of Aspergillus from A. glaucus to A. niger. The central points of the proposal by Pitt and Taylor (2014) are that retypification of Aspergillus on A. niger will make the classification of fungi with Aspergillus anamorphs: i) reflect the great phenotypic diversity in sexual morphology, physiology and ecology of the clades whose species have Aspergillus anamorphs; ii) respect the phylogenetic relationship of these clades to each other and to Penicillium; and iii) preserve the name Aspergillus for the clade that contains the greatest number of economically important species. Specifically, of the 11 teleomorph genera associated with Aspergillus anamorphs, the proposal of Pitt and Taylor (2014) maintains the three major teleomorph genera – Eurotium, Neosartorya and Emericella – together with Chaetosartorya, Hemicarpenteles, Sclerocleista and Warcupiella. Aspergillus is maintained for the important species used industrially and for manufacture of fermented foods, together with all species producing major mycotoxins. The teleomorph genera Fennellia, Petromyces, Neocarpenteles and Neopetromyces are synonymised with Aspergillus. The lists below are based on the List of “Names in Current Use” developed by Pitt and Samson (1993) and those listed in MycoBank (www.MycoBank.org), plus extensive scrutiny of papers publishing new species of Aspergillus and associated teleomorph genera as collected in Index of Fungi (1992-2104). -
Caractérisation De La Biodiversité Des Souches D'aspergillus De La Section
En vue de l'obtention du DOCTORAT DE L'UNIVERSITÉ DE TOULOUSE Délivré par : Institut National Polytechnique de Toulouse (Toulouse INP) Discipline ou spécialité : Pathologie, Toxicologie, Génétique et Nutrition Présentée et soutenue par : Mme JOYA MAKHLOUF le jeudi 11 juillet 2019 Titre : Caractérisation de la biodiversité des souches d'Aspergillus de la section Flavi isolées d'aliments commercialisés au Liban: approche moléculaire, métabolique et morphologique Ecole doctorale : Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingénieries (SEVAB) Unité de recherche : Toxicologie Alimentaire (ToxAlim) Directeur(s) de Thèse : M. JEAN-DENIS BAILLY M. MONZER HAMZE Rapporteurs : M. JEROME MOUNIER, UNIVERSITE DE BRETAGNE OCCIDENTALE Mme MIREILLE KALASSY AOUAD, UNIVERSITE ST JOSEPH DE BEYROUTH Membre(s) du jury : M. ZIAD DAOUD, UNIVERSITE DE BALAMAND, Président M. JEAN-DENIS BAILLY, ECOLE NATIONALE VETERINAIRE DE TOULOUSE, Membre M. MONZER HAMZE, UNIVERSITE LIBANAISE, Membre M. OLIVIER PUEL, INRA TOULOUSE, Membre TABLE DES MATIERES Liste des TABLEAUX ...................................................................................................... 5 Liste des FIGURES .............................................................................................. ……….6 Liste des ABRÉVIATIONS .............................................................................................. 7 INTRODUCTION ........................................................................................................... 9 Première Partie : DONNÉES BIBLIOGRAPHIQUES -
Agentes Comunes En Las Aspergilosis Humanas: Conceptos Prima
Bol. Micol. 2014; 29(2): 63-100 REVISIÓN Agentes comunes en las aspergilosis humanas: conceptos prima- rios en la diferenciación de sus complejos de especies (Common agent in human aspergillosis: primary concepts in their complex species differentiation) Eduardo Piontelli L. Universidad de Valparaíso, Escuela de Medicina. Cátedra de Micología Casilla 92 V Valparaíso <email: [email protected]> RESUMEN ABSTRACT Las especies del género Aspergillus P.Micheli ex Species of the genus Aspergillus P.Micheli ex Haller, Haller, son consideradas como importantes organismos in- are considered important members of the organisms of tegrantes de la microbiota en distintos tipos de suelos en mycrobiota in different tipes of soils in all latitudes. They todas las latitudes. Presentan grandes capacidades prsent large industrial fermentative capacity, are common fermentativas industriales, son agentes comunes en micro- agents in food microbiology, major biodeterioration agents biología de alimentos, grandes biodescomponedores junto with bacteria, contaminants in agricultural products, and a las bacterias, contaminantes de productos agrícolas y de important in human and animal health. The genus is importancia en salud humana y animal. El género se aso- associated with 9 or more teleomorphs, forming a cia a 9 o más teleomorfos, formando un clado monofilético monophyletic clade closely related to the genus Penicillium. estrechamente relacionado con el género Penicillium. De- Due to the high number of species, their taxonomic dynamic bido al elevado número de especies, su dinámica taxonómica and frequent changes in nomenclature have often complicated y sus frecuentes cambios en la nomenclatura, han compli- the researcher in any field of biology, especially when related cado a menudo al investigador en algún campo de la biolo- to industry or medicine. -
Phylogeny, Identification and Nomenclature of the Genus Aspergillus
available online at www.studiesinmycology.org STUDIES IN MYCOLOGY 78: 141–173. Phylogeny, identification and nomenclature of the genus Aspergillus R.A. Samson1*, C.M. Visagie1, J. Houbraken1, S.-B. Hong2, V. Hubka3, C.H.W. Klaassen4, G. Perrone5, K.A. Seifert6, A. Susca5, J.B. Tanney6, J. Varga7, S. Kocsube7, G. Szigeti7, T. Yaguchi8, and J.C. Frisvad9 1CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands; 2Korean Agricultural Culture Collection, National Academy of Agricultural Science, RDA, Suwon, South Korea; 3Department of Botany, Charles University in Prague, Prague, Czech Republic; 4Medical Microbiology & Infectious Diseases, C70 Canisius Wilhelmina Hospital, 532 SZ Nijmegen, The Netherlands; 5Institute of Sciences of Food Production National Research Council, 70126 Bari, Italy; 6Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture & Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; 7Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary; 8Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan; 9Department of Systems Biology, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark *Correspondence: R.A. Samson, [email protected] Abstract: Aspergillus comprises a diverse group of species based on morphological, physiological and phylogenetic characters, which significantly impact biotechnology, food production, indoor environments and human health. Aspergillus was traditionally associated with nine teleomorph genera, but phylogenetic data suggest that together with genera such as Polypaecilum, Phialosimplex, Dichotomomyces and Cristaspora, Aspergillus forms a monophyletic clade closely related to Penicillium. Changes in the International Code of Nomenclature for algae, fungi and plants resulted in the move to one name per species, meaning that a decision had to be made whether to keep Aspergillus as one big genus or to split it into several smaller genera. -
Two New Aflatoxin Producing Species, and an Overview of Aspergillus Section Flavi
Downloaded from orbit.dtu.dk on: Dec 18, 2017 Two new aflatoxin producing species, and an overview of Aspergillus section Flavi Varga, J.; Frisvad, Jens Christian; Samson, R. A. Published in: Studies in Mycology Link to article, DOI: 10.3114/sim.2011.69.05 Publication date: 2011 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Varga, J., Frisvad, J. C., & Samson, R. A. (2011). Two new aflatoxin producing species, and an overview of Aspergillus section Flavi. Studies in Mycology, 69(1), 57-80. DOI: 10.3114/sim.2011.69.05 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. available online at www.studiesinmycology.org StudieS in Mycology 69: 57–80. 2011. doi:10.3114/sim.2011.69.05 Two new aflatoxin producing species, and an overview of Aspergillus section Flavi J. Varga1,2*, J.C. -
Taxonomic Studies on the Genus Aspergillus
Studies in Mycology 69 (June 2011) Taxonomic studies on the genus Aspergillus Robert A. Samson, János Varga and Jens C. Frisvad CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands An institute of the Royal Netherlands Academy of Arts and Sciences Studies in Mycology The Studies in Mycology is an international journal which publishes systematic monographs of filamentous fungi and yeasts, and in rare occasions the proceedings of special meetings related to all fields of mycology, biotechnology, ecology, molecular biology, pathology and systematics. For instructions for authors see www.cbs.knaw.nl. ExEcutivE Editor Prof. dr dr hc Robert A. Samson, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands. E-mail: [email protected] Layout Editor Manon van den Hoeven-Verweij, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands. E-mail: [email protected] SciEntific EditorS Prof. dr Dominik Begerow, Lehrstuhl für Evolution und Biodiversität der Pflanzen, Ruhr-Universität Bochum, Universitätsstr. 150, Gebäude ND 44780, Bochum, Germany. E-mail: [email protected] Prof. dr Uwe Braun, Martin-Luther-Universität, Institut für Biologie, Geobotanik und Botanischer Garten, Herbarium, Neuwerk 21, D-06099 Halle, Germany. E-mail: [email protected] Dr Paul Cannon, CABI and Royal Botanic Gardens, Kew, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, U.K. E-mail: [email protected] Prof. dr Lori Carris, Associate Professor, Department of Plant Pathology, Washington State University, Pullman, WA 99164-6340, U.S.A. E-mail: [email protected] Prof. -
Ncomms2850.Pdf
ARTICLE Received 8 Nov 2012 | Accepted 8 Apr 2013 | Published 7 May 2013 DOI: 10.1038/ncomms2850 Characterization of salt-adapted secreted lignocellulolytic enzymes from the mangrove fungus Pestalotiopsis sp. Yonathan Arfi1, Didier Chevret2, Bernard Henrissat3, Jean-Guy Berrin1, Anthony Levasseur1 & Eric Record1 Fungi are important for biomass degradation processes in mangrove forests. Given the pre- sence of sea water in these ecosystems, mangrove fungi are adapted to high salinity. Here we isolate Pestalotiopsis sp. NCi6, a halotolerant and lignocellulolytic mangrove fungus of the order Xylariales. We study its lignocellulolytic enzymes and analyse the effects of salinity on its secretomes. De novo transcriptome sequencing and assembly indicate that this fungus possesses of over 400 putative lignocellulolytic enzymes, including a large fraction involved in lignin degradation. Proteomic analyses of the secretomes suggest that the presence of salt modifies lignocellulolytic enzyme composition, with an increase in the secretion of xylanases and cellulases and a decrease in the production of oxidases. As a result, cellulose and hemicellulose hydrolysis is enhanced but lignin breakdown is reduced. This study highlights the adaptation to salt of mangrove fungi and their potential for biotechnological applications. 1 INRA, UMR1163—Biotechnologie des Champignons Filamenteux, ESIL-Polytech, Aix-Marseille University, 13288 Marseille, France. 2 INRA, UMR1319 Micalis, Plateforme d’Analyse Prote´omique de Paris Sud-Ouest, 78352 Jouy-en-Josas, France. 3 CNRS, UMR6098 Architecture et Fonction des Macromole´cules Biologiques, 13288 Marseille, France. Correspondence and requests for materials should be addressed to Y.A. (email: yonathan.arfi@gmail.com). NATURE COMMUNICATIONS | 4:1810 | DOI: 10.1038/ncomms2850 | www.nature.com/naturecommunications 1 & 2013 Macmillan Publishers Limited. -
Classification of Aspergillus, Penicillium
available online at www.studiesinmycology.org STUDIES IN MYCOLOGY 95: 5–169 (2020). Classification of Aspergillus, Penicillium, Talaromyces and related genera (Eurotiales): An overview of families, genera, subgenera, sections, series and species J. Houbraken1*, S. Kocsube2, C.M. Visagie3, N. Yilmaz3, X.-C. Wang1,4, M. Meijer1, B. Kraak1, V. Hubka5, K. Bensch1, R.A. Samson1, and J.C. Frisvad6* 1Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; 2Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary; 3Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Hatfield, Pretoria, 0028, South Africa; 4State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3, 1st Beichen West Road, Chaoyang District, Beijing, 100101, China; 5Department of Botany, Charles University in Prague, Prague, Czech Republic; 6Department of Biotechnology and Biomedicine Technical University of Denmark, Søltofts Plads, B. 221, Kongens Lyngby, DK 2800, Denmark *Correspondence: J. Houbraken, [email protected]; J.C. Frisvad, [email protected] Abstract: The Eurotiales is a relatively large order of Ascomycetes with members frequently having positive and negative impact on human activities. Species within this order gain attention from various research fields such as food, indoor and medical mycology and biotechnology. In this article we give an overview of families and genera present in the Eurotiales and introduce an updated subgeneric, sectional and series classification for Aspergillus and Penicillium. Finally, a comprehensive list of accepted species in the Eurotiales is given. The classification of the Eurotiales at family and genus level is traditionally based on phenotypic characters, and this classification has since been challenged using sequence-based approaches. -
A Comparative Genomics Study of 23 Aspergillus Species from Section Flavi
ARTICLE https://doi.org/10.1038/s41467-019-14051-y OPEN A comparative genomics study of 23 Aspergillus species from section Flavi Inge Kjærbølling1, Tammi Vesth1, Jens C. Frisvad 1, Jane L. Nybo1, Sebastian Theobald1, Sara Kildgaard1, Thomas Isbrandt Petersen1, Alan Kuo2, Atsushi Sato3, Ellen K. Lyhne1, Martin E. Kogle1, Ad Wiebenga4, Roland S. Kun4, Ronnie J.M. Lubbers4, Miia R. Mäkelä 5, Kerrie Barry2, Mansi Chovatia2, Alicia Clum2, Chris Daum2, Sajeet Haridas 2, Guifen He2, Kurt LaButti 2, Anna Lipzen2, Stephen Mondo2, Jasmyn Pangilinan2, Robert Riley2, Asaf Salamov2, Blake A. Simmons 6, Jon K. Magnuson 6, Bernard Henrissat7, Uffe H. Mortensen 1, Thomas O. Larsen 1, Ronald P. de Vries 4, Igor V. Grigoriev 2,8, 9 6,10 1 1234567890():,; Masayuki Machida , Scott E. Baker & Mikael R. Andersen * Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clus- ters (73 per species) in section Flavi. However, the observed phenotypes (growth char- acteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi.