Identification and Phylogeny of Ascomycetous Yeasts from Analysis
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Final 130607
Jury: Prof. dr. ir. Walter Steurbaut (chairman) Prof. dr. ir. Erick Vandamme (promotor) Prof. dr. ir. Wim Soetaert (promotor) Prof. dr. ir. Nico Boon Prof. dr. ir. Monica Höfte Prof. dr. Els Van Damme Dr. Roel Bovenberg Dr. Thierry Dauvrin Promotors: Prof. dr. ir. Erick VANDAMME Prof. dr. ir. Wim SOETAERT Laboratory of Industrial Microbiology and Biocatalysis Department of Biochemical and Microbial Technology Ghent University Dean: Prof. dr. ir. Herman VAN LANGENHOVE Rector: Prof. dr. Paul VAN CAUWENBERGE S. De Maeseneire was supported by a fellowship of the Flemish Institute for the Promotion of Scientific and Technological Research in the Industry (IWT-Vlaanderen). The research was conducted at the Laboratory of Industrial Microbiology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University. ir. Sofie De Maeseneire MYROTHECIUM GRAMINEUM AS A NOVEL FUNGAL EXPRESSION HOST Thesis submitted in fulfilment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences Cell and Gene Biotechnology Titel van het doctoraatsproefschrift in het Nederlands: Myrothecium gramineum als een nieuwe fungale expressie-gastheer Cover illustration: ‘ Myrothecium gramineum’ by Sofie De Maeseneire (June 2007) To refer to this thesis: De Maeseneire, S. L. (2007) Myrothecium gramineum as a novel fungal expression host. PhD-thesis, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium, 308 p. ISBN-number: 978-90-5989-176-0 The author and the promotors give the authorisation to consult and to copy parts of this work for personal use only. Every other use is subject to copy right laws. Permission to reproduce any material contained in this work should be obtained from the author. -
Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)
| YEASTBOOK GENOME ORGANIZATION AND INTEGRITY Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina) Bernard A. Dujon*,†,1 and Edward J. Louis‡,§ *Department Genomes and Genetics, Institut Pasteur, Centre National de la Recherche Scientifique UMR3525, 75724-CEDEX15 Paris, France, †University Pierre and Marie Curie UFR927, 75005 Paris, France, ‡Centre for Genetic Architecture of Complex Traits, and xDepartment of Genetics, University of Leicester, LE1 7RH, United Kingdom ORCID ID: 0000-0003-1157-3608 (E.J.L.) ABSTRACT Considerable progress in our understanding of yeast genomes and their evolution has been made over the last decade with the sequencing, analysis, and comparisons of numerous species, strains, or isolates of diverse origins. The role played by yeasts in natural environments as well as in artificial manufactures, combined with the importance of some species as model experimental systems sustained this effort. At the same time, their enormous evolutionary diversity (there are yeast species in every subphylum of Dikarya) sparked curiosity but necessitated further efforts to obtain appropriate reference genomes. Today, yeast genomes have been very informative about basic mechanisms of evolution, speciation, hybridization, domestication, as well as about the molecular machineries underlying them. They are also irreplaceable to investigate in detail the complex relationship between genotypes and phenotypes with both theoretical and practical implications. This review examines these questions at two distinct levels offered by the broad evolutionary range of yeasts: inside the best-studied Saccharomyces species complex, and across the entire and diversified subphylum of Saccharomycotina. While obviously revealing evolutionary histories at different scales, data converge to a remarkably coherent picture in which one can estimate the relative importance of intrinsic genome dynamics, including gene birth and loss, vs. -
A Newsletter for Persons Interested in Yeast
ISSN 0513-5222 A Newsletter for Persons Interested in Yeast Official Publication of the International Commission on Yeasts of the International Union of Microbiological Societies (IUMS) JUNE 2010 Volume LIX, Number I Marc-André Lachance, Editor University of Western Ontario, London, Ontario, Canada N6A 5B7 <[email protected]> http://publish.uwo.ca/~lachance/YeastNewsletter.html Associate Editors Peter Biely Patrizia Romano Kyria Boundy-Mills Institute of Chemistry Dipartimento di Biologia, Difesa Herman J. Phaff Culture Slovak Academy of e Biotecnologie Agro-Forestali Collection Sciences Università della Basilicata, Department of Food Science and Dúbravská cesta 9, 842 3 Via Nazario Sauro, 85, 85100 Potenza, Technology 8 Bratislava, Slovakia Italy University of California Davis Davis California 95616-5224 F Hagen, Utrecht, The Netherlands . 19 HV Amorim, Pracicaba, Sao Paulo, Brazil . 29 JA Barnett, Norwich, United Kingdom . 20 D Begerow and A Yurkov, Bochum, Germany 29 CA Rosa, Belo Horizonte, D Kregiel, Lodz, Poland ................. 30 Minas Gerais, Brazil .............. 20 M Kopecká, Brno, Czech Republic . 32 WI Golubev, Puschino, Russia . 21 D Libkind, Bariloche, Argentina . 33 GI Naumov and E.S. Naumova, G. Miloshev, Sofia, Bulgaria . 33 Moscow, Russia .................. 22 JP Tamang, Tadong, India . 35 A Bakalinsky, Corvalis, Oregon, USA . 23 MA Lachance, London, Ontario, Canada . 35 H Lee, Guelph, Ontario, Canada . 24 Á Fonseca and JP Sampaio, WM Ingledew, Parksville, Capa Rica, Portugal ............... 36 British Columbia, Canada . 25 Recent Meeting ........................ 38 M Sipiczki, Debrecen, Hungary . 26 Forthcoming Meeting .................... 42 A Speers, Halifax, Nova Scotia, Canada . 27 Publications of interest ................... 43 SO Suh, Manassas, Virgina, USA . 27 Fifty Years Ago ........................ 47 P Venkov, Cherni vrah, Bulgaria . -
Présentée Par : Melle BELHOUCINE Latifa Les Champignons Associés Au Platypus Cylindrus Fab. (Coleoptera, Curculionidae, Platy
République Algérienne Démocratique Et Populaire Ministère de l’Enseignement Supérieure et de La Recherche Scientifique Université Abou Bakr Belkaid Tlemcen Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre et de l’Univers Département Des Sciences d’Agronomie et des Forêts Présentée par : Melle BELHOUCINE Latifa En vue de l’obtention du diplôme de Doctorat en Sciences Forestières Les champignons associés au Platypus cylindrus Fab. (Coleoptera, Curculionidae, Platypodinae) dans un jeune peuplement de chêne-liège de la forêt de M’Sila (Oran, nord-ouest d’Algérie) : Etude particulière de la biologie et l’épidémiologie de l’insecte Devant le jury composé de: Président : Pr. Letreuch- Belarouci N. Université de Tlemcen Directeur de thèse : Pr. Bouhraoua T.R. Université de Tlemcen Co- Directeur de thèse : Pr. Pujade i-Villar J. Université de Barcelone - Espagne Examinateur : Pr. Chakali G. Université INA Alger Examinateur : Pr. Bellahcene M. Université de Mostaganem Examinateur : Pr. Abdelwahid D. Université de Tlemcen Année 2012-2013 Que ce travail soit un témoignage de ma grande affection pour : - Mon très cher père ; - Ma défunte mère ; - Mes sœurs ; - Mes frères ; - Mes nièces et neveux ; - Mes belles sœurs et beaux frères ; - Mes amis. “It’s the journey that’s important, not the getting there” (John McLeod). L'écriture de cette thèse a été un voyage fascinant plein d'expériences inoubliables. La rédaction d'une thèse est un long voyage, et évidemment pas possible sans le soutien de nombreuses personnes. J'ai été vraiment privilégiée pour commencer mon voyage dans le monde de la science avec de nombreuses personnes inspirantes. -
Oenological Impact of the Hanseniaspora/Kloeckera Yeast Genus on Wines—A Review
fermentation Review Oenological Impact of the Hanseniaspora/Kloeckera Yeast Genus on Wines—A Review Valentina Martin, Maria Jose Valera , Karina Medina, Eduardo Boido and Francisco Carrau * Enology and Fermentation Biotechnology Area, Food Science and Technology Department, Facultad de Quimica, Universidad de la Republica, Montevideo 11800, Uruguay; [email protected] (V.M.); [email protected] (M.J.V.); [email protected] (K.M.); [email protected] (E.B.) * Correspondence: [email protected]; Tel.: +598-292-481-94 Received: 7 August 2018; Accepted: 5 September 2018; Published: 10 September 2018 Abstract: Apiculate yeasts of the genus Hanseniaspora/Kloeckera are the main species present on mature grapes and play a significant role at the beginning of fermentation, producing enzymes and aroma compounds that expand the diversity of wine color and flavor. Ten species of the genus Hanseniaspora have been recovered from grapes and are associated in two groups: H. valbyensis, H. guilliermondii, H. uvarum, H. opuntiae, H. thailandica, H. meyeri, and H. clermontiae; and H. vineae, H. osmophila, and H. occidentalis. This review focuses on the application of some strains belonging to this genus in co-fermentation with Saccharomyces cerevisiae that demonstrates their positive contribution to winemaking. Some consistent results have shown more intense flavors and complex, full-bodied wines, compared with wines produced by the use of S. cerevisiae alone. Recent genetic and physiologic studies have improved the knowledge of the Hanseniaspora/Kloeckera species. Significant increases in acetyl esters, benzenoids, and sesquiterpene flavor compounds, and relative decreases in alcohols and acids have been reported, due to different fermentation pathways compared to conventional wine yeasts. -
Phylogenetic Circumscription of Saccharomyces, Kluyveromyces
FEMS Yeast Research 4 (2003) 233^245 www.fems-microbiology.org Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora Cletus P. Kurtzman à Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University Street, Peoria, IL 61604, USA Received 22 April 2003; received in revised form 23 June 2003; accepted 25 June 2003 First published online Abstract Genera currently assigned to the Saccharomycetaceae have been defined from phenotype, but this classification does not fully correspond with species groupings determined from phylogenetic analysis of gene sequences. The multigene sequence analysis of Kurtzman and Robnett [FEMS Yeast Res. 3 (2003) 417^432] resolved the family Saccharomycetaceae into 11 well-supported clades. In the present study, the taxonomy of the Saccharomyctaceae is evaluated from the perspective of the multigene sequence analysis, which has resulted in reassignment of some species among currently accepted genera, and the proposal of the following five new genera: Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. ß 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved. Keywords: Saccharomyces; Kluyveromyces; New ascosporic yeast genera; Molecular systematics; Multigene phylogeny 1. Introduction support the maintenance of three distinct genera. Yarrow [8^10] revived the concept of three genera and separated The name Saccharomyces was proposed for bread and Torulaspora and Zygosaccharomyces from Saccharomyces, beer yeasts by Meyen in 1838 [1], but it was Reess in 1870 although species assignments were often di⁄cult. -
Use of Conventional Taxonomy, Electrophoretic Karyotyping and DNA–DNA Hybridization for the Classification of Fermentative Apiculate Yeasts
International Journal of Systematic and Evolutionary Microbiology (2000), 50, 1665–1672 Printed in Great Britain Use of conventional taxonomy, electrophoretic karyotyping and DNA–DNA hybridization for the classification of fermentative apiculate yeasts Ann Vaughan-Martini, Paola Angelini and Gianluigi Cardinali Author for correspondence: Ann Vaughan-Martini. Tel: j39 075 585 6479. Fax: j39 075 585 6470. e-mail: avaughan!unipg.it Industrial Yeasts Collection A taxonomic study was conducted that considered strains of the genera (DBVPG), Dipartimento di Hanseniaspora/Kloeckera held in the Industrial Yeasts Collection (DBVPG) of Biologia Vegetale, ' Universita' di Perugia, Sez. the Dipartimento di Biologia Vegetale of the Universita di Perugia, Italy. Microbiologia Applicata, Standard phenotypic as well as molecular criteria were considered in a effort Borgo XX Giugno 74, to revisit the classification of these strains, some of which have been in the 06121 Perugia, Italy collection for about 50 years. Results of salient physiological tests showed that some of the DBVPG and type strains could not be identified by current taxonomic keys. Electrophoretic karyotypes were identical for some species, with the type strains of the seven accepted species showing only five distinct chromosomal patterns. DNA–DNA hybridization analyses, using a non- radioactive dot-blot technique, allowed for the distinction of taxa. The taxonomic implications of these results are discussed. Keywords: Hanseniaspora, conventional and molecular taxonomy, non-radioactive dot-blot DNA reassociation, pulsed-field gel electrophoresis INTRODUCTION confirm sporulation in some strains of Hansenia and therefore assigned it to an anamorphic taxon of The genus Hanseniaspora was created when Klo$ cker fermenting, apiculate yeasts. He then proposed the (1912) described the species Hanseniaspora valbyensis, generic name Hanseniaspora for the perfect taxa. -
Oxylipin Distribution in Eremothecium
1 Oxylipin distribution in Eremothecium by Ntsoaki Joyce Leeuw Submitted in accordance with the requirements for the degree Magister Scientiae in the Department of Microbial, Biochemical and Food Biotechnology Faculty of Natural and Agricultural Sciences University of the Free State Bloemfontein South Africa Supervisor: Prof J.L.F. Kock Co- supervisors: Dr C.H. Pohl Prof P.W.J. Van Wyk November 2006 2 This dissertation is dedicated to the following people: My mother (Nkotseng Leeuw) My brother (Kabelo Leeuw) My cousins (Bafokeng, Lebohang, Mami, Thabang and Rorisang) Mr. Eugean Malebo 3 ACKNOWLEDGEMENTS I wish to thank and acknowledge the following: ) God, to You be the glory for the things You have done in my life. ) My family (especially my mom) – for always being there for me when I’m in need. ) Prof. J.L.F Kock for his patience, constructive criticisms and guidance during the course of this study. ) Dr. C.H. Pohl for her encouragement and assistance in the writing up of this dissertation. ) Mr. P.J. Botes for assistance with the GC-MS. ) Prof. P.W.J. Van Wyk and Miss B. Janecke for assistance with the CLSM and SEM. ) My fellow colleagues (especially Chantel and Desmond) for their assistance, support and encouragement. ) Mr. Eugean Malebo for always being there when I needed you. 4 CONTENTS Page Title page I Acknowledgements II Contents III CHAPTER 1 Introduction 1.1 Motivation 2 1.2 Definition and classification of yeasts 3 1.3 Classification of Eremothecium and related genera 5 1.4 Pathogenicity 12 1.5 Oxylipins 13 1.5.1 Definition -
Title Melon Aroma-Producing Yeast Isolated from Coastal
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Kyoto University Research Information Repository Melon aroma-producing yeast isolated from coastal marine Title sediment in Maizuru Bay, Japan Sutani, Akitoshi; Ueno, Masahiro; Nakagawa, Satoshi; Author(s) Sawayama, Shigeki Citation Fisheries Science (2015), 81(5): 929-936 Issue Date 2015-09 URL http://hdl.handle.net/2433/202563 The final publication is available at Springer via http://dx.doi.org/10.1007/s12562-015-0912-5.; The full-text file will be made open to the public on 28 July 2016 in Right accordance with publisher's 'Terms and Conditions for Self- Archiving'.; This is not the published version. Please cite only the published version. この論文は出版社版でありません。 引用の際には出版社版をご確認ご利用ください。 Type Journal Article Textversion author Kyoto University 1 FISHERIES SCIENCE ORIGINAL ARTICLE 2 Topic: Environment 3 Running head: Marine fungus isolation 4 5 Melon aroma-producing yeast isolated from coastal marine sediment in Maizuru Bay, 6 Japan 7 8 Akitoshi Sutani1 · Masahiro Ueno2 · Satoshi Nakagawa1· Shigeki Sawayama1 9 10 11 12 __________________________________________________ 13 (Mail) Shigeki Sawayama 14 [email protected] 15 16 1 Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, 17 Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan 18 2 Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto 19 University, Kyoto 625-0086, Japan 1 20 Abstract Researches on marine fungi and fungi isolated from marine environments are not 21 active compared with those on terrestrial fungi. The aim of this study was isolation of novel 22 and industrially applicable fungi derived from marine environments. -
1 Extensive Loss of Cell Cycle and DNA Repair Genes in an Ancient Lineage of Bipolar Budding
bioRxiv preprint doi: https://doi.org/10.1101/546366; this version posted February 11, 2019. 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 4.0 International license. 1 Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding 2 yeasts 3 4 Jacob L. Steenwyk1, Dana A. Opulente2, Jacek Kominek2, Xing-Xing Shen1, Xiaofan Zhou3, 5 Abigail L. Labella1, Noah P. Bradley1, Brandt F. Eichman1, Neža Čadež5, Diego Libkind6, 6 Jeremy DeVirgilio7, Amanda Beth Hulfachor4, Cletus P. Kurtzman7, Chris Todd Hittinger2*, and 7 Antonis Rokas1* 8 9 1. Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA 10 2. Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research 11 Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of 12 Wisconsin–Madison, Wisconsin 53706, USA 13 3. Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative 14 Microbiology Research Centre, South China Agricultural University, 510642 Guangzhou, China 15 4. Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow 16 Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, 17 USA 18 5. University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, 19 Jamnikarjeva 101, 1000 Ljubljana, Slovenia 20 6. Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática, Instituto Andino 21 Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del 22 Comahue - CONICET, San Carlos de Bariloche, 8400, Río Negro, Argentina 1 bioRxiv preprint doi: https://doi.org/10.1101/546366; this version posted February 11, 2019. -
Fungi Associated with Ips Acuminatus (Coleoptera: Curculionidae) in Ukraine with a Special Emphasis on Pathogenicity of Ophiostomatoid Species
EUROPEAN JOURNAL OF ENTOMOLOGYENTOMOLOGY ISSN (online): 1802-8829 Eur. J. Entomol. 114: 77–85, 2017 http://www.eje.cz doi: 10.14411/eje.2017.011 ORIGINAL ARTICLE Fungi associated with Ips acuminatus (Coleoptera: Curculionidae) in Ukraine with a special emphasis on pathogenicity of ophiostomatoid species KATERYNA DAVYDENKO 1, 2, RIMVYDAS VASAITIS 2 and AUDRIUS MENKIS 2 1 Ukrainian Research Institute of Forestry & Forest Melioration, Pushkinska st. 86, 61024 Kharkiv, Ukraine; e-mail: [email protected] 2 Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007, Uppsala, Sweden; e-mails: [email protected], [email protected] Key words. Coleoptera, Curculionidae, pine engraver beetle, Scots pine, Ips acuminatus, pathogens, Ophiostoma, Diplodia pinea, insect-fungus interaction Abstract. Conifer bark beetles are well known to be associated with fungal complexes, which consist of pathogenic ophiostoma- toid fungi as well as obligate saprotroph species. However, there is little information on fungi associated with Ips acuminatus in central and eastern Europe. The aim of the study was to investigate the composition of the fungal communities associated with the pine engraver beetle, I. acuminatus, in the forest-steppe zone in Ukraine and to evaluate the pathogenicity of six associated ophiostomatoid species by inoculating three-year-old Scots pine seedlings with these fungi. In total, 384 adult beetles were col- lected from under the bark of declining and dead Scots pine trees at two different sites. Fungal culturing from 192 beetles resulted in 447 cultures and direct sequencing of ITS rRNA from 192 beetles in 496 high-quality sequences. -
Comparative Genomics of Biotechnologically Important Yeasts Supplementary Appendix
Comparative genomics of biotechnologically important yeasts Supplementary Appendix Contents Note 1 – Summary of literature on ascomycete yeasts used in this study ............................... 3 CUG-Ser yeasts ................................................................................................................................................................ 3 Other Saccharomycotina ............................................................................................................................................. 5 Taphrinomycotina ....................................................................................................................................................... 10 Note 2 – Genomes overview .................................................................................................11 Yeast culturing, identification, DNA and total RNA extraction ................................................................. 12 Genome sequencing and assembly ....................................................................................................................... 12 Transcriptome sequencing and assembly ......................................................................................................... 13 Table S1. Genome statistics ..................................................................................................................................... 14 Table S2. Annotation statistics ..............................................................................................................................