TAXONOMIC STUDIES AND THE EVOLUTION OF HABITAT PREFERENCE IN THE CYSTOBASIDIOMYCETES by Pedro Pablo Parra Giraldo A Dissertation Submitted to the Faculty of Purdue University In Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy Department of Botany & Plant Pathology West Lafayette, Indiana August 2019 2 THE PURDUE UNIVERSITY GRADUATE SCHOOL STATEMENT OF COMMITTEE APPROVAL Dr. Mary Catherine Aime, Chair Department of Botany and Plant Pathology Dr. Jin-Rong Xu Department of Botany and Plant Pathology Dr. Stephen Goodwin Department of Botany and Plant Pathology Dr. Michael Gribskov Department of Biological Sciences Approved by: Dr. Christopher J. Staiger Head of the Graduate Program 3 To my mother for her tenacity and faith. To my father for teaching me the value of honesty and humbleness To Juanita, Mariangel and Carolina for being my motivation to never give up To Rato for loving me and teaching me so much. For making out of me a better man 4 ACKNOWLEDGMENTS Thank you Dr. Aime for your support, for giving me a life lesson and showing me the path to follow. Thanks to the members of my academic committee: Dr. Xu, Dr. Gribskov and Dr. Goodwin for your guidance and suggestions. Thanks to Dr. Mengiste for being a great prelim chair. Special thanks to Dr. Goldsbrough and Dr. Staiger for your unrestricted support and your guidance. Thanks to you my dear friend Jorge for opening the doors of your house since day one. Thank you for your support, for your advice and encouragement, for always being willing to discuss and provide accurate and useful input. Thanks to all the Aime Lab, great current and past members (if I mention all of them it would be a whole chapter of this dissertation) for putting a piece of your knowledge and life into mine. Thank you, John Cavaletto, for showing me how a passionate teacher should look like, for your cooperation and guidance. Thank you, Katherine Rivera, for your support, for being such a good listener, for always being there, for your happiness and laughter. Thanks, Rapu for all the happy moments, for the amazing years, for your love. Thanks to Rodrigo Rodriguez, for always being available to listen to me, to my stories and for showing me a different way to understand life. Hansel, thank you for your advice and helping me keep on track. Thanks to Eliana, for the good moments. Thanks to Vanessa, best roommate ever. Thank you, Lisa, Pam, Stacey for being so helpful and nice. Thanks to Dr. Morris Levy and Maria Levy for trusting in me and being so supportive along these years. Thanks to Dr. Bernhard and Dr. Alonso for teaching me the love for Science. To my friends in Colombia, David, Jesus, German and Nodier. Thanks to Hector, I still remember those words. Thanks to all of my friends that I may forget to mention in this paragraph. I am thankful for having all of you in my life. 5 TABLE OF CONTENTS LIST OF TABLES .......................................................................................................................... 8 LIST OF FIGURES ........................................................................................................................ 9 ABSTRACT .................................................................................................................................. 12 A LITERATURE REVIEW OF THE CYSTOBASIDOMYCETES ................. 14 Naohidea .................................................................................................................. 15 Cystobasidium ......................................................................................................... 16 Occultifur ................................................................................................................ 17 Erythrobasidium ...................................................................................................... 17 Bannoa ..................................................................................................................... 18 Cyrenella ................................................................................................................. 19 Hasegawazyma ........................................................................................................ 19 Cyphobasidium ........................................................................................................ 19 Symmetrospora ........................................................................................................ 20 Buckleyzyma ........................................................................................................... 21 Sakaguchia .............................................................................................................. 21 Microsporomyces .................................................................................................... 22 Halobasidium .......................................................................................................... 22 NEW SPECIES OF BANNOA DESCRIBED FROM THE TROPICS AND THE FIRST REPORT OF THE GENUS IN SOUTH AMERICA ....................................................... 26 2.1 Abstract ........................................................................................................................... 26 2.2 Introduction .................................................................................................................... 26 2.3 Material and Methods ..................................................................................................... 28 Sample collection and storage ................................................................................. 28 Morphological characterization ............................................................................... 28 Physiological studies ............................................................................................... 28 DNA extraction, sequencing, and phylogenetic analyses ....................................... 29 Mating intercompatibility ........................................................................................ 30 2.4 Results ............................................................................................................................ 31 Phylogenetic analyses ............................................................................................. 31 6 Physiological tests ................................................................................................... 37 Mating intercompatibility experiments ................................................................... 41 2.5 Taxonomy ....................................................................................................................... 43 2.6 Discussion ....................................................................................................................... 47 NEW SPECIES IN THE CYSTOBASIDIOMYCETES .................................... 50 3.1 Buckleyzyma butyrosa and Sakaguchia warrensis: new species in the Buckleyzymales and Sakaguchiales ...................................................................................................................... 50 Abstract ................................................................................................................... 50 Introduction ............................................................................................................. 50 Material and Methods .............................................................................................. 53 3.1.3.1 Sample collection and storage .............................................................................. 53 3.1.3.2 Morphological and physiological studies ............................................................. 53 3.1.3.3 DNA extraction and phylogenetic studies ............................................................ 54 Results ..................................................................................................................... 55 3.1.4.1 Phylogenetic placement of collected strains ........................................................ 55 Taxonomy ................................................................................................................ 58 Discussion ............................................................................................................... 73 3.2 Halobasidium umbonatum sp. nov. and the first report of H. xiangyangense in North America ...................................................................................................................................... 74 Abstract ................................................................................................................... 74 Introduction ............................................................................................................. 75 Materials and Methods ............................................................................................ 76 3.2.3.1 Sample collection and storage .............................................................................. 76 3.2.3.2 Morphological and physiological studies ............................................................. 76 3.2.3.3 DNA extraction, sequencing and phylogenetic studies ........................................ 77 Results ..................................................................................................................... 78 3.2.4.1 Phylogenetic studies ............................................................................................