AN ABSTRACT OF THE DISSERTATION OF C. Alisha Quandt for the degree of Doctor of Philosophy in Botany and Plant Pathology presented on July 17, 2014 Title: Systematic, Genomic, and Transcriptomic Analysis of Mycoparasitic Tolypocladium Species and their Elaphomyces Hosts. Abstract approved:________________________________________________________ Joseph W. Spatafora Fungi in the genus Tolypocladium are diverse in their host associations, but the predominant ecologies include parasites of the ectomycorrhizal genus Elaphomyces and pathogens of insects. The aim of this dissertation research is to examine the evolution of these fungi and their host associations. To accomplish this several lines of data collection, analyses and experimentation, including nomenclatural changes, genome sequencing, differential RNA expression, and metagenomic sequencing of a host sporocarp, were pursued in an integrated manner. The first chapter is an introduction to the study systems and a background of fungal genomics. Nomenclatural issues are addressed in family Ophiocordycipitaceae and Tolypocladium that were brought about by changes in the International Code of Nomenclature for algae, fungi, and plants, abolishing a system where a single fungal species could have different generic names at different parts of its life cycle. Proposals for names to be protected and suppressed are made for the family in addition to new combinations in Tolypocladium. The genome sequence of T. ophioglossoides reveals a great number of secondary metabolite genes and clusters, including three, large peptaibiotic genes. The evolution of these genes, which have only been identified in Tolypocladium and Trichoderma species, is different within these two genera. Phylogenomic analyses of Peptaibiotics reveal a pattern that is consistent with speciation in the genus Trichoderma, while peptaibiotic diversity within Tolypocladium is inferred to be the product of lineage sorting and is inconsistent with the organismal phylogeny of the genus. To determine which genes are involved in the mycoparasitic infection in Tolypocladium, in Chapter 4 an RNA-Seq study identifies differentially expressed genes when T. ophioglossoides is grown on media containing host and non-host tissues. A chitinase, several G-protein coupled receptors hypothesized to play a role in host recognition, an adhesin involved in cellular attachment, and several secondary metabolite genes were found to be differentially expressed on the Elaphomyces-media created for the study. With the addition of two more Tolypocladium genome sequences, the Elaphomyces-parastite T. capitatum and the cicada pathogen T. paradoxum, Chapter 5 explores the evolution of host-jumping within Tolypocladium using genome scale datasets. A large number of genes within Tolypocladium have undergone lineage sorting, as the diversification of the genus happened relatively quickly and is inferred to be the product of host-mediated speciation events. The Elaphomyces granulatus metagenome as sequenced from sporocarp tissue is the subject of Chapter 6. Like other ectomycorrhizal Ascomycota, E. granulatus is expanded in genome size, but has a reduction in CAZymes compared to its closest sequenced relatives. The E. granulatus sporocarp microbiome is taxonomically diverse but the most common community component is Bradyrhizobiaceae bacteria. Despite the large amount of sequence data, the microbiome shows signatures of functional reduction. This dissertation uses advances in systematics, genomics, and transcriptomics to add to the understanding of how Tolypocladium and Elaphomyces utilize specific sources of nutrition, and what gene repertoires may tell us about these organisms’ life histories. ©Copyright by C. Alisha Quandt July 17, 2014 All Rights Reserved Systematic, Genomic, and Transcriptomic Analysis of Mycoparasitic Tolypocladium Species and their Elaphomyces Hosts. by C. Alisha Quandt A DISSERTATION submitted to Oregon State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Presented July 17, 2014 Commencement June 2015 Doctor of Philosophy dissertation of C. Alisha Quandt presented on July 17, 2014 APPROVED: _____________________________________________________________________ Major Professor, representing Botany and Plant Pathology _____________________________________________________________________ Head of the Department of Botany and Plant Pathology _____________________________________________________________________ Dean of the Graduate School I understand that my dissertation will become part of the permanent collection of Oregon State University libraries. My signature below authorizes release of my dissertation to any reader upon request. _____________________________________________________________________ C. Alisha Quandt, Author ACKNOWLEDGEMENTS This thesis would not exist in its present form or maybe even at all without the guidance, advice, support, and encouragement of many people. Hopefully, I can accurately express my sincere appreciation to everyone who has been instrumental in this journey for me. I would like to thank the Department of Botany and Plant Pathology (BPP) for providing a welcoming and supportive community in which to grow as a doctoral student. Dianne Simpson, Blaine Baker, Katie Remiyac, and Carleen Nutt graciously assisted in all manner of logistical matters, and I truly appreciate the time that they put into their jobs and helping me, which resulted in my education running smoothly. Linda Ciuffetti, our department chair, is amazingly supportive of graduate students and their experience in the department, and I have seen this and appreciated it personally. Since moving to Corvallis, BPP grads have been an integral part of my support system, and many, past and present, will be close friends for the rest of my life. BPP has been an incredibly positive and supportive environment with people knowledgeable in almost every aspect of biology, and I consider myself lucky to have worked in such a wonderful environment with a great group of people. I want to thank Mark Desanko and Chris Sullivan of the Center for Genome Research and Biocomputing (CGRB) for all their help with sequencing and computational support throughout my dissertation. My mother and father have always encouraged me to take my education seriously and to work diligently toward my goals. They may not have always understood why I chose the path that I did, but they have supported me nonetheless. Back during my undergraduate degree, my sister, Jessica, was the first person to give me a mycology text book that I wanted, and she has always been supportive of my eccentric interests and inspiring to me in her pursuit of her own. My extended family has also been amazingly supportive, even though I saw them so rarely during this time working on my degree. So many friends in Corvallis and beyond have helped me and encouraged me throughout my Ph.D. There were housemates who made Corvallis a real ‘home’ for me, BPP-ers who helped me relax after hard days in the lab, softball teammates, rock climbing buddies, La Conga Challenge conspirators, and so many others I dare not try to list them all by name here, lest I forget someone. I want to thank all of my foreign collaborators for their hospitality when visiting their labs. In China, Professor Li and his group (including Mingjun) at Anhui Agricultural University planned several amazing collecting trips in different regions of the country, and it was there that I collected my first cordyceps s.l. (Ophiocordyceps nutans). In Korea, Gi-Ho Sung and his lab were so accommodating during my stay and collecting, and as a result I now have a younger Korean brother, fellow graduate student, Jun-Sang Oh. It was an honor to work for three months in the lab of Francis Martin at INRA in Nancy, France. Everyone was very helpful with the various aspects of my project, and Stéphan Uroz even tried to convince a bank manager to give me back my credit card that was eaten by an ATM machine, to no avail. The graduate students and other foreign researchers at INRA made my time in Nancy, away from home, really enjoyable and I appreciate their willingness to hang out with a ‘loud American.’ I want to thank my committee members, Aaron Liston, Carol Mallory-Smith, Chris Marshall, and Pat Muir for their encouragement and willingness to ask tough, interesting questions, and point out ways in which I can grow as a scientist. The lab of Joey Spatafora has been an amazing environment in which to become a mycologist. Former post-docs in the lab, including Conrad Schoch, Barbara Robbertse, Gi-Ho Sung, Mingjun Chen, and Kathryn Bushley, helped me in different capacities over the years. Mingjun and Gi-Ho were wonderful hosts to me when I visited their countries, and Barbara and Conrad were also gracious hosts to me on the other side of this country during a conference. Former graduate student Cedar Hesse really got me started in bioinformatics and is still a source of advice for dealing with fungal community data. Former graduate student/ former housemate/ climbing buddy, etc., Ryan Kepler has remained a close friend, a Cordyceps ally, field hand, and collaborator since leaving the lab. His willingness to share knowledge, databases, and literature with me at the beginning of my project gave me a headstart, and his feedback and edits on my NSF GRF proposal are not forgotten or unappreciated. Fellow graduate student Alija Mujic has always been there through long Illumina preps to beers at Bombs, and I am