OVARIAN TRANSCRIPTOMICS OF D. MELANOGASTER REVEAL CANDIDATE GENES UNDERLYING WOLBACHIA-ASSOCIATED PLASTIC RECOMBINATION by SOPHIA I FRANTZ A THESIS Presented to the Department of Biology and the Graduate School of the University of Oregon in partial fulfillment of the requirements for the degree of Master of Science June 2020 THESIS APPROVAL PAGE Student: Sophia I Frantz Title: Ovarian Transcriptomics of D. melanogaster Reveal Candidate Genes Underlying Wolbachia-Associated Plastic Recombination This thesis has been accepted and approved in partial fulfillment of the requirements for the Master of Science degree in the Department of Biology by: Dr. Nadia Singh Chairperson Dr. William Cresko Chairperson Dr. Peter Ralph Member and Kate Mondloch Interim Vice Provost and Dean of the Graduate School Original approval signatures are on file with the University of Oregon Graduate School. Degree awarded June 2020 ii © 2020 Sophia I Frantz iii THESIS ABSTRACT Sophia I Frantz Master of Science Department of Biology June 2020 Title: Ovarian Transcriptomics of D. melanogaster Reveal Candidate Genes Underlying Wolbachia-Associated Plastic Recombination Phenotypic plasticity is prevalent in nature, and its study facilitates understanding of how organisms acclimate to stressful environments. Recombination rate is plastic in a diversity of organisms and under a variety of stressful conditions. However, the recent finding that Wolbachia pipientis induces plastic recombination in Drosophila melanogaster deviates from previous patterns, because Wolbachia is not strictly considered a stressor to this host. We investigate the molecular mechanisms of Wolbachia-associated plastic recombination by comparing the ovarian transcriptomes of D. melanogaster infected and uninfected with Wolbachia. Our data suggest infection explains a small amount of transcriptional variation but specifically affects genes related to cell cycle, translation, and metabolism. We also find enrichment of cell division and recombination processes. Broadly, the transcriptomic changes identified in this study provide insight for the mechanisms of microbe-mediated plastic recombination, an important but poorly understood facet of host-microbe dynamics. This thesis includes previously unpublished, co-authored material. iv CURRICULUM VITAE NAME OF AUTHOR: SOPHIA I FRANTZ GRADUATE AND UNDERGRADUATE SCHOOLS ATTENDED: University of Oregon, Eugene OR Swarthmore College, Swarthmore PA PROFESSIONAL EXPERIENCE: Graduate Teaching Assistant, Department of Biology, University of Oregon, Eugene, OR, 2018-2020 Research Assistant, Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, 2017-2018 Research Assistant, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 2016-2017 v TABLE OF CONTENTS Chapter Page I. INTRODUCTION ................................................................................................ 1 II. OVARIAN TRANSCRIPTOMICS OF D. MELANOGASTER REVEAL CANDIDATE GENES UNDERLYING WOLBACHIA-ASSOCIATED PLASTIC RECOMBINATION .......................................................................... 3 Introduction ....................................................................................................... 3 Methods ............................................................................................................. 7 Results ............................................................................................................... 11 1 Wolbachia’s Influence on Global Transcription Differences is Variable while the Influence of Genotype is Consistent across Samples .............. 11 2 Wolbachia Infection Induces Differential Gene Expression ....................... 14 3 Differentially Expressed Genes are Randomly Distributed across the Genome ................................................................................ 14 4 Differentially Expressed Genes are Enriched in Cell Division Processes ... 16 Discussion ......................................................................................................... 17 III. CONCLUSIONS ............................................................................................... 25 APPENDICES A. SUPPLEMENTARY FIGURES ................................................................... 27 B. SUPPLEMENTARY TABLES ..................................................................... 28 REFERENCES CITED ........................................................................................... 53 vi LIST OF FIGURES Figure Page 1. Global ovarian transcriptome nMDS ordination ................................................. 12 2. Location of differentially expressed genes across the genome for each chromosome .............................................................................................. 15 vii LIST OF TABLES Table Page 1. Summary of perMANOVA test results .............................................................. 13 viii CHAPTER I INTRODUCTION Phenotypic plasticity, the phenomenon by which one genotype produces multiple phenotypes in response to different environmental conditions, contributes to phenotypic diversity and is pervasive across a wide variety of taxa (Bradshaw, 1965). Cases of phenotypic plasticity often involve morphological, behavioral or life history traits, but genetic recombination itself can also be plastic (Plough, 1917; Hussin et al., 2011; Stapley et al., 2017). Such plastic recombination has consequences for the genetic diversity of the next generation of a population. Although previous studies have documented many instances of stress-induced plastic recombination, the recent finding that the endosymbiont Wolbachia pipientis induces plastic recombination in its Drosophila melanogaster host deviates from these studies (Singh, 2019), since this microbe is not considered a stressor to D. melanogaster (Hoffman et al., 1998). Thus, the phenomenon of Wolbachia-induced plastic recombination lies at the intersection of fundamental questions of evolutionary biology, such as the role of phenotypic plasticity in evolution, the determinants of recombination rate variation, and the evolution of host- microbe symbioses. However, an understanding of this phenomenon and its implications for evolution requires an understanding of the molecular basis of Wolbachia-associated plastic recombination. In chapter II, I describe a co-authored study that serves as the initial step toward elucidating the molecular mechanism of Wolbachia-associated plastic recombination. Since recombination occurs in the ovaries and Wolbachia colonize the ovaries, we compared the ovarian transcriptomes of Wolbachia-infected and uninfected flies. We characterized the global ovarian transcriptome response and identify specific 1 genes that may mediate the interaction between Wolbachia and host recombination processes. I also discuss the implications of this study for understanding plastic recombination and host-microbe interactions. 2 CHAPTER II OVARIAN TRANSCRIPTOMICS OF D. MELANOGASTER REVEAL CANDIDATE GENES UNDERLYING WOLBACHIA-ASSOCIATED PLASTIC RECOMBINATION This chapter includes co-authored material. Dr. Nadia Singh designed the experiment and advised with analyses and manuscript preparation. Dr. William Cresko and Dr. Clayton Small advised with analyses and manuscript preparation. I performed all analyses and wrote the manuscript. Introduction Under a changing or stressful environment, populations may adapt over generations, and, more immediately, individuals in these populations may acclimate within a lifetime via phenotypic plasticity. Phenotypic plasticity is the phenomenon by which one genotype produces multiple phenotypes in response to different environmental conditions (Bradshaw, 1965). Phenotypic plasticity is pervasive in nature and includes well-studied examples such as seasonal color changes of Precis octavia butterflies (Brakefield, 2008) and predator-induced morphological changes in Daphnia (Brehm, 1909; Tollrian, 1995). Triggering conditions may be exogenous— such as temperature (Scheepens et al., 2018), or endogenous— such as microbial presence (Verbon & Liberman, 2016). Although many cases of phenotypic plasticity have involved morphological, behavioral or life history traits, genetic recombination itself can also be plastic (for review see (Modliszewski & Copenhaver, 2017; Stapley et al., 2017). Plastic recombination has been documented in diverse organisms and under a variety of environmental conditions, such as in yeast under osmotic stress (Gao et al., 2008), in 3 mice under social stress (Balyaev DK & Borodin PM, 1982), and in humans with increasing maternal age (Hussin et al., 2011). The mechanistic link between environmental stress and plastic recombination is largely unknown, though studies in yeast have identified known stress response genes that also regulate recombination rate at specific genomic locations (Gao et al., 2008; Kon et al., 1998). Plastic recombination is a major contributor to variation in recombination rate (Agrawal 2005), and its contribution to genetic diversity overall requires understanding of the conditions in which it manifests. The study of recombination in the genetic model organism Drosophila melanogaster led to key insights about conditions that trigger plastic recombination: recombination was altered in response to extreme temperature (Plough, 1917; Graubard 1932; Grell 1978), starvation (Neel, 1941), and age (Stern, 1926; Hayman and Parsons 1960). Recent work also supports the effect of