Doctor of Philosophy, The Ohio State University, 2018, Evolution, Ecology and Organismal Biology

Most broadly, this study aimed to develop a better understanding of how organisms evolve novel functions and traits, and examine how seemingly complex adaptive trait syndromes can convergently evolve. As an ideal example of this, the carnivorous plants were chosen. This polyphyletic grouping contains taxa derived from multiple independent evolutionary origins, in at least five plant orders, and has resulted in striking convergence of niche and morphology. First, a database study was performed, with the goal of understanding the evolutionary trends that impact carnivorous plants as a whole. Using carnivorous and non-carnivorous plant genomes available from GenBank. An a priori list of Gene Ontology-coded functions implicated in plant carnivory by earlier studies was constructed via literature review. Experimental and control samples were tested for statistical overrepresentation of these functions. It was found that, while some functions were significant in some taxa, there was no overall shared signal of plant carnivory, with each taxon presumably having selected for a different subset of these functions. Next, analyses were performed that targeted Sarracenia alata specifically. A reference genome for S. alata was assembled using PacBio, Illumina, and BioNano data and annotated using MAKER-P with additional preliminary database filtration. From these, it was found that Sarracenia alata possesses significant and substantial overrepresentation of genes with functions associated with plant carnivory, at odds with the hypothesis that the plant primarily relies on symbioses. Finally, pitcher fluid was collected from S. alata in the field. RNA was extracted from the fluid, sequenced via Illumina, and assembled with Trinity. Sequences were sorted into host plant and microbiome based on BLAST match to the S. alata reference genome. It was found that, while S. alata contributes two-thirds of the transcripts, these encode no digestive enzymes and a very limited set o (open full item for complete abstract)

Committee: Bryan Carstens Ph.D. (Advisor); Marymegan Daly Ph.D. (Committee Member); Zakee Sabree Ph.D. (Committee Member); Andrea Wolfe Ph.D. (Committee Member) Subjects: Bioinformatics; Biology; Botany

Doctor of Philosophy, The Ohio State University, 2024, Microbiology

Candida albicans is a diploid fungus and common human commensal that colonizes the skin, gastrointestinal tract, and urogenital system of its host. It is also one of the most clinically relevant fungal pathogens, capable of overgrowing its natural niches and causing cutaneous or mucosal infections in immunocompromised individuals. Access to the bloodstream can facilitate dissemination through the body and progress to life-threatening systemic infections associated with high mortality rates, presenting a significant healthcare burden. As such, C. albicans – in particular the genome reference strain SC5314 – has been the subject of many investigations to better understand the mechanisms behind its ability to cause human disease. One of the key factors allowing C. albicans to function as both a commensal and a pathogen is its ability to transition between a variety of phenotypically distinct morphologies. While it typically grows as a round-to-ovoid yeast (also known as the white state), C. albicans can adopt a range of cell states and morphologies including pseudohyphae, hyphae, opaque, and other less common cell types. Different morphologies interact with the human host to produce commensal or pathogenic outcomes. For example, hyphae are more readily recognized by immune cells and inflict damage upon the host by penetrating through tissue and lysing phagocytic cells. In contrast, opaque cells are phagocytosed less efficiently by macrophage and neutrophils relative to their white state counterparts and colonize the gastrointestinal tract more thoroughly in some cases. Advancing our understanding of the mechanisms regulating these morphological transitions between them is critical to understanding how this pathogenic yeast interacts with the host. In Chapter 2, we investigate the role of the histone deacetylase SIR2 in C. albicans phenotypic switching. Preliminary work using a previously-constructed strain set in the BWP17 background – an SC5314 derivative – identi (open full item for complete abstract)

Committee: Matthew Anderson (Advisor); Chad Rappleye (Committee Member); Mark Parthun (Committee Member); Patrick Bradley (Committee Member) Subjects: Genetics; Microbiology

Doctor of Philosophy, Case Western Reserve University, 2023, Biology

Tylosema esculentum (marama bean) is an underutilized legume, long considered as a local potential crop due to its rich nutritional value. The reference plastome and mitogenome were assembled using a hybrid method with both Illumina and PacBio data. The diversity was explored with the WGS data of 84 samples from various geographic locations in Namibia and Pretoria. Phylogenetic analysis revealed two cytotypes with distinct plastomes and mitogenomes with differing levels of variability. Deep sequencing has identified heteroplasmy with both types of organellar genomes present, albeit one at a very low frequency. The inheritance of this complex of organellar genomes appears to be fairly constant, providing a conundrum of how the two genomes co-exist and are propagated through generations. The type 1 mitogenome has two autonomous rings with a total length of 399,572 bp, which can be restructured into five smaller circular molecules through recombination on 3 pairs of long direct repeats. The type 2 mitogenome contains a unique 2,108 bp sequence, which connects distant segments to form a new structure consisting of three circular molecules and one linear chromosome. This increased the copy number of nad9, rrns, rrn5, trnC, and trnfM. The two mitogenomes differed at another 230 loci, with only one nonsynonymous substitution in matR. cpDNA insertions were concentrated in one subgenomic ring of the mitogenome, including a 9,798 bp long fragment that contains potential psbC, rps14, psaA, and psaB pseudogenes. The two types of plastomes range in length from 161,537 bp to 161,580 bp, differing at 122 loci and at a 230 bp inversion. The chloroplast genes rpoC2, rpoB, and ndhD were found to be more diverse than other genes in marama plastome. 21.6 Gb PacBio HiFi data was assembled using Canu v2.2 into an unphased assembly of 1.24 Gb. k-mer analysis indicated that marama may be ancient tetraploid with an estimated genome size of only 277 Mb. The generated assembly has an N50 v (open full item for complete abstract)

Committee: Christopher Cullis (Advisor); Hillel Chiel (Committee Chair); Peter Zimmerman (Committee Member); Jean Burns (Committee Member); Sarah Bagby (Committee Member) Subjects: Bioinformatics; Genetics; Plant Biology

Doctor of Philosophy, The Ohio State University, 2018, Plant Pathology

Numerous diseases affect soybean [Glycine max (L.) Merr] yields throughout the growing season in Ohio. Two soil borne pathogens Fusarium graminearum and Phytophthora sojae are known to reduce stand and yield. Currently, fungicide seed treatments are used to manage these pathogens, however, host plant resistance is often the best management strategy for field crops. Thus, the overall objective of the five chapters this dissertation was to identify mechanisms and candidate genes of resistance that are effective towards seed, seedling, and root rots caused by Fusarium graminearum and P. sojae in soybean. Quantitative disease resistance loci (QDRL) have been mapped in two separate recombinant inbred line (RIL) populations for resistance to Fusarium graminearum . In the F7:8 RIL derived from a cross Magellan X PI 567516C, one major QDRL was mapped. Fine mapping of this region identified four putative candidate genes for resistance to Fusarium graminearum . In an additional population of Wyandot x PI 567301B, a major and minor QDRL was mapped to chromosome 8 and 6, respectively. Hybrid genome assembly, fine mapping, and RNA sequencing analysis narrowed the major QDRL to 2.5 cM containing three putative candidate genes for resistance or susceptibility. To validate these candidate genes functional analysis needs to be assessed at the seed level. To achieve this we modified the Apple latent spherical virus (ASLV) which allowed for direct inoculation of VIGS-triggering ALSV agro-infiltrated Nicotiana benthamiana leaves onto soybean unifoliates. However, this method is genotype dependent; the virus is detected in numerous reproductive structures including pods, embryos, stems, leaves, and roots. The last objective of this dissertation focuses on mechanisms of partial resistance to Phytophthora sojae . This oomycete is a leading pathogen of soybean, causing root and stem rot (PRR) across the North Central Region in the U.S. Twenty phenotypic quantitative trait loci ( (open full item for complete abstract)

Committee: Anne Dorrance Dr. (Advisor); Leah McHale Dr. (Committee Member); Christopher Taylor Dr. (Committee Member); Feng Qu Dr. (Committee Member) Subjects: Genetics; Plant Biology; Plant Pathology; Plant Sciences