Riley Mcglynn

Date of Award

January 2018

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Biology

First Advisor

Brian Darby

Abstract

Oscheius tipulae is a species of free-living soil nematode that can be found in ecosystems worldwide. Because of this, individuals must be able to respond to heat, freezing, and desiccation stresses in order to survive. They do this by producing a suite of cellular responses, some of which are necessary to survive multiple stresses, and some are stress-specific. While these cellular responses are well known, the ways in which they are regulated in a genome-wide context are not. In this project, multiple high throughput sequencing and bioinformatics analyses were utilized to answer this question. First, the O. tipulae genome was sequenced via Illumina HiSeq, assembled, and annotated. An RNA-Seq experiment was performed to determine transcription patterns within stress responses. Pooled nematode samples were subjected to heat, freezing, or desiccation stress prior to RNA sequencing and read mapping. Results showed that shared cellular responses were controlled by the upregulation of both shared and stress-specific genes. This suggests that the genome remains efficient by utilizing overlapping response genes and reinforcing them with stress-specific genes. Whole genome bisulfite sequencing and MethylCap-Seq analyses were performed to assess DNA cytosine methylation presence in O. tipulae and the model organism Caenorhabditis elegans and to determine its role in the abiotic stress response process in O. tipulae. Methylated cytosines were found in both O. tipulae and C. elegans, contradicting the historical belief that cytosine methylation is absent in nematodes. Changes in DNA methylation were not associated with the abiotic stress response as very few methylation cites were found within upregulated genes. This project utilized new sequencing technologies and various bioinformatics programs to provide an in-depth look into the genome-wide responses to abiotic stress in O. tipulae.

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