Date of Award

Winter 2023

Project Type

Dissertation

Program or Major

Molecular and Evolutionary Systems Biology

Degree Name

Doctor of Philosophy

First Advisor

W. Kelley Thomas

Second Advisor

David Plachetzki

Third Advisor

Mathew MacManes

Abstract

DNA and RNA sequencing is an indispensable tool for the surveillance and monitoring of organisms. Technological advances and research opportunities over the past several years have transformed and driven my research questions; from understanding the impacts of environmental perturbations on complex benthic communities, to tracking and understanding emerging pathogens like SARS-CoV-2. All of them revolve around the use of DNA sequencing to ask fundamental questions about our understanding genomes and their relationship to phenotype and the environment. The advent of sequencing-based characterization has revolutionized our approach to studying organismal communities on a large scale, offering the ability to analyze vast numbers of samples efficiently, bypassing the extensive time and extensive expertise that were once essential. However, these methods bring upon a new viewpoint that has highlighted our lack of understanding of the associated biology. My Ph.D. research aims to shed light on the associated pitfalls and promises. Importantly, how does the underlying biology of these organisms relate to the techniques we use to study them? Three main groups are covered in this work, bacterial communities, benthic animal communities, and viral communities, however, the implications and conclusions are applicable across all of life. Chapter one “from barcodes to genomes”, is divided into three main sections and focuses on identifying the limitations associated with standard DNA barcoding approaches and providing avenues for improvement. The first section of this chapter provides a large-scale comparison of marker gene sequence identity and its relationship to the functional capacity of microbes. The second section provides an overview of how DNA and RNA sequencing is used to study meiofaunal communities, a particularly difficult task due to the dynamic and seemingly cosmopolitan and ubiquitous nature of the group. The methodological limitations that exist in meiofaunal groups mirror those in bacterial communities, primarily the inability of current methods to disentangle the diversity of these organisms. In section three we utilize a set of seventy novel meiofaunal genomes and publicly available animal genome datasets to develop a new method of enriching complete mitochondrial genomes from samples. This new method coupled with novel computational methods for mitochondrial metagenomics is applied to mock animal communities and provides a promising approach for researchers. Chapter two, which was driven by the ongoing covid-19 pandemic, shifts to analyzing the biology and evolution of emerging pathogens. This chapter is divided into two sections covering the University of New Hampshire SARS-CoV-2 testing program and the wastewater surveillance program. The chapter highlights the importance of surveillance programs and the ability for wastewater-based epidemiology to identify and track existing and emerging pathogens using DNA and RNA sequencing. The final chapter emphasizes the critical role of bioinformatics training and the necessity of workforce development for applicable and far-reaching science. This chapter discusses the implementation of comprehensive bioinformatics training programs, from workshops for students and researchers to the development of accessible online resources. It underscores the importance of equipping scientists with the skills needed to effectively analyze and interpret complex genomic data.

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