Date of Award

Summer 6-2022

Degree Type


Degree Name

Doctor of Philosophy (PhD)


Biological, Environmental, and Earth Sciences

Committee Chair

Dr. Alex Sutton Flynt

Committee Chair School

Biological, Environmental, and Earth Sciences

Committee Member 2

Dr. Shahid Karim

Committee Member 2 School

Biological, Environmental, and Earth Sciences

Committee Member 3

Dr. Dmitri Mavrodi

Committee Member 3 School

Biological, Environmental, and Earth Sciences

Committee Member 4

Dr. Glenmore Shearer

Committee Member 4 School

Biological, Environmental, and Earth Sciences

Committee Member 5

Dr. Chaoyang Zhang

Committee Member 5 School

Computing Sciences and Computer Engineering



RNA interference (RNAi) is a pervasive gene regulatory mechanism in eukaryotes based on the action of multiple classes of small RNA (sRNA). Exploiting RNAi pathways in non-model systems have great potential for creating potent RNAi technologies. Here, we accessed RNAi-mediated control of gene expression in the two-spotted spider mite, Tetranychus urticae (T. urticae) using engineered dsRNA designed to modulate the host RNAi pathway and increase RNAi efficacy. Analysis of Dicer (Dcr) generated fragments revealed how exogenous RNAs access the host RNAi pathway in this animal, opening avenues for designing RNAi technology for their control. Further, some organisms incorporate RNA-dependent RNA polymerases (RdRPs) activity into RNAi pathways either through precursor amplification or by directly generating sRNAs from Dcr-generated fragments. While this enzymatic activity has prominent roles in plants and fungi, the involvement of RdRP in RNAi pathways of many animals is controversial. In this work, we investigated the contribution of RdRP to sRNA biogenesis in Branchiostoma floridae (B. floridae), as well as their potential role in the RNAi pathways of Crassostrea gigas (C. gigas) challenged with oyster herpes virus type 1 (OsHV-1). With adequate RdRP transcripts expressed in a variety of organs and tissues and at different stages of development in these animals, their translation is highly likely. Through inhibiting RNA Pol II’s activity and analyzing potentially RdRP synthesized nascent RNAs, we detected RdRP activity restricted to a few loci. Using this approach, we implicated RdRPs in playing a critical role in somatic genome protection through transposon repression. Although we failed to recover a wide coverage of RdRP activity in Amphioxus genome. Our observation suggests a scenario where RdRP function has become marginal, consistent with their loss in several animal lineages such as vertebrates. These explain the challenges of detecting a role in the creation of dsRNA. This observation shows a framework for how an essential gene regulation mechanism slowly decays on its way to being lost.