Evolution of P-element Repression in Drosophila Melanogaster through the Piwi-Interacting RNA Pathway

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dc.contributor.advisorKelleher, Erin S.
dc.contributor.committeeMemberAzevedo, Ricardo B. R.
dc.contributor.committeeMemberStewart, Alexander J.
dc.contributor.committeeMemberCasola, Claudio
dc.creatorZhang, Shuo 1989-
dc.date.accessioned2019-09-15T21:47:39Z
dc.date.available2019-09-15T21:47:39Z
dc.date.createdAugust 2019
dc.date.issued2019-08
dc.date.submittedAugust 2019
dc.date.updated2019-09-15T21:47:39Z
dc.description.abstractTransposable elements (TEs) are ubiquitous and selfish genetic entities whose mobilization poses a significant threat to their host. In the germline of metazoan, the Piwi-interacting RNAs (piRNAs) derived from TE-enriched loci (called piRNA clusters) regulate TE activity in a sequence specific manner. However, the emergence and dynamics of piRNA-mediated repressor alleles to an invading TE remain elusive. P-element, a DNA transposon that recently invaded the D. melanogaster genome around 1950, provides a unique opportunity to study the evolution of host repression. In this dissertation, I first adapted a targeted sequencing strategy and developed a computational pipeline to annotate P-element insertions in a sequenced Drosophila melanogaster genome. My approach precisely determined P-element insertion breakpoints and found new P-element insertions, which were undetected by previously methods. Next, I modified the pipeline to annotate P-element insertions in the Drosophila melanogaster genetic reference panel (DGRP), a panel composed of 205 fully sequenced inbred lines. I found over 90% of DGRP genomes have P-elements in ancestral piRNA clusters that are active prior to the P-element invasion. This indicates de novo mutation, in which P-elements transpose into pre-existing piRNA clusters, is the predominant mechanism for the origin of repressor alleles. Moreover, I detected no fewer than 84 independent P-element insertions in ancestral piRNA clusters. Finally, I observed that P-element insertions in piRNA clusters segregate at significant higher frequency than P-elements outside of piRNA clusters, suggesting that cluster P-elements confer a selective advantage. Taken together, my results revealed a striking example of polygenic adaptation, in which a plethora of de novo beneficial P-element insertions into multiple piRNA clusters, fueled the evolution of a ubiquitous repressive phenotype in <60 years.
dc.description.departmentBiology and Biochemistry, Department of
dc.format.digitalOriginborn digital
dc.format.mimetypeapplication/pdf
dc.identifier.citationPortions of this document appear in: Zhang, Shuo, and Erin S. Kelleher. "Targeted identification of TE insertions in a Drosophila genome through hemi-specific PCR." Mobile DNA 8, no. 1 (2017): 10.
dc.identifier.urihttps://hdl.handle.net/10657/4697
dc.language.isoeng
dc.rightsThe author of this work is the copyright owner. UH Libraries and the Texas Digital Library have their permission to store and provide access to this work. UH Libraries has secured permission to reproduce any and all previously published materials contained in the work. Further transmission, reproduction, or presentation of this work is prohibited except with permission of the author(s).
dc.subjectTransposable element
dc.subjectP-element
dc.subjectPiRNA
dc.subjectDe novo mutation
dc.subjectPolygenic adaptation
dc.titleEvolution of P-element Repression in Drosophila Melanogaster through the Piwi-Interacting RNA Pathway
dc.type.dcmiText
dc.type.genreThesis
thesis.degree.collegeCollege of Natural Sciences and Mathematics
thesis.degree.departmentBiology and Biochemistry, Department of
thesis.degree.disciplineBiology
thesis.degree.grantorUniversity of Houston
thesis.degree.levelDoctoral
thesis.degree.nameDoctor of Philosophy

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