Degree Type
Dissertation
Date of Award
2015
Degree Name
Doctor of Philosophy
Department
Genetics, Development and Cell Biology
Major
Genetics; Bioinformatics and Computational Biology
First Advisor
Thomas Peterson
Second Advisor
Dan Nettleton
Abstract
Segmental duplications are prevalent in both plant and animal genomes, and have played important roles in genome evolution. The focus of my project is to understand the transposition-mediated mechanisms that lead to the formation of segmental duplications, and the immediate impact of recently generated large (up to 14.6 Mb) tandem duplications in maize. We applied a variety of genetic, molecular, statistical and bioinformatics approaches, including genetic screening, PCR, Southern blotting, qRT-PCR, microarray, mRNA-sequencing, small RNA-sequencing, and a self-developed program (STRAND: Search for Transposon-Induced Tandem Direct Duplications) to study these questions. We discovered new genome rearrangement mechanisms, including transposition of paired DNA transposon termini that can generate tandem direct duplications (TDD) and novel structures termed Composite Insertions. Genomic study revealed that these mechanisms have played an important role in generating TDD in 8 of 22 examined plant genomes. We also found a significant dosage-dependent effect of a 14.6 Mb duplication on phenotypic variation, and expression of mRNA and small RNA transcripts. This work expands our current knowledge of how DNA transposons contribute to rapid genome expansion, extends our understanding of the significance of DNA transposons in altering genome structure, and provides new insight into the transcriptional expression and phenotypic effect of a specific and recent maize duplication.
DOI
https://doi.org/10.31274/etd-180810-4482
Copyright Owner
Tao Zuo
Copyright Date
2015
Language
en
File Format
application/pdf
File Size
181 pages
Recommended Citation
Zuo, Tao, "Mechanisms and impact of alternative transposition-induced segmental duplications" (2015). Graduate Theses and Dissertations. 14883.
https://lib.dr.iastate.edu/etd/14883