Mechanisms and impact of alternative transposition-induced segmental duplications

dc.contributor.advisor Thomas Peterson
dc.contributor.advisor Dan Nettleton Zuo, Tao
dc.contributor.department Genetics, Development and Cell Biology 2018-08-11T14:56:51.000 2020-06-30T02:59:52Z 2020-06-30T02:59:52Z Thu Jan 01 00:00:00 UTC 2015 2016-12-02 2015-01-01
dc.description.abstract <p>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.</p>
dc.format.mimetype application/pdf
dc.identifier archive/
dc.identifier.articleid 5890
dc.identifier.contextkey 8436116
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath etd/14883
dc.language.iso en
dc.source.bitstream archive/|||Fri Jan 14 20:28:00 UTC 2022
dc.subject.disciplines Bioinformatics
dc.subject.disciplines Genetics
dc.subject.keywords Genetics
dc.subject.keywords Bioinformatics and Computational Biology
dc.subject.keywords alterantive transposition
dc.subject.keywords dosage effect
dc.subject.keywords maize
dc.subject.keywords segmental duplications
dc.subject.keywords transposon
dc.title Mechanisms and impact of alternative transposition-induced segmental duplications
dc.type article
dc.type.genre dissertation
dspace.entity.type Publication
relation.isOrgUnitOfPublication 9e603b30-6443-4b8e-aff5-57de4a7e4cb2 Genetics; Bioinformatics and Computational Biology dissertation Doctor of Philosophy
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