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dc.contributor.advisor Dietrich, Fred S. en_US
dc.contributor.author Kavanaugh, Laura Anne en_US
dc.date.accessioned 2008-05-14T16:28:57Z
dc.date.available 2008-05-14T16:28:57Z
dc.date.issued 2008-04-23 en_US
dc.identifier.uri http://hdl.handle.net/10161/597
dc.description Dissertation en_US
dc.description.abstract The rapid development of large-scale genomic sequencing has dramatically changed the field of genetics, in part through the development of comparative genomics. Fungal comparative genomics is particularly powerful given the large number of genomes currently available, their compact architecture, and their relative ease of genetic manipulation. Fungal comparative genomics was employed in this work to address two related questions. First, it was used along with computational thermodynamic methods to predict non-coding RNA (ncRNA) in Saccharomyces cerevisiae. Sets of positive and negative control genes were evaluated to determine the effect of window sizes and step sizes on the sensitivity of ncRNA identification. The approach was then applied to predict ncRNA genes on chromosome 6 of S. cerevisiae and S. bayanus. Northern blot analysis, rapid amplification of cDNA ends (RACE), and publicly available cDNA library data were used to test the predictions. Strong experimental evidence was accumulated for four new ncRNA genes. Potential structural elements in the 5' and 3' untranslated regions (UTRs) of six annotated protein-coding genes were also identified. This work shows that thermodynamic approaches, coupled with comparative genomics, are powerful tools for predicting structural ncRNA. Second, comparative genomic approaches were employed to identify a non-reciprocal transfer event from Cryptococcus neoformans var. grubii to var. neoformans ~2 million years ago involving a 14 gene (~40 kb) region. The majority of clinical and environmental var. neoformans strains from around the world contain this sequence obtained from var. grubii. The introgression event likely occurred via an incomplete inter-varietal sexual cycle creating a hybrid intermediate where mobile elements common to both lineages mediated the exchange. The subsequent duplication in laboratory strains of a fragment of this same genomic region supports evolutionary theories that instabilities in subtelomeric regions promote adaptive evolution through gene amplification and subsequent adaptation. These data indicate that DNA exchange between closely related sympatric varieties or species may be a recurrent theme in the evolution of fungal species. It further suggests that while evolutionary divergence is the primary force driving speciation, rare introgression events also play a potentially important role. en_US
dc.format.extent 5182874 bytes
dc.format.mimetype application/pdf
dc.language.iso en_US
dc.subject Biology, Genetics en_US
dc.subject Saccharomyces en_US
dc.subject Cryptococcus en_US
dc.subject non-coding RNA en_US
dc.subject Comparative Genomics en_US
dc.subject DNA Introgression en_US
dc.title Use of Comparative Genomics for Non-coding Rna Prediction and Investigation of Dna Introgression in Yeast en_US
dc.type Dissertation en_US
dc.department Genetics and Genomics en_US

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