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Language
English
Date Submitted
Spring 4-15-2015
Research Mentor and Department
Sarah CR Elgin
Restricted/Unrestricted
Dissertation/Thesis
Abstract
The Drosophila melanogaster Muller F element is a small autosome (~4.2 Mb) that is primarily packaged in a heterochromatic state. However, the distal 1.3 Mb of this autosome contains ~80 genes (including several essential genes) and the proper expression of these genes is important to the overall fitness of the organism. The D. ananassae F element is unusual because it is substantially larger (~20 Mb) than the F elements in the other Drosophila species. Concomitant with this expansion, we observe that some of the D. ananassae F element genes are much larger than their D. melanogaster orthologs. To characterize the gene structure on the D. ananassae F element, with the goal of elucidating those aspects that contribute to F element gene expression in a heterochromatic environment, I performed a comparative analysis of the genes found on the D. melanogaster and D. ananassae F elements. To facilitate this analysis, other undergraduates and I improved ~1.4 Mb from three D. ananassae F element scaffolds and carefully annotated the twelve F element genes located therein. I analyzed these twelve genes along several parameters (e.g. GC content, codon bias) to identify factors that correlate with the size of the coding spans. My analysis shows that there is a strong correlation between coding span and intron size, in contrast to no correlation with several other parameters. The data indicate that most of the changes in the size of D. ananassae F element genes can be attributed to a change in intron size, not to the size or the number of coding exons. No other gene characteristics examined (GC content of introns and exons, codon bias, expression type and maximum expression level) show a strong correlation with the size of the coding spans. However, this study is limited by the small sample size. As we annotate more F element genes in the future, we can incorporate those genes into the analysis pipeline that I have developed to search for additional correlations that might provide some insight into the organization and successful functioning of these genes.